Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 103 of 120
Found at i:30234479 original size:113 final size:114
Alignment explanation
Indices: 30234126--30234514 Score: 491
Period size: 113 Copynumber: 3.4 Consensus size: 114
30234116 AGCACCAATC
** * *
30234126 TACCTCAGGACCAAACGGTGCGTTTTGGTTAAGATA-TTTGCGGCGCTTTTTGTAATACGCAGCT
1 TACCTCAAAACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTGTAATACGCCGCT
*
30234190 AATACTATTCTTTAGCGGCGTTTTATCGTAAACGCCACTAATTCTAATA
66 AATACTGTTCTTTAGCGGCGTTTTATCGTAAACGCCACTAATTCTAATA
* * **** *
30234239 TACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGATTACAAATAA-ACGCCAC
1 TACCTCAAAACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT-TTTGTAATACGCCGC
* ** * ** *
30234303 TAATGA-TGTTCTTTTA-CGGCGTTTTTTAATAAGCGCCACTAACACTAATC
65 TAAT-ACTGTTC-TTTAGCGGCGTTTTATCGTAAACGCCACTAATTCTAATA
* * *
30234353 TACCTCAAGACCAAACGGTGCATTTTGGTTAAGATA-TTTGCGGCGCTTTTTGTAATACGCCGCT
1 TACCTCAAAACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTGTAATACGCCGCT
* *
30234417 AATACTGTTCTTTAGCGGCATTTTATCGTAAATGCCACTAATTCTAATA
66 AATACTGTTCTTTAGCGGCGTTTTATCGTAAACGCCACTAATTCTAATA
*
30234466 TACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTT
1 TACCTCAAAACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT
30234515 ACAAATAAAC
Statistics
Matches: 226, Mismatches: 42, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
112 8 0.04
113 115 0.51
114 95 0.42
115 8 0.04
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (114 bp):
TACCTCAAAACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTGTAATACGCCGCT
AATACTGTTCTTTAGCGGCGTTTTATCGTAAACGCCACTAATTCTAATA
Found at i:30234570 original size:114 final size:114
Alignment explanation
Indices: 30234220--30234570 Score: 455
Period size: 114 Copynumber: 3.1 Consensus size: 114
30234210 TTTTATCGTA
30234220 AACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCG
1 AACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCG
*
30234285 ATTACAAATAAACGCCACTAATGATGTTCTTTTACGGCG-TTTTTTAAT
66 CTTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTTAAT
** * * * * *
30234333 AAGCGCCACTAACACTAATCTACCTCAAGACCAAACGGTGCATTTTGGTTAAGATA-TTTGCGGC
1 AA-CGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
**** * * *
30234397 GCTT-TTTGTAATACGCCGCTAAT-ACTGTTC-TTTAGCGGCATTTTATCGT-A-
65 GCTTACAAATAA-ACGCCACTAATGA-TGTTCTTTTA-CGGCGTTTT-T-TTAAT
*
30234447 AATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCG
1 AACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCG
30234512 CTTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTTAAT
66 CTTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTTAAT
30234561 AACGCCACTA
1 AACGCCACTA
30234571 GTTGTTCGGG
Statistics
Matches: 194, Mismatches: 31, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
112 9 0.05
113 79 0.41
114 95 0.49
115 10 0.05
116 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (114 bp):
AACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCG
CTTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTTAAT
Found at i:30238737 original size:23 final size:23
Alignment explanation
Indices: 30238711--30238762 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
30238701 ATTAATAATG
*
30238711 ATATTATTAATGAAATTTA-AATA
1 ATATTATTAATAAAATTTATAA-A
*
30238734 ATATTTTTAATAAAATTTATAAA
1 ATATTATTAATAAAATTTATAAA
30238757 ATATTA
1 ATATTA
30238763 CCAATAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATTATTAATAAAATTTATAAA
Found at i:30238976 original size:31 final size:29
Alignment explanation
Indices: 30238941--30239004 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
30238931 TCTTAAAAAA
*
30238941 TATATATAAACTTTGGTTTAATGTGTAATTT
1 TATATATAAACTTTGATTT--TGTGTAATTT
* * *
30238972 TATATGTGAATTTTGATTTTGTGTAATTT
1 TATATATAAACTTTGATTTTGTGTAATTT
30239001 TATA
1 TATA
30239005 CATGAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.48
31 15 0.52
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (29 bp):
TATATATAAACTTTGATTTTGTGTAATTT
Found at i:30238983 original size:13 final size:14
Alignment explanation
Indices: 30238957--30239004 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
30238947 TAAACTTTGG
30238957 TTTA-ATGTGTAAT
1 TTTATATGTGTAAT
30238970 TTTATATGTG-AAT
1 TTTATATGTGTAAT
*
30238983 TTTGATTTTGTGTAAT
1 TTT-A-TATGTGTAAT
30238999 TTTATA
1 TTTATA
30239005 CATGAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 10 0.34
14 7 0.24
15 6 0.21
16 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (14 bp):
TTTATATGTGTAAT
Found at i:30242310 original size:43 final size:43
Alignment explanation
Indices: 30242217--30242389 Score: 195
Period size: 43 Copynumber: 4.0 Consensus size: 43
30242207 GTTTTTAGAA
***
30242217 ATAAACGCCGCTATAGATCACGACTTTTAGCGGCGCTTTTCCC
1 ATAAACGCCGCTATAGATCACGACTTTTAGCGGCGCTTTTTTT
* *
30242260 ACT-AACGCCGTTATAGATCATGACTTTTAGCGGCGCTTTTTTT
1 A-TAAACGCCGCTATAGATCACGACTTTTAGCGGCGCTTTTTTT
* * * * * *
30242303 ATAAACGCCGTTATAAATAATGACTTTTAGCGGTGATTTTTTT
1 ATAAACGCCGCTATAGATCACGACTTTTAGCGGCGCTTTTTTT
* * * *
30242346 ATAAACGCCGCTAAAGAACACGACCTTTAGCGGCGTTTTTTTT
1 ATAAACGCCGCTATAGATCACGACTTTTAGCGGCGCTTTTTTT
30242389 A
1 A
30242390 AAAAAACACC
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.01
43 108 0.98
44 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (43 bp):
ATAAACGCCGCTATAGATCACGACTTTTAGCGGCGCTTTTTTT
Found at i:30245710 original size:21 final size:21
Alignment explanation
Indices: 30245659--30245717 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
30245649 CCTCTGCTCA
*
30245659 GCTTCCCTCGCTGCAGCCTCT
1 GCTTCCCTCGCTGCTGCCTCT
* * *
30245680 GCTTCTCTCGCTGCTGTCTTT
1 GCTTCCCTCGCTGCTGCCTCT
*
30245701 GTTTCCCTCGCTGCTGC
1 GCTTCCCTCGCTGCTGC
30245718 ATTAACTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.41, G:0.20, T:0.37
Consensus pattern (21 bp):
GCTTCCCTCGCTGCTGCCTCT
Found at i:30246930 original size:12 final size:12
Alignment explanation
Indices: 30246913--30246937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30246903 CATGGTCTCA
30246913 TAAAAATCCAAT
1 TAAAAATCCAAT
30246925 TAAAAATCCAAT
1 TAAAAATCCAAT
30246937 T
1 T
30246938 CATTACCTGG
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:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAAAATCCAAT
Found at i:30248420 original size:22 final size:22
Alignment explanation
Indices: 30248394--30248451 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
30248384 TCAAAAAAGT
*
30248394 AATTAAACCCTAAAACCCGTAA
1 AATTAAACCCTAAAACCCATAA
* * *
30248416 CATTAAACCTTTAAACCCATAA
1 AATTAAACCCTAAAACCCATAA
*
30248438 AATTAAAGCCTAAA
1 AATTAAACCCTAAA
30248452 GCCTAAACCT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.03, T:0.22
Consensus pattern (22 bp):
AATTAAACCCTAAAACCCATAA
Found at i:30248694 original size:41 final size:41
Alignment explanation
Indices: 30248622--30248872 Score: 331
Period size: 41 Copynumber: 6.1 Consensus size: 41
30248612 TAAATTATTT
* *
30248622 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCGC
* ** *
30248663 TAAAGCCCTGAGCATTAGCGTCGCTACCTCAAAAACACCGC
1 TAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCGC
* * * *
30248704 TAAAGCCCTGAGCACTCGCGACGCTTTTTCAAAAACGTCGC
1 TAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCGC
* * * * *
30248745 TAAATCCCTGAGCACTAGCGACGCTTTCTCAAAAAAGTCAC
1 TAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCGC
* * *
30248786 TAAATCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCGC
*
30248827 TAAAGCCCTGAGCATTAGCGACGCTTTCGCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCGC
30248868 TAAAG
1 TAAAG
30248873 TCCCGAAAGC
Statistics
Matches: 182, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 182 1.00
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCGC
Found at i:30251618 original size:13 final size:14
Alignment explanation
Indices: 30251585--30251619 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
30251575 TTAACGATCT
30251585 TAAAGAAAAAAATA
1 TAAAGAAAAAAATA
*
30251599 TAAAGAATAAAATA
1 TAAAGAAAAAAATA
30251613 -AAAGAAA
1 TAAAGAAA
30251620 GATATGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (14 bp):
TAAAGAAAAAAATA
Found at i:30255131 original size:131 final size:130
Alignment explanation
Indices: 30254911--30255558 Score: 697
Period size: 131 Copynumber: 5.0 Consensus size: 130
30254901 GTTTAACATG
* * ** * *
30254911 AACAACTCACTGATTAAAGATCACAACTGATATTATTAAGGCTCATTGATTTATGATCATAGTCT
1 AACAACTCGCTGATTTAAGATCACAACTGATATTATTAAGGCTCGCTGATTTATGATCACA-ACT
* * * *
30254976 AAGTTCATTTGATTTACTAACATGAACAATTTTATCTGAGTTAGATGATTTTCTATCGTTTCTCC
65 AAGTTCATTTGATTTACTATCATGAACAATTTTATCTGAGTTAGCTGATTTTCTATCGCTGCTCC
30255041 A
130 A
* *
30255042 AACAACTCGCTGATTTAAGATAACAACTGATATTATTAAGGCTCGCTGATTAATGATCACAACAT
1 AACAACTCGCTGATTTAAGATCACAACTGATATTATTAAGGCTCGCTGATTTATGATCACAAC-T
* * * * *
30255107 AAGTTCATTTGATTTATTATCATGAACAATTTCATTTGAGTTAGCTAATTTTCTATCACTGCTCC
65 AAGTTCATTTGATTTACTATCATGAACAATTTTATCTGAGTTAGCTGATTTTCTATCGCTGCTCC
30255172 A
130 A
** * * * * *
30255173 AACAACTCATTGATTTAAGA-CGACAACTAATATTATTAAGGCTCGCTGATTTACGGTTACATTC
1 AACAACTCGCTGATTTAAGATC-ACAACTGATATTATTAAGGCTCGCTGATTTATGATCACA-AC
* * * *
30255237 TAAGTTCATTTGATTTACTATCATGAACAATTTTATTTAAGTTAGTTGATTTTCTATCACTGCTC
64 TAAGTTCATTTGATTTACTATCATGAACAATTTTATCTGAGTTAGCTGATTTTCTATCGCTGCTC
*
30255302 TA
129 CA
* * * * ** * * *
30255304 AATAGCTCGTTGATTTAAGATCACAACTGATATTATTCAGGCTAACTAATTTACGATCAAAACCT
1 AACAACTCGCTGATTTAAGATCACAACTGATATTATTAAGGCTCGCTGATTTATGATCACAA-CT
* * ** * * * *
30255369 AAGTTCA-TTGATTTACTATCATGAACACTTTAATCAAAGTTAGTTTATTTTCTATCGCTACTCA
65 AAGTTCATTTGATTTACTATCATGAACAATTTTATCTGAGTTAGCTGATTTTCTATCGCTGCTCC
30255433 A
130 A
** * * ** * * * *
30255434 AACAGTTTGCTAATTTAAGATCACAACTGGCATTATTAAGGTTTGTTGATTTGTGATCACAACTT
1 AACAACTCGCTGATTTAAGATCACAACTGATATTATTAAGGCTCGCTGATTTATGATCACAAC-T
* * *
30255499 AAATTTATTTGATTTACTATCATGAACAATTTTCTCTGAGTTAGCTGATTTTCTATCGCT
65 AAGTTCATTTGATTTACTATCATGAACAATTTTATCTGAGTTAGCTGATTTTCTATCGCT
30255559 ATCCCGAACA
Statistics
Matches: 433, Mismatches: 77, Indels: 14
0.83 0.15 0.03
Matches are distributed among these distances:
129 1 0.00
130 103 0.24
131 327 0.76
132 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (130 bp):
AACAACTCGCTGATTTAAGATCACAACTGATATTATTAAGGCTCGCTGATTTATGATCACAACTA
AGTTCATTTGATTTACTATCATGAACAATTTTATCTGAGTTAGCTGATTTTCTATCGCTGCTCCA
Found at i:30257361 original size:24 final size:24
Alignment explanation
Indices: 30257334--30257398 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
30257324 AGCTCATGCG
*
30257334 AGCCAATATCGGGTAGCTCCGAAA
1 AGCCAATATCGGGAAGCTCCGAAA
* * * *
30257358 AGCCATTAACAGGAAGCTCCGAAT
1 AGCCAATATCGGGAAGCTCCGAAA
30257382 AGCCATATATCGGGAAG
1 AGCCA-ATATCGGGAAG
30257399 TTCAAGTGAG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 24 0.75
25 8 0.25
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (24 bp):
AGCCAATATCGGGAAGCTCCGAAA
Found at i:30264496 original size:25 final size:25
Alignment explanation
Indices: 30264468--30264518 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
30264458 TATCTAGATT
30264468 TAGTTCAATTTATCATGCCATAATA
1 TAGTTCAATTTATCATGCCATAATA
30264493 TAGTTCAATTTATCATGCCATAATA
1 TAGTTCAATTTATCATGCCATAATA
30264518 T
1 T
30264519 GGCTTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (25 bp):
TAGTTCAATTTATCATGCCATAATA
Found at i:30274017 original size:23 final size:23
Alignment explanation
Indices: 30273982--30274026 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
30273972 TGGAGTATAA
* *
30273982 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
30274005 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
30274027 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:30274075 original size:2 final size:2
Alignment explanation
Indices: 30274070--30274096 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30274060 TATATATATA
30274070 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
30274097 ACTTAAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:30274438 original size:2 final size:2
Alignment explanation
Indices: 30274431--30274459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30274421 TGTATTAAGT
30274431 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 T
30274460 GTTCAGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30274680 original size:42 final size:42
Alignment explanation
Indices: 30274633--30274798 Score: 255
Period size: 42 Copynumber: 4.0 Consensus size: 42
30274623 GCCTATCAGG
*
30274633 CTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGA
1 CTTAATGCCGGTGAAACAATATCAGACTTTATGTCTAGCAGA
* * *
30274675 CTTAATGCCGGTGAAATAATTTCAGACTTTATGTCTAGCAGG
1 CTTAATGCCGGTGAAACAATATCAGACTTTATGTCTAGCAGA
30274717 CTTAATGCCGGTGAAACAATATCAGACTTTATGTCTAGCAGGA
1 CTTAATGCCGGTGAAACAATATCAGACTTTATGTCTAGCA-GA
* *
30274760 -TTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAGCAG
1 CTTAATGCCGGTGAAACAATATCAGACTTTATGTCTAGCAG
30274799 GCTAAGTGTC
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 20 0.18
42 92 0.81
43 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (42 bp):
CTTAATGCCGGTGAAACAATATCAGACTTTATGTCTAGCAGA
Found at i:30274770 original size:84 final size:83
Alignment explanation
Indices: 30274629--30274801 Score: 294
Period size: 84 Copynumber: 2.1 Consensus size: 83
30274619 CAGTGCCTAT
30274629 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGACTTAATGCCGGTGAAATAA
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGACTTAATGCCGGTGAAA-AA
*
30274694 TTTCAGACTTTATGTCTAG
65 TTTCAGACTATATGTCTAG
* *
30274713 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTATGTCTAGCAGGA-TTAATGCCGGTGAAACA
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCA-GACTTAATGCCGGTGAAAAA
30274777 TTTCAGACTATATGTCTAG
65 TTTCAGACTATATGTCTAG
30274796 CAGGCT
1 CAGGCT
30274802 AAGTGTCGGT
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
83 25 0.29
84 58 0.68
85 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (83 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGACTTAATGCCGGTGAAAAAT
TTCAGACTATATGTCTAG
Found at i:30283557 original size:133 final size:130
Alignment explanation
Indices: 30283358--30283737 Score: 363
Period size: 133 Copynumber: 2.8 Consensus size: 130
30283348 GCGCTTCCCC
* * * * * * *
30283358 AAAAACGCCGCAAAAAATTGGAATATAGCGGCGTTTTCTGAGAAACACTGGTAACGATAAT-GAA
1 AAAAACGCCGCAAAGAA-TGGCATATAGCGGCGTTTTC-GGGAAACGCCGGTAAAGAT-ATCTAA
* *
30283422 TTTGAGGAAAATATCTGAGCAAAACAGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCAC
63 TTTGAGGAAAA-ATTTG-GCAAAAC-GTACCGTTTTGTTGTTTCATTTTATTTCCTTAGTGGCAC
*
30283487 ATTTTA
125 ATTGTA
** * *
30283493 AAAAACGATGGCGAAGAAT-GCA-GTAGCGGCGTTTTCAGGGAAACGCCGGTAAAGATATCTAAT
1 AAAAACG-CCGCAAAGAATGGCATATAGCGGCGTTTTC-GGGAAACGCCGGTAAAGATATCTAAT
* * *
30283556 TTGAGGAAAAAATTTGGACAAAACGCTACCGTTTTATTGCTTCATTTTATTTCCTTAGTGGCGCA
64 TTGAGG-AAAAATTTGG-CAAAACG-TACCGTTTTGTTGTTTCATTTTATTTCCTTAGTGGCACA
30283621 TTGTA
126 TTGTA
* * * ** *
30283626 AAAAACGCCGCAAATATTGGGATATAATGGCGTTATT-GGAGAAACGCCGGTAAAGAAATCTAAT
1 AAAAACGCCGCAAAGAATGGCATATAGCGGCGTT-TTCGG-GAAACGCCGGTAAAGATATCTAAT
* *
30283690 TTGAGGAAAAATTTAGGGCAAAACGGTACAGTTTTGTTGTTTCCTTTT
64 TTGAGGAAAAATTT--GGCAAAAC-GTACCGTTTTGTTGTTTCATTTT
30283738 TATGCTTTAG
Statistics
Matches: 201, Mismatches: 32, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
132 10 0.05
133 105 0.52
134 67 0.33
135 13 0.06
136 6 0.03
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (130 bp):
AAAAACGCCGCAAAGAATGGCATATAGCGGCGTTTTCGGGAAACGCCGGTAAAGATATCTAATTT
GAGGAAAAATTTGGCAAAACGTACCGTTTTGTTGTTTCATTTTATTTCCTTAGTGGCACATTGTA
Found at i:30286154 original size:19 final size:16
Alignment explanation
Indices: 30286104--30286155 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 16
30286094 AAATAAAGAC
30286104 ATATTAAATATTATAA
1 ATATTAAATATTATAA
* *
30286120 AAATTGAATATTTATAA
1 ATATTAAATA-TTATAA
30286137 ATTTATTAAATATGTATAA
1 A--TATTAAATAT-TATAA
30286156 TTCAAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 1 0.04
19 12 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
ATATTAAATATTATAA
Found at i:30288545 original size:17 final size:17
Alignment explanation
Indices: 30288523--30288555 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30288513 TTAATATCTA
30288523 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
30288540 TATAAGTTTTCTAAAT
1 TATAAGTTTTCTAAAT
30288556 AAGTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:30288586 original size:16 final size:15
Alignment explanation
Indices: 30288562--30288602 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
30288552 AAATAAGTTA
*
30288562 ATTAAATTTATTTGT
1 ATTAAATTTATTAGT
30288577 ATTAAAATTTATTAGT
1 ATT-AAATTTATTAGT
30288593 ATTAAATTTA
1 ATTAAATTTA
30288603 CTTCGTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
ATTAAATTTATTAGT
Found at i:30288845 original size:21 final size:21
Alignment explanation
Indices: 30288821--30288899 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
30288811 TGTTATAATA
30288821 CATAACTGT-TATATAAGCTTG
1 CATAACT-TATATATAAGCTTG
*
30288842 CATAACTTATATTTAAGCTTG
1 CATAACTTATATATAAGCTTG
* * *
30288863 CATAACTTACATAATAA-TTTA
1 CATAACTTATAT-ATAAGCTTG
30288884 CATAACTTATATATAA
1 CATAACTTATATATAA
30288900 TAGCATAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 5 0.10
21 42 0.84
22 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (21 bp):
CATAACTTATATATAAGCTTG
Found at i:30288853 original size:116 final size:116
Alignment explanation
Indices: 30288726--30288966 Score: 432
Period size: 116 Copynumber: 2.1 Consensus size: 116
30288716 TTATATAATA
30288726 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACA-A
1 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
30288790 CATAAATTACATAATACTTTATGTTATAATACATAAC-TGTTATATAAGCTTG
66 -ATAAATTACATAATACTTTATGTTATAATACATAACTTG-TATATAAGCTTG
* *
30288842 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACATAACTTATATATAATAGCATA
1 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
30288907 ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
66 ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
30288958 CATAACTTA
1 CATAACTTA
30288967 CATAAATTAA
Statistics
Matches: 121, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
116 118 0.98
117 3 0.02
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (116 bp):
CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
Found at i:30288980 original size:9 final size:9
Alignment explanation
Indices: 30288958--30289010 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
30288948 TATAAGCTTG
*
30288958 CATAACTTA
1 CATAAATTA
30288967 CATAAATTA
1 CATAAATTA
* *
30288976 AATAACTTA
1 CATAAATTA
*
30288985 CATAACTTA
1 CATAAATTA
*
30288994 CATAAAATTG
1 CAT-AAATTA
30289004 CATAAAT
1 CATAAAT
30289011 ATTTTTATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
9 30 0.81
10 7 0.19
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (9 bp):
CATAAATTA
Found at i:30288998 original size:18 final size:18
Alignment explanation
Indices: 30288935--30288998 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
30288925 TATGTTATAA
*
30288935 TACATAACTTGTATATAAGCT
1 TACATAAC-T-TACATAA-CT
* *
30288956 TGCATAACTTACATAAAT
1 TACATAACTTACATAACT
*
30288974 TAAATAACTTACATAACT
1 TACATAACTTACATAACT
30288992 TACATAA
1 TACATAA
30288999 AATTGCATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 22 0.61
19 6 0.17
20 1 0.03
21 7 0.19
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (18 bp):
TACATAACTTACATAACT
Found at i:30289376 original size:42 final size:42
Alignment explanation
Indices: 30289279--30289488 Score: 316
Period size: 42 Copynumber: 5.0 Consensus size: 42
30289269 TTTGTGAAAT
30289279 AAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTCTTCCC
1 AAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTT-TTCCC
30289322 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCC
* *
30289364 AAGCGCCGCTAAAGAACATGATATTTAGCGGCGTTTTCTTCCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TTCCC
* *
30289407 AAGCGCCGCTAAAGAATATGATCTTTAGCGGCGTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCC
* *
30289449 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCTTTTTTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTC
30289489 TGTAAGCGCC
Statistics
Matches: 157, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
42 84 0.54
43 72 0.46
44 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCC
Found at i:30289495 original size:85 final size:85
Alignment explanation
Indices: 30289278--30289505 Score: 334
Period size: 85 Copynumber: 2.7 Consensus size: 85
30289268 GTTTGTGAAA
* * *
30289278 TAAGCGCCGCTAAAGAACA-CTACTTTTAGCGGCGTTTTCTTCCCAAGCGCCGCTAAAGAACATG
1 TAAGCGCCGCTAAAGAACATGTTC-TTTAGCGGCGTTTTCTTCCTAAGCGCCGCTAAAGAACATG
30289342 ATCTTTAGCGGCGTTTTTTCC
65 ATCTTTAGCGGCGTTTTTTCC
* * * *
30289363 CAAGCGCCGCTAAAGAACATGATATTTAGCGGCGTTTTCTTCCTAAGCGCCGCTAAAGAATATGA
1 TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTCTTCCTAAGCGCCGCTAAAGAACATGA
30289428 TCTTTAGCGGCGTTTTTTCC
66 TCTTTAGCGGCGTTTTTTCC
* * *
30289448 TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC-TTTTTTTCTGTAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTCTTC-CTAAGCGCCGCTAAAG
30289506 TTAGCAACGT
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
84 7 0.05
85 121 0.95
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (85 bp):
TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTCTTCCTAAGCGCCGCTAAAGAACATGA
TCTTTAGCGGCGTTTTTTCC
Found at i:30289712 original size:26 final size:26
Alignment explanation
Indices: 30289683--30289732 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
30289673 TCTAGCAAAT
*
30289683 AACCCATTTCGATATTTATTTTTGTA
1 AACCCATCTCGATATTTATTTTTGTA
*
30289709 AACCCATCTCGGTATTTATTTTTG
1 AACCCATCTCGATATTTATTTTTG
30289733 AGTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (26 bp):
AACCCATCTCGATATTTATTTTTGTA
Found at i:30294227 original size:254 final size:255
Alignment explanation
Indices: 30293777--30294284 Score: 820
Period size: 254 Copynumber: 2.0 Consensus size: 255
30293767 CAACTGCAGC
* *
30293777 TCAACATGTGTTTTGAAAGACAAGAAGGCTTGTAATGCATCAAACTTTTTCATAAGAAAATTAAA
1 TCAACATGTGTTTTGAAAGACAAGAAGGCTTGCAATGCATCAAACTTTTGCATAAGAAAATTAAA
* * *
30293842 TCCAAGCATGAATTTAAAATGTATCCACAAAGGAGATATAGTATTAATAGCCTGAAGAGTAACAA
66 TCCAAGCATGAATTGAAAATGCATCAACAAAGGAGATATAGTATTAATAGCCTGAAGAGTAACAA
* * * * * * *
30293907 GAGGCTAGACCCCACAAGTCAGTAACAATTAACTCGAGAGGAGTAGAGTACACTGATTTAATGGA
131 GAGGCCAGACCCCAAAACTCAGTAACAATAAACTCAAGAGGAGCAGAGTACACTAATTTAATGGA
* *
30293972 CATAAATGGCAGTTTGTGGCTTTTACCAAGCTCACAAACATTACATAAAGAGAATGACTG
196 CATAAATGGCAGTTTGTGGCGTTTACCAAGCTCACAAACATTACACAAAGAGAATGACTG
*
30294032 TCAACATGTGTTTTGAAAGACAAGAAGGCTTGCAATGCATCAAACTTTTGCTTAAGAAAATT-AA
1 TCAACATGTGTTTTGAAAGACAAGAAGGCTTGCAATGCATCAAACTTTTGCATAAGAAAATTAAA
* * *
30294096 TCCAAGTATGAATTGAAAATGCATCAATAAAGGAGATATAGTATTGATAGCCTGAAGAGTAACAA
66 TCCAAGCATGAATTGAAAATGCATCAACAAAGGAGATATAGTATTAATAGCCTGAAGAGTAACAA
* *
30294161 GGGGCCAGACCCCAAAACTCAGTCACAATAAACTCAAGAGGAGCAGAGTACACTAATTTAATGGA
131 GAGGCCAGACCCCAAAACTCAGTAACAATAAACTCAAGAGGAGCAGAGTACACTAATTTAATGGA
*
30294226 CATAAATGGCAGTTTGTGGCGTTTACCAAGCTCACAAGCATTACACAAAGAGAATGACT
196 CATAAATGGCAGTTTGTGGCGTTTACCAAGCTCACAAACATTACACAAAGAGAATGACT
30294285 TATTCTTGGG
Statistics
Matches: 232, Mismatches: 21, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
254 173 0.75
255 59 0.25
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.24
Consensus pattern (255 bp):
TCAACATGTGTTTTGAAAGACAAGAAGGCTTGCAATGCATCAAACTTTTGCATAAGAAAATTAAA
TCCAAGCATGAATTGAAAATGCATCAACAAAGGAGATATAGTATTAATAGCCTGAAGAGTAACAA
GAGGCCAGACCCCAAAACTCAGTAACAATAAACTCAAGAGGAGCAGAGTACACTAATTTAATGGA
CATAAATGGCAGTTTGTGGCGTTTACCAAGCTCACAAACATTACACAAAGAGAATGACTG
Found at i:30306278 original size:10 final size:10
Alignment explanation
Indices: 30306263--30306297 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
30306253 TTTTATTAGT
30306263 ATATATAAAA
1 ATATATAAAA
30306273 ATATATTAAAA
1 ATATA-TAAAA
*
30306284 ATATAAAAAA
1 ATATATAAAA
30306294 ATAT
1 ATAT
30306298 TTTTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATATATAAAA
Found at i:30306321 original size:20 final size:20
Alignment explanation
Indices: 30306284--30306332 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
30306274 TATATTAAAA
* * *
30306284 ATATAAAAAAATATTTTTTT
1 ATATCAAAAAATAGTTTTTC
*
30306304 ATATCAAAAATTAGTTTTTC
1 ATATCAAAAAATAGTTTTTC
*
30306324 ATGTCAAAA
1 ATATCAAAA
30306333 TTTAATTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (20 bp):
ATATCAAAAAATAGTTTTTC
Found at i:30307449 original size:32 final size:34
Alignment explanation
Indices: 30307400--30307471 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 34
30307390 CCGTTTTGAC
* *
30307400 ATTTTTAGATTCCTT-AAAGCTT-G-AAGAAAAAA
1 ATTTTTAGATTCATTAAAAG-TTGGTAAAAAAAAA
30307432 ATTTTTA-AGTTCATTAAAAGTTGGTAAAAAAAAA
1 ATTTTTAGA-TTCATTAAAAGTTGGTAAAAAAAAA
30307466 ATTTTT
1 ATTTTT
30307472 GACCCTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 1 0.03
32 14 0.41
33 5 0.15
34 14 0.41
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (34 bp):
ATTTTTAGATTCATTAAAAGTTGGTAAAAAAAAA
Found at i:30307482 original size:33 final size:31
Alignment explanation
Indices: 30307445--30307543 Score: 99
Period size: 33 Copynumber: 3.1 Consensus size: 31
30307435 TTTAAGTTCA
30307445 TTAAAAGTTGGTAAAAAAAAAATTTTTGACCCT
1 TTAAAAGTT-G-AAAAAAAAAATTTTTGACCCT
* * *
30307478 TTAAAAGTTTCAAAAAAAAAAAATTTTAACCCT
1 TTAAAAG-TT-GAAAAAAAAAATTTTTGACCCT
* * * *
30307511 TTAAAAATTGAAAAACAATATTTTGGACCCT
1 TTAAAAGTTGAAAAAAAAAATTTTTGACCCT
30307542 TT
1 TT
30307544 TTAGCCTTGG
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 18 0.33
32 2 0.04
33 32 0.59
34 2 0.04
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (31 bp):
TTAAAAGTTGAAAAAAAAAATTTTTGACCCT
Found at i:30310051 original size:26 final size:26
Alignment explanation
Indices: 30310001--30310053 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
30309991 TTATATGATG
*
30310001 AAATAAATAATAAATTATATAATATT
1 AAATAAATAATAAATTAAATAATATT
*
30310027 AAATAAATAAATAAA-TAAATTATATT
1 AAATAAAT-AATAAATTAAATAATATT
30310053 A
1 A
30310054 TATATAACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AAATAAATAATAAATTAAATAATATT
Found at i:30310351 original size:23 final size:25
Alignment explanation
Indices: 30310325--30310376 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
30310315 ATGATAAAAA
30310325 TTTAAT-AATGAG-AAAATTATTAT
1 TTTAATCAATGAGTAAAATTATTAT
* *
30310348 TTT-ATCAATGAGTAAAATTGTTGT
1 TTTAATCAATGAGTAAAATTATTAT
30310372 TTTAA
1 TTTAA
30310377 GTATCAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 2 0.08
23 9 0.38
24 12 0.50
25 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
TTTAATCAATGAGTAAAATTATTAT
Found at i:30313385 original size:14 final size:15
Alignment explanation
Indices: 30313356--30313411 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
30313346 CAAACACACC
*
30313356 CTTAGTTTTTCAATA
1 CTTAATTTTTCAATA
30313371 CTTAATTTTTC-ATA
1 CTTAATTTTTCAATA
* *
30313385 CTTAAATTTTCAACA
1 CTTAATTTTTCAATA
30313400 CTTAATTTTTCA
1 CTTAATTTTTCA
30313412 CTTTATCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
14 13 0.36
15 23 0.64
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (15 bp):
CTTAATTTTTCAATA
Found at i:30314401 original size:8 final size:8
Alignment explanation
Indices: 30314388--30314412 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
30314378 AATTATTATT
30314388 TTTTAAAA
1 TTTTAAAA
30314396 TTTTAAAA
1 TTTTAAAA
30314404 TTTTAAAA
1 TTTTAAAA
30314412 T
1 T
30314413 ATTGATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:30316037 original size:19 final size:18
Alignment explanation
Indices: 30316010--30316045 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30316000 CCTATTTGTT
*
30316010 ATTAGTTATTTATTACTAA
1 ATTAATTATTT-TTACTAA
30316029 ATTAATTATTTTTACTA
1 ATTAATTATTTTTACTA
30316046 TTATTCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTAATTATTTTTACTAA
Found at i:30316130 original size:23 final size:24
Alignment explanation
Indices: 30316104--30316155 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
30316094 ATAACCATAT
*
30316104 TTATACATACATTTTCTATAA-TA
1 TTATACATACATTTTCTAAAATTA
*
30316127 TTATACATACATTTTTTAAAATTA
1 TTATACATACATTTTCTAAAATTA
30316151 TTATA
1 TTATA
30316156 AATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATACATACATTTTCTAAAATTA
Found at i:30324769 original size:88 final size:88
Alignment explanation
Indices: 30324620--30325447 Score: 1208
Period size: 88 Copynumber: 9.4 Consensus size: 88
30324610 TGGAACCACA
* * * *
30324620 AGCCTAATTTCCCTGAGCAACAGTGGAGTAGGTTGAAAATAGCAGATTTTGTCTTCCTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
*
30324685 CAGCGAAGTAGATCGAAGATACC
66 CAGCGAAGTAGATCGAAGACACC
* * * * *
30324708 AGCCTTATTTCCCTAAGCAGCAGTGGAGTAGGTTAAAAATAGTAGATCTTGTCTTTCTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
30324773 CAGCGAAGTAGATCGAAGACACC
66 CAGCGAAGTAGATCGAAGACACC
* *
30324796 AGCCTTATCT-CTTAAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
*
30324860 CAGCGAAGTAGATCGAAGATACC
66 CAGCGAAGTAGATCGAAGACACC
* * *
30324883 AGCCTTATTTCCCTAAGCAGCAGTGAAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
*
30324948 CAGTGAAGTAGATCGAAGACACC
66 CAGCGAAGTAGATCGAAGACACC
** **
30324971 AGCCTTATCTCCCTGAGCAATAGTGGAGTAGGTTGAAAATAATAGATCTTGTCTTCCTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* *
30325036 CGGCGAAGTAGATCGAAGATACC
66 CAGCGAAGTAGATCGAAGACACC
** * * *
30325059 AGCCTTATCTCTATGAGCAGCAGTGGAGTTGGTTGAAAATAGCAAATTTTGTCTTCCTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* *
30325124 TAGCGAAGTAGATCGAAGATACC
66 CAGCGAAGTAGATCGAAGACACC
* * * *
30325147 AGCCTTATCTCCCTGAGCAGTAGTGGAATAGGTTAAAAATAGCAGATCTTGTCTTCTTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
30325212 CAGCGAAGTAGATCGAAGACACC
66 CAGCGAAGTAGATCGAAGACACC
* * * * *
30325235 AGCCTTATCTCCCTGAGCAGCAATAGAGTAGGTTGAAAATAACAGATCTTGTCTTCCTATATTAG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
* *
30325300 CAGCAAAATAGATCGAAGACACC
66 CAGCGAAGTAGATCGAAGACACC
* * * *
30325323 AGCCTTATCTCCTTGAGCAGTAGTGGAGTTGGTTAAAAATAGCAGATCTTGTCTTCCTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
*
30325388 CAGCAAAGTAGATCGAAGACACC
66 CAGCGAAGTAGATCGAAGACACC
* * *
30325411 AGCCTTATCTCCTTGAGCAGCAGCGAAGTAGGTTGAA
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAA
30325448 GCAACAAGTC
Statistics
Matches: 662, Mismatches: 77, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
87 81 0.12
88 581 0.88
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (88 bp):
AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGG
CAGCGAAGTAGATCGAAGACACC
Found at i:30325461 original size:43 final size:43
Alignment explanation
Indices: 30325414--30325509 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 43
30325404 AGACACCAGC
** * *
30325414 CTTATCTCCTTGAGCAGCAGCGAAGTAGGTTGAAGCAACAAGT
1 CTTATCTCCTAAAGCAGCAGCGAAGCAGGTTAAAGCAACAAGT
** * *
30325457 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAGCAACAAGT
1 CTTATCT-CCTAAAGCAGCAGCGAAGCAGGTTAAAGCAACAAGT
30325501 CTTATCTCC
1 CTTATCTCC
30325510 CTGAAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 9 0.20
44 35 0.80
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (43 bp):
CTTATCTCCTAAAGCAGCAGCGAAGCAGGTTAAAGCAACAAGT
Found at i:30325494 original size:44 final size:44
Alignment explanation
Indices: 30325440--30325525 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
30325430 GCAGCGAAGT
*
30325440 AGGTTGAAGCAACAAGTCTTATCTCCCT-AAAGTTGCAGTGGAGC
1 AGGTTAAAGCAACAAGTCTTATCTCCCTGAAA-TTGCAGTGGAGC
*
30325484 AGGTTAAAGCAACAAGTCTTATCTCCCTGAAATTGTAGTGGA
1 AGGTTAAAGCAACAAGTCTTATCTCCCTGAAATTGCAGTGGA
30325526 ACAGACACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 36 0.92
45 3 0.08
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
AGGTTAAAGCAACAAGTCTTATCTCCCTGAAATTGCAGTGGAGC
Found at i:30325965 original size:18 final size:18
Alignment explanation
Indices: 30325942--30325977 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
30325932 CAGCGCTCCA
30325942 CACGTTTTTCTTCCCTCG
1 CACGTTTTTCTTCCCTCG
30325960 CACGTTTTTCTTCCCTCG
1 CACGTTTTTCTTCCCTCG
30325978 TATGCCTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.39, G:0.11, T:0.44
Consensus pattern (18 bp):
CACGTTTTTCTTCCCTCG
Found at i:30329689 original size:21 final size:20
Alignment explanation
Indices: 30329649--30329692 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
30329639 AATATGATTA
* *
30329649 AAATAATTTATTATTTTAAT
1 AAATAATTTAATATTATAAT
30329669 AAATAATTTAATATTAATAAT
1 AAATAATTTAATATT-ATAAT
30329690 AAA
1 AAA
30329693 ATTTATCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATTTAATATTATAAT
Found at i:30329709 original size:13 final size:12
Alignment explanation
Indices: 30329677--30329772 Score: 62
Period size: 11 Copynumber: 8.4 Consensus size: 12
30329667 ATAAATAATT
*
30329677 TAATATTAATAA
1 TAATATTTATAA
*
30329689 TAAAATTTATCAA
1 TAATATTTAT-AA
30329702 TAATATTT-TAA
1 TAATATTTATAA
30329713 -AAT-TTTAATAA
1 TAATATTT-ATAA
* *
30329724 TATTATTAAT-A
1 TAATATTTATAA
* *
30329735 TATTATTGA-AA
1 TAATATTTATAA
*
30329746 -AATATTTATAT
1 TAATATTTATAA
30329757 TAATATTT-TAA
1 TAATATTTATAA
30329768 TAATA
1 TAATA
30329773 AATATATGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
9 3 0.05
10 9 0.14
11 23 0.35
12 20 0.30
13 11 0.17
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (12 bp):
TAATATTTATAA
Found at i:30329722 original size:19 final size:22
Alignment explanation
Indices: 30329689--30329732 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
30329679 ATATTAATAA
30329689 TAAAATTTATCAATAATATT-T
1 TAAAATTTATCAATAATATTAT
30329710 TAAAATTT-T-AATAATATTAT
1 TAAAATTTATCAATAATATTAT
30329730 TAA
1 TAA
30329733 TATATTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 5 0.23
21 8 0.36
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAATTTATCAATAATATTAT
Found at i:30329775 original size:27 final size:27
Alignment explanation
Indices: 30329682--30329777 Score: 74
Period size: 27 Copynumber: 3.5 Consensus size: 27
30329672 TAATTTAATA
*
30329682 TTAATAATAAA-ATTTATCAATAATATT
1 TTAATAATAAATATTTAT-ATTAATATT
* * *
30329709 TTAA-AATTTTAATA-ATATTATTAATATA
1 TTAATAA--TAAATATTTA-TATTAATATT
*
30329737 TTATTGAA-AAATATTTATATTAATATT
1 TTAAT-AATAAATATTTATATTAATATT
30329764 TTAATAATAAATAT
1 TTAATAATAAATAT
30329778 ATGTTAAATT
Statistics
Matches: 52, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
26 4 0.08
27 27 0.52
28 17 0.33
29 2 0.04
30 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (27 bp):
TTAATAATAAATATTTATATTAATATT
Found at i:30329869 original size:11 final size:11
Alignment explanation
Indices: 30329853--30329892 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
30329843 TGGGGATTTT
30329853 TACTAAAATAA
1 TACTAAAATAA
30329864 TACTAAAA-AA
1 TACTAAAATAA
*
30329874 TA--AAAAAAA
1 TACTAAAATAA
30329883 TACTAAAATA
1 TACTAAAATA
30329893 GTATAACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
8 4 0.16
9 4 0.16
10 4 0.16
11 13 0.52
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (11 bp):
TACTAAAATAA
Found at i:30330047 original size:3 final size:3
Alignment explanation
Indices: 30330034--30330098 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
30330024 CAGCCCAGCT
* ** *
30330034 GAA GGA GAA GAA GAA GAA GAGA GCT GAA GGA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA
30330080 GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA G
30330099 GTGGTGCCGG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 51 0.96
4 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.38, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:30330520 original size:76 final size:77
Alignment explanation
Indices: 30330315--30330526 Score: 225
Period size: 76 Copynumber: 2.7 Consensus size: 77
30330305 GTTTAGTTAT
* *
30330315 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-T-GTTAGTTAT
30330380 TAGGATTAGTAAAAACCC
60 TAGGATTAGTAAAAACCC
* *** * * ***
30330398 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACATTA-TATTATTGTTAGTTATTATTT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGTTAGTTATTAGGA
30330461 TTAGT-AAAACCC
65 TTAGTAAAAACCC
30330473 TAATTATTATTGTTAGTTAGTATTATT-TTGAGTAAAAAACTATTATTATTGTTA
1 TAATTATTATTGTTAGTTAGTATTATTGTT-AGTAAAAAACTATTATTATTGTTA
30330527 TTGTGTTAGT
Statistics
Matches: 108, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
75 25 0.23
76 43 0.40
77 1 0.01
78 1 0.01
79 5 0.05
80 2 0.02
82 18 0.17
83 13 0.12
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (77 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGTTAGTTATTAGGAT
TAGTAAAAACCC
Found at i:30334507 original size:26 final size:26
Alignment explanation
Indices: 30334477--30334557 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
30334467 TTCGATCACG
30334477 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
30334503 TGTGTA-T-CGGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
30334528 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
30334554 TGTG
1 TGTG
30334558 AACCGAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 21 0.50
27 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:30334556 original size:51 final size:49
Alignment explanation
Indices: 30334376--30334557 Score: 197
Period size: 51 Copynumber: 3.6 Consensus size: 49
30334366 GATGGTCATG
* * **
30334376 TGTGTAGTACTCTGTGCAGGCTACTACGTGTACCGGAT-TGATAGGTTGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTA-CGGATGT-ATAGGTCACA
* * * * * *
30334426 TGTGTAGTACTATGTGCAGGCTACTATGCGTACTGAATAGTTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTAC-GGAT-GTATAGGTCACA
30334477 TGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATGGTA-ATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTA-CGGAT-GTATA-GGTCACA
30334528 TGTGTAGTACTATGTGCAGGCTACTATGTG
1 TGTGTAGTACTATGTGCAGGCTACTATGTG
30334558 AACCGAACAT
Statistics
Matches: 110, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 32 0.29
51 75 0.68
52 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.34
Consensus pattern (49 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTACGGATGTATAGGTCACA
Found at i:30334615 original size:45 final size:45
Alignment explanation
Indices: 30334559--30334644 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
30334549 TACTATGTGA
* * *
30334559 ACCGAACATCATTGATTAGTAAGGTTGTTACTATGTGCTGATTCT
1 ACCGAACATCATTGATTAATAAGGTGGTTACCATGTGCTGATTCT
* *
30334604 ACCGGACATCATTGATTAATAAGGTGGTTGCCATGTGCTGA
1 ACCGAACATCATTGATTAATAAGGTGGTTACCATGTGCTGA
30334645 ATCCATCGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTACCATGTGCTGATTCT
Found at i:30338678 original size:157 final size:153
Alignment explanation
Indices: 30338263--30338852 Score: 748
Period size: 157 Copynumber: 3.9 Consensus size: 153
30338253 ACAAATTAGT
* *
30338263 AAAAAACTCTTATTTCGGCCCTTTGTTCGTATTTTTTT-CCTTG-ATTTTATTAC-TT--AAAAA
1 AAAAAACCCTTATTTCGGCCCTTTGTTCATATTTTTTTACC--GAATTTTATTACTTTCAAAAAA
* *
30338323 TATACTATTTTC-TAATTTTATTATTTTACATTATTTTTAGTACATTATGTTTGAAATGTATTAA
64 TATATTATTTTCATAATTTTATTATTTTACATTA-TTTTAGTACATTATGTTTGAAATGCATTAA
* *
30338387 TTTAATGTGTTTTTTAAATAAA-TT-
128 TTTAGTATGTTTTTTAAATAAATTTA
*
30338411 AAAAAACTCTTATTTCGGCCCTTTGTTCATATTTTTTT-CCTGAA--TT-TTACTTTCAATAAAA
1 AAAAAACCCTTATTTCGGCCCTTTGTTCATATTTTTTTACC-GAATTTTATTACTTTC-A-AAAA
30338472 ATATATTATTTT-ATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGCATTAA
63 ATATATTATTTTCATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGCATTAA
30338536 TTTAGTATGTTTTTTAAATAAATTTCA
128 TTTAGTATGTTTTTTAAATAAATTT-A
*
30338563 AAAATTAACCCTTATTTTGGCCCTTTGTTCGA-ATTTTTTT-CTCGAATTTTATTACTTTCAATC
1 AAAA--AACCCTTATTTCGGCCCTTTGTTC-ATATTTTTTTAC-CGAATTTTATTACTTTCAA--
* * *
30338626 AAAATATATTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAC
60 AAAATATATTATTTTCATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGCAT
* *
30338690 TAATTTAGTGTGTTTTTCAAATAAATTTA
125 TAATTTAGTATGTTTTTTAAATAAATTTA
* * ** *
30338719 GAAAAAAACCTTATTTCGGCCATTTGTTCATATTTTTTTACCGAAGCCTTATT-GTTTCAAAAAA
1 -AAAAAACCCTTATTTCGGCCCTTTGTTCATATTTTTTTACCGAA-TTTTATTACTTTCAAAAAA
*
30338783 TATATTATTTTCAT-ATTTTATTATTTTACGTTATTTTAGTACATTATGTTTGAAATGCATTAAT
64 TATATTATTTTCATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGCATTAAT
30338847 TTAGTA
129 TTAGTA
30338853 AAAAACCCTT
Statistics
Matches: 395, Mismatches: 23, Indels: 43
0.86 0.05 0.09
Matches are distributed among these distances:
145 4 0.01
146 4 0.01
147 2 0.01
148 40 0.10
149 49 0.12
150 38 0.10
152 4 0.01
153 69 0.17
154 35 0.09
155 42 0.11
156 10 0.03
157 97 0.25
158 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (153 bp):
AAAAAACCCTTATTTCGGCCCTTTGTTCATATTTTTTTACCGAATTTTATTACTTTCAAAAAATA
TATTATTTTCATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGCATTAATTT
AGTATGTTTTTTAAATAAATTTA
Found at i:30338825 original size:310 final size:302
Alignment explanation
Indices: 30338271--30338852 Score: 858
Period size: 310 Copynumber: 1.9 Consensus size: 302
30338261 GTAAAAAACT
* *
30338271 CTTATTTCGGCCCTTTGTTCGTATTTTTTTCCTTGATTTTATTACTTAAAAATATACTATTTTCT
1 CTTATTTCGGCCCTTTGTTCGAATTTTTTTCCTCGATTTTATTACTTAAAAATATACTATTTTCT
*
30338336 AATTTTATTATTTTACATTATTTTTAGTACATTATGTTTGAAATGTATTAATTTAATGTGTTTTT
66 AATTTTATTATTTTACATTATTTTTAGTACATTATGTTTGAAATGTACTAATTTAATGTGTTTTT
* *
30338401 TAAATAAATTAAAAAACTCTTATTTCGGCCCTTTGTTCATATTTTTTTCCTGAATTTTACTTTCA
131 CAAATAAATTAAAAAACTCTTATTTCGGCCATTTGTTCATATTTTTTTCCTGAATTTTACTTTCA
30338466 ATAAAAATATATTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGC
196 ATAAAAATATATTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGC
30338531 ATTAATTTAGTATGTTTTTTAAATAAATTTCAAAAATTAACC
261 ATTAATTTAGTATGTTTTTTAAATAAATTTCAAAAATTAACC
* *
30338573 CTTATTTTGGCCCTTTGTTCGAATTTTTTT-CTCGAATTTTATTACTTTCAATCAAAATATATTA
1 CTTATTTCGGCCCTTTGTTCGAATTTTTTTCCTCG-ATTTTATTAC-TT--A--AAAATATACTA
*
30338637 TTTTCGT-ATTTTATTATTTTACATTA-TTTTAGTACATTATGTTTGAAATGTACTAATTTAGTG
60 TTTTC-TAATTTTATTATTTTACATTATTTTTAGTACATTATGTTTGAAATGTACTAATTTAATG
30338700 TGTTTTTCAAATAAATTTAGAAAAAAAC-CTTATTTCGGCCATTTGTTCATATTTTTTTACC-GA
124 TGTTTTTCAAATAAA-TT---AAAAAACTCTTATTTCGGCCATTTGTTCATATTTTTTT-CCTGA
* *
30338763 AGCCTTATT-GTTTC-A-AAAAATATATTATTTTCAT-ATTTTATTATTTTACGTTATTTTAGTA
184 A---TT-TTACTTTCAATAAAAATATATTATTTT-ATAATTTTATTATTTTACATTATTTTAGTA
30338824 CATTATGTTTGAAATGCATTAATTTAGTA
244 CATTATGTTTGAAATGCATTAATTTAGTA
30338853 AAAAACCCTT
Statistics
Matches: 253, Mismatches: 10, Indels: 26
0.88 0.03 0.09
Matches are distributed among these distances:
301 3 0.01
302 38 0.15
303 2 0.01
305 1 0.00
306 49 0.19
307 36 0.14
308 1 0.00
309 32 0.13
310 80 0.32
311 3 0.01
312 6 0.02
313 2 0.01
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (302 bp):
CTTATTTCGGCCCTTTGTTCGAATTTTTTTCCTCGATTTTATTACTTAAAAATATACTATTTTCT
AATTTTATTATTTTACATTATTTTTAGTACATTATGTTTGAAATGTACTAATTTAATGTGTTTTT
CAAATAAATTAAAAAACTCTTATTTCGGCCATTTGTTCATATTTTTTTCCTGAATTTTACTTTCA
ATAAAAATATATTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGC
ATTAATTTAGTATGTTTTTTAAATAAATTTCAAAAATTAACC
Found at i:30338963 original size:130 final size:131
Alignment explanation
Indices: 30338713--30338949 Score: 329
Period size: 130 Copynumber: 1.8 Consensus size: 131
30338703 TTTTCAAATA
*
30338713 AATTTAGAAAAAAACCTTATTTCGGCCATTTGTTCATATTTTTTTACCGAAGCCTTATTGTTTCA
1 AATTTAGAAAAAAACCTTATTTCGGCCATTTGTTCATATTTTTTTACCGAAGCCTTATTCTTTCA
30338778 AAAAATATATTATTTTCATATTTTATTATTTTACGTTATTTTAGTACATTATGTTTGAAATGCAT
66 AAAAATATATTATTTTCATATTTTATTATTTTACGTTATTTTAGTACATTATGTTTGAAATGCAT
30338843 T
131 T
* * * **
30338844 AATTTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTA-TTTTTT-CC--AGATTTTATTACTT
1 AATTTAG-AAAAAAACCTTATTTCGGCCATTTGTTCATATTTTTTTACCGAAG-CCTTATT-CTT
* * * *
30338905 TTAAAAAATATTTTATTTTCGTATTTTATTATTTTACGTTCTTTT
63 TCAAAAAATATATTATTTTCATATTTTATTATTTTACGTTATTTT
30338950 CATATTTTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
128 2 0.02
129 5 0.05
130 45 0.48
131 13 0.14
132 28 0.30
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (131 bp):
AATTTAGAAAAAAACCTTATTTCGGCCATTTGTTCATATTTTTTTACCGAAGCCTTATTCTTTCA
AAAAATATATTATTTTCATATTTTATTATTTTACGTTATTTTAGTACATTATGTTTGAAATGCAT
T
Found at i:30339150 original size:28 final size:29
Alignment explanation
Indices: 30339094--30339151 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
30339084 GGGTTTTTTC
* * * *
30339094 ATGCTAAATAAATTTCATAAAATATATAT
1 ATGCTAAATAAATATAATAAAACACATAT
30339123 ATGCTAAATAAA-ATAATAAAACACATAT
1 ATGCTAAATAAATATAATAAAACACATAT
30339151 A
1 A
30339152 ATGTACATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (29 bp):
ATGCTAAATAAATATAATAAAACACATAT
Found at i:30339228 original size:10 final size:10
Alignment explanation
Indices: 30339213--30339349 Score: 124
Period size: 10 Copynumber: 14.2 Consensus size: 10
30339203 TACTTATTTT
30339213 TTTTTCTTTC
1 TTTTTCTTTC
*
30339223 TTTTTCCTTC
1 TTTTTCTTTC
*
30339233 CTTTTC-TTC
1 TTTTTCTTTC
* *
30339242 TTCTCCTTTC
1 TTTTTCTTTC
*
30339252 CTTTTCTTTC
1 TTTTTCTTTC
30339262 TTTTTCTTTC
1 TTTTTCTTTC
30339272 ---TTC--TC
1 TTTTTCTTTC
30339277 TTTTTCTTCTC
1 TTTTTCTT-TC
*
30339288 CTTTTCTTTC
1 TTTTTCTTTC
30339298 TTTTTCTTTC
1 TTTTTCTTTC
* *
30339308 TTCTCCTTTC
1 TTTTTCTTTC
* *
30339318 CTTTCCTTTC
1 TTTTTCTTTC
*
30339328 CTTTTCTTTC
1 TTTTTCTTTC
30339338 TTTTTCTTTC
1 TTTTTCTTTC
30339348 TT
1 TT
30339350 CTCCTTCTTT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
5 2 0.02
7 3 0.03
8 3 0.03
9 6 0.06
10 80 0.78
11 9 0.09
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:30339339 original size:76 final size:77
Alignment explanation
Indices: 30339214--30339365 Score: 231
Period size: 76 Copynumber: 2.0 Consensus size: 77
30339204 ACTTATTTTT
*
30339214 TTTTCTTTCTTTTTCCTTCCTTTTCTTCTTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTCT-CT
1 TTTTCTTTCTTTTTCCTTCCTTTCCTTCTTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTCTCCT
30339278 T-TTTCTTCTCC
66 TCTTTCTTCTCC
*
30339289 TTTTCTTTCTTTTT-CTTTCTTCTCCTTTCCTT-TCCTTTCCTTTTCTTTCTTTTTCTTTCTTCT
1 TTTTCTTTCTTTTTCCTTCCTT-TCC-TT-CTTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTCT
30339352 CCTTCTTTCTTCTC
63 CCTTCTTTCTTCTC
30339366 TCCAGCTGAA
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
74 6 0.09
75 16 0.23
76 33 0.47
77 6 0.09
78 9 0.13
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (77 bp):
TTTTCTTTCTTTTTCCTTCCTTTCCTTCTTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTCTCCT
TCTTTCTTCTCC
Found at i:30339447 original size:40 final size:40
Alignment explanation
Indices: 30339392--30339471 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
30339382 CCCCAACCCA
30339392 ATATAAGGGCTGGTGTCAACCTCTGCCACTGGCACCACTG
1 ATATAAGGGCTGGTGTCAACCTCTGCCACTGGCACCACTG
30339432 ATATAAGGGCTGGTGTCAACCTCTGCCACTGGCACCACTG
1 ATATAAGGGCTGGTGTCAACCTCTGCCACTGGCACCACTG
30339472 GTGCCGCCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (40 bp):
ATATAAGGGCTGGTGTCAACCTCTGCCACTGGCACCACTG
Found at i:30346824 original size:6 final size:6
Alignment explanation
Indices: 30346813--30346838 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30346803 ATATACACAG
30346813 TCAGAT TCAGAT TCAGAT TCAGAT TC
1 TCAGAT TCAGAT TCAGAT TCAGAT TC
30346839 GAACTTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (6 bp):
TCAGAT
Found at i:30347045 original size:27 final size:27
Alignment explanation
Indices: 30347007--30347065 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
30346997 TCTTTTCGAT
*
30347007 ACATACTAGATAATATGCACTTCCTCC
1 ACATACCAGATAATATGCACTTCCTCC
30347034 ACATACCAGATAATATGCACTTCCTCC
1 ACATACCAGATAATATGCACTTCCTCC
30347061 ACATA
1 ACATA
30347066 TACAAAACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.36, C:0.31, G:0.07, T:0.27
Consensus pattern (27 bp):
ACATACCAGATAATATGCACTTCCTCC
Found at i:30347426 original size:38 final size:38
Alignment explanation
Indices: 30347365--30347437 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
30347355 GGTCTCACTC
* *
30347365 GTGTGGCTCACACGGCTTGGCCCATTGCCCACACGTCT
1 GTGTGGCTCACACGCCTTGGCCCATTACCCACACGTCT
* *
30347403 GTGTGTCTCACACGACCTT-GCCCATTATCCACACG
1 GTGTGGCTCACACG-CCTTGGCCCATTACCCACACG
30347438 CCCATGTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 27 0.90
39 3 0.10
ACGTcount: A:0.16, C:0.37, G:0.22, T:0.25
Consensus pattern (38 bp):
GTGTGGCTCACACGCCTTGGCCCATTACCCACACGTCT
Found at i:30348930 original size:6 final size:6
Alignment explanation
Indices: 30348919--30348945 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30348909 TTACCATCTC
30348919 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
30348946 GCCACAAGAT
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:30353227 original size:25 final size:25
Alignment explanation
Indices: 30353199--30353252 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
30353189 TAGCTCACAT
*
30353199 GAGCATCCCAATATTTAGTTCTTAC
1 GAGCATCCCAATATATAGTTCTTAC
* * *
30353224 GAGCTTCCCATTATATGGTTCTTAC
1 GAGCATCCCAATATATAGTTCTTAC
30353249 GAGC
1 GAGC
30353253 TTCTCATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (25 bp):
GAGCATCCCAATATATAGTTCTTAC
Found at i:30353508 original size:25 final size:25
Alignment explanation
Indices: 30353463--30353533 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
30353453 ATGAGCTTCC
* *
30353463 CGTTACATGGCTCACATGAGCCTCT
1 CGTTACATGACTCACAAGAGCCTCT
*
30353488 CGTTACATGACTCGA-AAGAGCTTCT
1 CGTTACATGACTC-ACAAGAGCCTCT
* *
30353513 CGTTTATAT-ACTCACATGAGC
1 CG-TTACATGACTCACAAGAGC
30353534 ATTCCTGAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 1 0.03
25 31 0.82
26 6 0.16
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (25 bp):
CGTTACATGACTCACAAGAGCCTCT
Found at i:30357907 original size:37 final size:37
Alignment explanation
Indices: 30357854--30357938 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
30357844 TATGTGACAC
**
30357854 AAGTTTAGCTCAGACGAGTAACTTAATGTTGTTTTAT
1 AAGTTTAGCTCAGACGAGTAACTTAATGTCATTTTAT
** *
30357891 AAGTTTAGCTTGGACGAGTAACTTGATGTCATTTTAT
1 AAGTTTAGCTCAGACGAGTAACTTAATGTCATTTTAT
30357928 AAGTTTAGCTC
1 AAGTTTAGCTC
30357939 GGATGGCTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (37 bp):
AAGTTTAGCTCAGACGAGTAACTTAATGTCATTTTAT
Found at i:30358847 original size:24 final size:24
Alignment explanation
Indices: 30358820--30358871 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
30358810 TACCCATGCT
*
30358820 ATTCAAAATATATTAAATTCTTTA
1 ATTCAAAATATATTAAATTCCTTA
** *
30358844 ATTCCCAATGTATTAAATTCCTTA
1 ATTCAAAATATATTAAATTCCTTA
30358868 ATTC
1 ATTC
30358872 CCAATTTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTCAAAATATATTAAATTCCTTA
Found at i:30358872 original size:24 final size:24
Alignment explanation
Indices: 30358830--30358876 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
30358820 ATTCAAAATA
*
30358830 TATTAAATTCTTTAATTCCCAATG
1 TATTAAATTCCTTAATTCCCAATG
30358854 TATTAAATTCCTTAATTCCCAAT
1 TATTAAATTCCTTAATTCCCAAT
30358877 TTCTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (24 bp):
TATTAAATTCCTTAATTCCCAATG
Found at i:30359308 original size:22 final size:22
Alignment explanation
Indices: 30359280--30359351 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
30359270 AGTAGGCATC
30359280 GAAGTGCAAATTACTAAGCACT
1 GAAGTGCAAATTACTAAGCACT
* * *
30359302 GAAGTGCAAAATAGTGA-CACT
1 GAAGTGCAAATTACTAAGCACT
* * *
30359323 AAAGTGCAGAATGAC-AAGCACC
1 GAAGTGCA-AATTACTAAGCACT
30359345 GAAGTGC
1 GAAGTGC
30359352 GAAACGGTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 12 0.32
22 26 0.68
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.17
Consensus pattern (22 bp):
GAAGTGCAAATTACTAAGCACT
Found at i:30361180 original size:20 final size:20
Alignment explanation
Indices: 30361157--30361195 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
30361147 CTTACACATG
30361157 GGCGTGTAGACCACCACACA
1 GGCGTGTAGACCACCACACA
*
30361177 GGCGTGTAGACCTCCACAC
1 GGCGTGTAGACCACCACAC
30361196 GATTGGGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.36, G:0.26, T:0.13
Consensus pattern (20 bp):
GGCGTGTAGACCACCACACA
Found at i:30368920 original size:12 final size:13
Alignment explanation
Indices: 30368889--30368921 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
30368879 TAATAGAAGT
30368889 GATAACAAAAATG
1 GATAACAAAAATG
*
30368902 GATAACAAAATTG
1 GATAACAAAAATG
30368915 GA-AACAA
1 GATAACAA
30368922 TATAACTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.61, C:0.09, G:0.15, T:0.15
Consensus pattern (13 bp):
GATAACAAAAATG
Found at i:30369764 original size:617 final size:605
Alignment explanation
Indices: 30368043--30369769 Score: 2324
Period size: 617 Copynumber: 2.8 Consensus size: 605
30368033 GACAAAAAAC
* * * * * *
30368043 TTACTATCATCTATAAGAATTGCCACTTTTTGAGAAGCAAAGGCAAAGGGTTTGAAGAACTTCCA
1 TTACTATCATCTACAAGAATTGCCGCTTTTTGAGAAGCAAA-GTAAGGGGATTGAAGAACTTCCC
* ** * * *
30368108 ATGTGTAAATTTTGTTGAGACTGCAGAA-CC--CATTGAAGCAATGATCAACAAAAAAATAACTT
65 AT-TTTTGA-TTT-TTGAGACTGCAGAATCCATGATTGAAGCAACGATCAACAAAAAAATAGCTT
* * *
30368170 TGATACCATACTAGAAATATAAAAGAAAAAGAGTAATTCATTAATCATACTCTTAGAATATAGGG
127 TGATACCATACTAGAAATAT-AGAGAAGAAGAGTAATTCATTAATCATACTCTTAGAATACAGGG
* * *
30368235 GCCTTTGTGTATTTATACACTAGAGGCTTAACAGAAGTTATAACAAAAAAGGATAACATG-AATG
191 GCC-TTGTGTATTTATACACTGGAGGCTTAACAGAAGTGATAACAAAAATGGATAACA-GAAATG
* * *
30368299 GAAACTACACATAACTAGATTTAGTTGAGCCTAACTTACAACAATTATCTAGTTACTTCCTCTAA
254 GAAACTACTCATAACTAGATTTAGTTGAGCCTAACTT---AC----AGCTAGTTACTTCCTCTAC
* * * * *
30368364 TATTCCATAGGCACAGGGAGGGGAACCAAGTAGCTAATAGTATGGTTGCCTTTGTCGGAAATCTC
312 TATTCCATAGGTATA-GGAAGGGAACCAAGTAGCTAATAGCATGGTTGCCTTTGTTGGAAATCTC
* * *
30368429 CCTTTACGCCTTCATGTTTGTGCATCTCCCTATGACTTTATTTTAAAAGGCTCTATATGATGTTT
376 CCTTTACGCCTTCATGTTTATGCATCTCTCTATGACTTTATTTTAAAAGGCTCTATATGATGATT
* * *
30368494 GTGGCATGGTTTTGCCTAGATTAGTTACTATGTCATTGTTTTATTTTCCCCATTTAAAAAAATAA
441 GTAGCATGGTTTTGCCTAGATTAGTTACTATGTAATTGTTCTATTTTCCCCATTTAAAAAAATAA
** *
30368559 ATTCAATTATTGATATGCAATCAATCATAAAAAAAATTGATAAACTTTTTTGGGTGTAAATTCAA
506 ATTCAACAATTGAAATGCAATCAATCATAAAAAAAATTGATAAACTTTTTTGGGTGTAAATTCAA
* *
30368624 GATGTTTGGAAGTTACATTTAACTTGAGACGCAAG
571 AATGTTTGGAAGTTACATTCAACTTGAGACGCAAG
*
30368659 TTACTATCATCTACAAGAATTGCCGCTTTTTGAGAAGCAAAGATAAGGGGATTGGAGAACTTCCC
1 TTACTATCATCTACAAGAATTGCCGCTTTTTGAGAAGCAAAG-TAAGGGGATTGAAGAACTTCCC
** **
30368724 ATTTGTTGATTTTTGAGACTATAGAATCCATGATTGAAGCAACGATCGGCAAAAAAATAGCTTTG
65 ATTT-TTGATTTTTGAGACTGCAGAATCCATGATTGAAGCAACGATCAACAAAAAAATAGCTTTG
*
30368789 ATACCATACTAGAAATATAGAAGAAGAAGAGTAATTCATTAATAATACTCTTAGAATACAGGGGC
129 ATACCATACTAGAAATATAG-AGAAGAAGAGTAATTCATTAATCATACTCTTAGAATACAGGGGC
*
30368854 CTTGTGTATTTATACACTGGAGGCTTAATAGAAGTGATAACAAAAATGGATAACA-AAATTGGAA
193 CTTGTGTATTTATACACTGGAGGCTTAACAGAAGTGATAACAAAAATGGATAACAGAAA-TGGAA
* * * *
30368918 AC-AAT-ATAACTAGATTTACTTGAGTCTAACTTATAGAATTTATCTAGTTACTTCCTCTACTAT
257 ACTACTCATAACTAGATTTAGTTGAGCCTAACTTACAG-------CTAGTTACTTCCTCTACTAT
* * * *
30368981 TCCATAGGTATAAGAAGGGGAACCAAGTAGCTAATATCATGGTTGTCTTTGATGGAAATCTCCCT
315 TCCATAGGTATAGGAA-GGGAACCAAGTAGCTAATAGCATGGTTGCCTTTGTTGGAAATCTCCCT
* *
30369046 TTACGCCTTCATGTTTATTCATCTCTCTATGAATTTATTTTAAAAGGCTCTATATGATGATTGTA
379 TTACGCCTTCATGTTTATGCATCTCTCTATGACTTTATTTTAAAAGGCTCTATATGATGATTGTA
* *
30369111 GCATGGCTTTGCCTAGATTAGTTACTATGTAATTGTTCTATTTTCCCTCTTTTAAAAAAAAAATA
444 GCATGGTTTTGCCTAGATTAGTTACTATGTAATTGTTCTATTTTCCC-CATTT---AAAAAAATA
* * * *
30369176 AATTCAACAATTGAAATGC-ATCCAGTCATACAAAAAAAAATTGATACATTTTCTTTTGGTGTAA
505 AATTCAACAATTGAAATGCAAT-CAATCAT---AAAAAAAATTGATAAACTTT-TTTGGGTGTAA
*
30369240 ATTCAAAATGTTTGGAAGTTACATTCCACTTGAGACGCAAG
565 ATTCAAAATGTTTGGAAGTTACATTCAACTTGAGACGCAAG
*
30369281 TTACTATCATTTACAAGAATTGCCGCTTTTTGAGAAGCAAATGTAAGGGGATTGAAGAACTTCCC
1 TTACTATCATCTACAAGAATTGCCGCTTTTTGAGAAGCAAA-GTAAGGGGATTGAAGAACTTCCC
*
30369346 ATTTTTCGATTCTATTGAGATTGCAGAATCCATGATTGAAGCAACGATCAACAAAAAAATAGCTT
65 ATTTTT-GATT-T-TTGAGACTGCAGAATCCATGATTGAAGCAACGATCAACAAAAAAATAGCTT
** * * *
30369411 TGATAATATACTAGAAATATAGAGTAAGAAGAGTAATTGATTAATCATACTCTTAAAATACAAGG
127 TGATACCATACTAGAAATATAGAG-AAGAAGAGTAATTCATTAATCATACTCTTAGAATACAGGG
*
30369476 GCCTTGTGTATTTATACACTGGAGGCTTAACAGAAGTGATAACAAAAATGGATAATAGAAATGGA
191 GCCTTGTGTATTTATACACTGGAGGCTTAACAGAAGTGATAACAAAAATGGATAACAGAAATGGA
*
30369541 AACTACTCATAACTAGATTTAGTTGAGCCTAACTTACAGC-AGTT-CTTCCTTTACTATTCCATA
256 AACTACTCATAACTAGATTTAGTTGAGCCTAACTTACAGCTAGTTACTTCCTCTACTATTCCATA
* * *
30369604 GGTATTAGGAAGGGAACCAAGTAGCTAATAGCATGGCTG-CTTGTGTTGGAAATCTCCTTTTATG
321 GGTA-TAGGAAGGGAACCAAGTAGCTAATAGCATGGTTGCCTT-TGTTGGAAATCTCCCTTTACG
*
30369668 CCTTCATGTTTATGCATCTCTCTATGACTTTATTTTAAAAGGCTCTATATGATGATTGTAGCTTG
384 CCTTCATGTTTATGCATCTCTCTATGACTTTATTTTAAAAGGCTCTATATGATGATTGTAGCATG
30369733 GTTTTGCCTAGATTAGTTACTATGTAATTGTTCTATT
449 GTTTTGCCTAGATTAGTTACTATGTAATTGTTCTATT
30369770 CCTCCCCCCC
Statistics
Matches: 985, Mismatches: 91, Indels: 69
0.86 0.08 0.06
Matches are distributed among these distances:
607 1 0.00
611 1 0.00
613 2 0.00
614 212 0.22
615 14 0.01
616 121 0.12
617 255 0.26
618 40 0.04
619 1 0.00
621 20 0.02
622 117 0.12
623 4 0.00
624 164 0.17
625 5 0.01
626 28 0.03
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (605 bp):
TTACTATCATCTACAAGAATTGCCGCTTTTTGAGAAGCAAAGTAAGGGGATTGAAGAACTTCCCA
TTTTTGATTTTTGAGACTGCAGAATCCATGATTGAAGCAACGATCAACAAAAAAATAGCTTTGAT
ACCATACTAGAAATATAGAGAAGAAGAGTAATTCATTAATCATACTCTTAGAATACAGGGGCCTT
GTGTATTTATACACTGGAGGCTTAACAGAAGTGATAACAAAAATGGATAACAGAAATGGAAACTA
CTCATAACTAGATTTAGTTGAGCCTAACTTACAGCTAGTTACTTCCTCTACTATTCCATAGGTAT
AGGAAGGGAACCAAGTAGCTAATAGCATGGTTGCCTTTGTTGGAAATCTCCCTTTACGCCTTCAT
GTTTATGCATCTCTCTATGACTTTATTTTAAAAGGCTCTATATGATGATTGTAGCATGGTTTTGC
CTAGATTAGTTACTATGTAATTGTTCTATTTTCCCCATTTAAAAAAATAAATTCAACAATTGAAA
TGCAATCAATCATAAAAAAAATTGATAAACTTTTTTGGGTGTAAATTCAAAATGTTTGGAAGTTA
CATTCAACTTGAGACGCAAG
Found at i:30370118 original size:20 final size:20
Alignment explanation
Indices: 30370093--30370160 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
30370083 GTATCCCCTT
*
30370093 ATAATTTTTTATGCATCCTC
1 ATAATTTTTTATGCTTCCTC
*
30370113 ATAATTTTTTATACTTCCTC
1 ATAATTTTTTATGCTTCCTC
* *
30370133 ACATTTTTTTGATG-TTCCCTC
1 ATAATTTTTT-ATGCTT-CCTC
30370154 ATAATTT
1 ATAATTT
30370161 CAAAAGGAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 28 0.72
21 11 0.28
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.53
Consensus pattern (20 bp):
ATAATTTTTTATGCTTCCTC
Found at i:30370667 original size:19 final size:20
Alignment explanation
Indices: 30370643--30370686 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
30370633 TATTAAAAAT
30370643 ATTTTT-ATATCAAAAATTA
1 ATTTTTCATATCAAAAATTA
* *
30370662 ATTTTTCATGTCAAAATTTA
1 ATTTTTCATATCAAAAATTA
30370682 ATTTT
1 ATTTT
30370687 GAAAATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTTTCATATCAAAAATTA
Found at i:30371650 original size:30 final size:28
Alignment explanation
Indices: 30371614--30371694 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
30371604 AAGTTGGTAA
*
30371614 AAAAAAAAATTTTGACCCTTTAAAAGTTT
1 AAAAAAAAATTTTGACCCTTTAAAA-ATT
* ** *
30371643 CAAAAAAAATTTAAACCCCTTAAAAATT
1 AAAAAAAAATTTTGACCCTTTAAAAATT
30371671 AAAAAACAATATTTTGGACCCTTT
1 AAAAAA-AA-ATTTT-GACCCTTT
30371695 TGACCTTGGG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 7 0.17
29 23 0.57
30 4 0.10
31 6 0.15
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (28 bp):
AAAAAAAAATTTTGACCCTTTAAAAATT
Found at i:30373157 original size:2 final size:2
Alignment explanation
Indices: 30373150--30373185 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30373140 AGTTCATGAA
30373150 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
30373186 TTGGGTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30374764 original size:19 final size:19
Alignment explanation
Indices: 30374720--30374766 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
30374710 TTTGATGTCA
30374720 CAATAAAA-ATTTAAGTAT
1 CAATAAAATATTTAAGTAT
* *
30374738 GAAAAAAATATTTAAGTAT
1 CAATAAAATATTTAAGTAT
*
30374757 CAGTAAAATA
1 CAATAAAATA
30374767 CTTACAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (19 bp):
CAATAAAATATTTAAGTAT
Found at i:30376469 original size:42 final size:41
Alignment explanation
Indices: 30376401--30376484 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 41
30376391 TATATATGCC
* *
30376401 ACACAGCCTGGGCACACCCTTGTGTCCTTGCCCGTATGGTTT
1 ACACAGCCTGGGCACACCC-TATGTCCTTGCCCATATGGTTT
*
30376443 ACACAGCCTGGGCACATGCCC-ATGTCCTTGCCCATGTGGTTT
1 ACACAGCCTGGGCACA--CCCTATGTCCTTGCCCATATGGTTT
30376485 TAAAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 34 0.92
44 3 0.08
ACGTcount: A:0.15, C:0.33, G:0.24, T:0.27
Consensus pattern (41 bp):
ACACAGCCTGGGCACACCCTATGTCCTTGCCCATATGGTTT
Found at i:30378451 original size:49 final size:49
Alignment explanation
Indices: 30378383--30378478 Score: 129
Period size: 49 Copynumber: 2.0 Consensus size: 49
30378373 ATAATCAACG
* * *
30378383 TCAACTGGGGGCTCAAGTTATACCTCAACCTGTGACCACATAACCACCA
1 TCAACTGGGAGCCCAAGTTATACCTCAACCTCTGACCACATAACCACCA
* * * *
30378432 TCAACTGGGAGCCCTAGTTATACTTCAACTTCTGACCATATAACCAC
1 TCAACTGGGAGCCCAAGTTATACCTCAACCTCTGACCACATAACCAC
30378479 GGTGAACTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (49 bp):
TCAACTGGGAGCCCAAGTTATACCTCAACCTCTGACCACATAACCACCA
Found at i:30380980 original size:15 final size:17
Alignment explanation
Indices: 30380953--30380987 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
30380943 TAATTAATAG
30380953 AAATAATAAAAC-AACA
1 AAATAATAAAACAAACA
30380969 AAATAA-AAAACAAACA
1 AAATAATAAAACAAACA
30380985 AAA
1 AAA
30380988 ACAATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.80, C:0.11, G:0.00, T:0.09
Consensus pattern (17 bp):
AAATAATAAAACAAACA
Found at i:30383633 original size:6 final size:6
Alignment explanation
Indices: 30383622--30383651 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30383612 CTTTTCTTTC
*
30383622 TTCTGT TTCTGT TTCTGT TTCTGC TTCTGT
1 TTCTGT TTCTGT TTCTGT TTCTGT TTCTGT
30383652 CCTTTGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.20, G:0.17, T:0.63
Consensus pattern (6 bp):
TTCTGT
Found at i:30385939 original size:13 final size:13
Alignment explanation
Indices: 30385921--30385945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30385911 TTTTTGAGTC
30385921 AAAAGTGTTTTTA
1 AAAAGTGTTTTTA
30385934 AAAAGTGTTTTT
1 AAAAGTGTTTTT
30385946 CAACTCAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
AAAAGTGTTTTTA
Found at i:30387494 original size:23 final size:23
Alignment explanation
Indices: 30387468--30387514 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
30387458 ATCTAGATAG
*
30387468 AAAAACAACTAATTGATATATTT
1 AAAAACAACTAATCGATATATTT
30387491 AAAAACAACTAATCGATATATTT
1 AAAAACAACTAATCGATATATTT
30387514 A
1 A
30387515 GTAAGCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (23 bp):
AAAAACAACTAATCGATATATTT
Found at i:30388003 original size:2 final size:2
Alignment explanation
Indices: 30387992--30388021 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
30387982 GTCTAATTGT
30387992 TA TA -A 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 T
30388022 GTAATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30395395 original size:11 final size:11
Alignment explanation
Indices: 30395379--30395408 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
30395369 CTGCTTTTCT
30395379 GCATTTTCTTG
1 GCATTTTCTTG
*
30395390 GCATTTTGTTG
1 GCATTTTCTTG
30395401 GCATTTTC
1 GCATTTTC
30395409 CTGGATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.10, C:0.17, G:0.20, T:0.53
Consensus pattern (11 bp):
GCATTTTCTTG
Found at i:30397955 original size:33 final size:33
Alignment explanation
Indices: 30397916--30397983 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
30397906 AAACACCATG
30397916 ACCACCCACAAATACTGAACCACAT-ATTGAACC
1 ACCACCCACAAATACTGAACCACATGA-TGAACC
30397949 ACCACCCACAAATACTGAACCACATGATGAACC
1 ACCACCCACAAATACTGAACCACATGATGAACC
30397982 AC
1 AC
30397984 ATATGAACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.43, C:0.37, G:0.07, T:0.13
Consensus pattern (33 bp):
ACCACCCACAAATACTGAACCACATGATGAACC
Found at i:30397991 original size:11 final size:12
Alignment explanation
Indices: 30397964--30397994 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
30397954 CCACAAATAC
30397964 TGAACCACATGA
1 TGAACCACATGA
30397976 TGAACCACAT-A
1 TGAACCACATGA
30397987 TGAACCAC
1 TGAACCAC
30397995 CAACTCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.42, C:0.29, G:0.13, T:0.16
Consensus pattern (12 bp):
TGAACCACATGA
Found at i:30401139 original size:19 final size:19
Alignment explanation
Indices: 30401087--30401130 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
30401077 TAGTTATGCG
*
30401087 AAAAA-TTCTTAAAATTTT
1 AAAAAGTTCATAAAATTTT
*
30401105 AAAATGTTCATAAAATTTT
1 AAAAAGTTCATAAAATTTT
30401124 AAAAAGT
1 AAAAAGT
30401131 ATTAAAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAAAGTTCATAAAATTTT
Found at i:30403507 original size:89 final size:90
Alignment explanation
Indices: 30403364--30403600 Score: 239
Period size: 89 Copynumber: 2.6 Consensus size: 90
30403354 CAGACGTTTG
* * * * ** * *
30403364 TGAATACACAACATTATTGCAGATAAAAGTTGCCAAATAATGGGTGGGTGAACCACCAAAGGCTG
1 TGAATACACAACATTTTTGCAGATAAAAATTGCTAGATAATATGTGGATGAACCACCAAA-GCTA
*
30403429 TA-GGCTAT-G-CTGCCAGATGGTTC
65 CATGGCTATAGTCTGCCAGATGGTTC
* * * * **
30403452 TGAATACACAACCTTTTTTGCATATAAAAATT-ATCAGGTAATATGTGGATGAACCACCAAATTT
1 TGAATACACAA-CATTTTTGCAGATAAAAATTGCT-AGATAATATGTGGATGAACCACCAAAGCT
** *
30403516 ACATGTTTATAGTCTGCCAGATGGTTG
64 ACATGGCTATAGTCTGCCAGATGGTTC
* *
30403543 TGAATACACAACATTTTTGTAGATAAAAGTTGCTAGATAATATGTGGATGAACCACCA
1 TGAATACACAACATTTTTGCAGATAAAAATTGCTAGATAATATGTGGATGAACCACCA
30403601 GATTTGCAGA
Statistics
Matches: 119, Mismatches: 24, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
88 13 0.11
89 41 0.34
90 40 0.34
91 25 0.21
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (90 bp):
TGAATACACAACATTTTTGCAGATAAAAATTGCTAGATAATATGTGGATGAACCACCAAAGCTAC
ATGGCTATAGTCTGCCAGATGGTTC
Found at i:30403597 original size:90 final size:88
Alignment explanation
Indices: 30403315--30403626 Score: 286
Period size: 90 Copynumber: 3.5 Consensus size: 88
30403305 CACATCGGGT
* * * * * *
30403315 TGTGGATGAACCACCAAATGTTGTAGGTTAATACGCTACCAGACGTTTGTGAATACACAACATTA
1 TGTGGATGAACCACCAAAT-TTGCA-GTTTATA-GCTGCCAGATGGTTGTGAATACACAACATTT
* * *
30403380 TTGCAGATAAAAGTTGCCAAATAATG
63 TTGCAGATAAAAGTTGCTAGATAATA
* * ** * ** * *
30403406 GGTGGGTGAACCACCAAAGGCTGTAGGCTAT-GCTGCCAGATGGTTCTGAATACACAACCTTTTT
1 TGTGGATGAACCACCAAA-TTTGCAGTTTATAGCTGCCAGATGGTTGTGAATACACAA-CATTTT
* * * *
30403470 TGCATATAAAAATT-ATCAGGTAATA
64 TGCAGATAAAAGTTGCT-AGATAATA
*
30403495 TGTGGATGAACCACCAAATTTACATGTTTATAGTCTGCCAGATGGTTGTGAATACACAACATTTT
1 TGTGGATGAACCACCAAATTTGCA-GTTTATAG-CTGCCAGATGGTTGTGAATACACAACATTTT
*
30403560 TGTAGATAAAAGTTGCTAGATAATA
64 TGCAGATAAAAGTTGCTAGATAATA
* *
30403585 TGTGGATGAACCACCAGATTTGCAGATTTATAGTTTGCCAGA
1 TGTGGATGAACCACCAAATTTGCAG-TTTATAG-CTGCCAGA
30403627 ACTTCCTCCT
Statistics
Matches: 175, Mismatches: 38, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
88 24 0.14
89 42 0.24
90 64 0.37
91 45 0.26
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (88 bp):
TGTGGATGAACCACCAAATTTGCAGTTTATAGCTGCCAGATGGTTGTGAATACACAACATTTTTG
CAGATAAAAGTTGCTAGATAATA
Found at i:30405456 original size:33 final size:33
Alignment explanation
Indices: 30405404--30405475 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
30405394 TTAATTTCAA
**
30405404 AAATTTAAAAATTCAAAAAATTATTTAAAAATT
1 AAATTTAAAAATTCAAAAAATTATAAAAAAATT
30405437 AAATTTCAAAAATTC-AAAAATTATAAAAAAATT
1 AAATTT-AAAAATTCAAAAAATTATAAAAAAATT
30405470 ATAATT
1 A-AATT
30405476 GTTTTTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
33 23 0.66
34 12 0.34
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (33 bp):
AAATTTAAAAATTCAAAAAATTATAAAAAAATT
Found at i:30407458 original size:2 final size:2
Alignment explanation
Indices: 30407451--30407488 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
30407441 CTCTTACTTT
30407451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30407489 AAAGAGTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30417290 original size:10 final size:10
Alignment explanation
Indices: 30417277--30417355 Score: 51
Period size: 10 Copynumber: 8.2 Consensus size: 10
30417267 AAAAGTTATA
30417277 AAAATTATTT
1 AAAATTATTT
*
30417287 AAAA--ATTA
1 AAAATTATTT
30417295 AAAATTA-TT
1 AAAATTATTT
*
30417304 AAAATAATTT
1 AAAATTATTT
* *
30417314 AAAA-AATATA
1 AAAATTAT-TT
*
30417324 AAAATATTTTT
1 AAAAT-TATTT
30417335 AAAATT-TTT
1 AAAATTATTT
*
30417344 AAAATTAATT
1 AAAATTATTT
30417354 AA
1 AA
30417356 TTGCTAACAT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
8 7 0.13
9 19 0.35
10 21 0.39
11 6 0.11
12 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AAAATTATTT
Found at i:30417306 original size:28 final size:27
Alignment explanation
Indices: 30417255--30417351 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 27
30417245 TAATTAAACT
*
30417255 TTTAAAAATTCAAAAAGTTATAAAAATTA
1 TTTAAAAATT-AAAAA-TTATTAAAATTA
*
30417284 TTTAAAAATTAAAAATTATTAAAATAA
1 TTTAAAAATTAAAAATTATTAAAATTA
*
30417311 TTTAAAAAATATAAAAATATTTTTAAAATT-
1 TTT-AAAAAT-T-AAAA-ATTATTAAAATTA
30417341 TTT-AAAATTAA
1 TTTAAAAATTAA
30417352 TTAATTGCTA
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.03
27 14 0.23
28 16 0.27
29 11 0.18
30 7 0.12
31 10 0.17
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
TTTAAAAATTAAAAATTATTAAAATTA
Found at i:30417317 original size:20 final size:20
Alignment explanation
Indices: 30417275--30417353 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
30417265 CAAAAAGTTA
*
30417275 TAAAAATTATTTAAA-AA-T
1 TAAAAATTATTAAAATAATT
30417293 TAAAAATTATTAAAATAATT
1 TAAAAATTATTAAAATAATT
* * *
30417313 TAAAAAATATAAAAATATTT
1 TAAAAATTATTAAAATAATT
* *
30417333 TTAAAATTTTTAAAATTAATT
1 TAAAAATTATTAAAA-TAATT
30417354 AATTGCTAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
18 14 0.29
19 2 0.04
20 29 0.59
21 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAAATTATTAAAATAATT
Found at i:30421366 original size:215 final size:215
Alignment explanation
Indices: 30420989--30421416 Score: 757
Period size: 215 Copynumber: 2.0 Consensus size: 215
30420979 GAGTTGATCA
30420989 AAACTATAGCTTATGGGTGTTGTAGGGTCTAAGATTGGGAAAGCACAAGTAGCCAAAAACTCGAA
1 AAACTATAGCTTATGGGTGTTGTAGGGTCTAAGATTGGGAAAGCACAAGTAGCCAAAAACTCGAA
* * *
30421054 GATATGAATAGCTTGGTTGAACCTAAAAGAGCTTTTCATACGGTGAGATGTTGCCTAAGGGAAAA
66 GAGATGAATAGCTTAGTTGAACCTAAAAGAGCTTTTCATACGGTGAGATGTTGCCTAAAGGAAAA
* * *
30421119 TAAGGCAAATTGTTTATTAAGTATACTGCACTACTGAAGGCATCATTCCAGTAGGTTAAGGGCAT
131 GAAGGCAAACTGTTTATCAAGTATACTGCACTACTGAAGGCATCATTCCAGTAGGTTAAGGGCAT
30421184 AGATGCATGAGCCAGTATCG
196 AGATGCATGAGCCAGTATCG
*
30421204 AAACTGTAGCTTATGGGTGTTGTAGGGTCTAAGATTGGGAAAGCACAAGTAGCCAAAAACTCGAA
1 AAACTATAGCTTATGGGTGTTGTAGGGTCTAAGATTGGGAAAGCACAAGTAGCCAAAAACTCGAA
* * *
30421269 GAGATGAATAGCTTAGTTGAAGCTGAAAGAGTTTTTCATACGGTGAGATGTTGCCTAAAGGAAAA
66 GAGATGAATAGCTTAGTTGAACCTAAAAGAGCTTTTCATACGGTGAGATGTTGCCTAAAGGAAAA
*
30421334 GAAGGCAACCTGTTTATCAAGTATACTGCACTACTGAAGGCATCATTCCAGTAGGTTAAGGGCAT
131 GAAGGCAAACTGTTTATCAAGTATACTGCACTACTGAAGGCATCATTCCAGTAGGTTAAGGGCAT
30421399 AGATGCATGAGCCAGTAT
196 AGATGCATGAGCCAGTAT
30421417 GGAAGGACCA
Statistics
Matches: 202, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
215 202 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (215 bp):
AAACTATAGCTTATGGGTGTTGTAGGGTCTAAGATTGGGAAAGCACAAGTAGCCAAAAACTCGAA
GAGATGAATAGCTTAGTTGAACCTAAAAGAGCTTTTCATACGGTGAGATGTTGCCTAAAGGAAAA
GAAGGCAAACTGTTTATCAAGTATACTGCACTACTGAAGGCATCATTCCAGTAGGTTAAGGGCAT
AGATGCATGAGCCAGTATCG
Found at i:30423493 original size:42 final size:42
Alignment explanation
Indices: 30423391--30423549 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 42
30423381 AATGTGATAT
*
30423391 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTT--GA-TTA
* * * *
30423435 CGTGTAATACCATGTCTGGGACATTGGCGTCGTATATGATTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTA
* *
30423477 CGTGTAAGACC-CTGTCTGGGACAGTGACATCGTTATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCG-TATTTGATTA
* **
30423520 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACATTGGCAT
30423550 TGTACGAGCC
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 29 0.31
43 34 0.36
44 29 0.31
45 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTA
Found at i:30423526 original size:43 final size:42
Alignment explanation
Indices: 30423432--30423540 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
30423422 GATTTGAGAT
* * * * *
30423432 TTACGTGTAATACCATGTCTGGGACATTGGCGTCGTATATGA
1 TTACGTGTAAGACCCTGTCTGGGACAGTGACATCGTATATGA
*
30423474 TTACGTGTAAGACCCTGTCTGGGACAGTGACATCGTTATTTGA
1 TTACGTGTAAGACCCTGTCTGGGACAGTGACATCG-TATATGA
*
30423517 TTACATGTAAGACCAC-GTCTGGGA
1 TTACGTGTAAGACC-CTGTCTGGGA
30423541 TGTTGGCATT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
42 30 0.52
43 27 0.47
44 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (42 bp):
TTACGTGTAAGACCCTGTCTGGGACAGTGACATCGTATATGA
Found at i:30426510 original size:23 final size:22
Alignment explanation
Indices: 30426467--30426524 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
30426457 AAAGGGTATC
* *
30426467 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
30426488 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
30426511 TGCATATCATATCT
1 TACAAATCATATCT
30426525 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:30428797 original size:2 final size:2
Alignment explanation
Indices: 30428790--30428831 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
30428780 CAAGCCTAGA
30428790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30428832 CAATAGCAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30434523 original size:16 final size:15
Alignment explanation
Indices: 30434485--30434523 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
30434475 AATATTTTTG
30434485 TATTTTTATATATTT
1 TATTTTTATATATTT
*
30434500 TAAATTTTATATATTAT
1 T-ATTTTTATATATT-T
30434517 TATTTTT
1 TATTTTT
30434524 TGTCAACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 17 0.85
17 2 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTATATATTT
Found at i:30436031 original size:2 final size:2
Alignment explanation
Indices: 30436026--30436057 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30436016 ATATTTACCC
30436026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30436058 AGCACTTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30438650 original size:18 final size:19
Alignment explanation
Indices: 30438620--30438656 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
30438610 TCAATAAATA
30438620 TTTTATATAAT-AATTTAG
1 TTTTATATAATAAATTTAG
30438638 TTTTA-ATATATAAATTTAG
1 TTTTATATA-ATAAATTTAG
30438657 AGTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 7 0.41
19 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTATATAATAAATTTAG
Found at i:30440416 original size:18 final size:18
Alignment explanation
Indices: 30440393--30440429 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30440383 TACTCATTCT
30440393 TTTGCTCATCATTACAGG
1 TTTGCTCATCATTACAGG
30440411 TTTGCTCATCATTACAGG
1 TTTGCTCATCATTACAGG
30440429 T
1 T
30440430 GCCTAACACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (18 bp):
TTTGCTCATCATTACAGG
Found at i:30442017 original size:100 final size:101
Alignment explanation
Indices: 30441891--30442089 Score: 373
Period size: 100 Copynumber: 2.0 Consensus size: 101
30441881 AAAAGGAATA
*
30441891 ATAAAATAACACAAAAAAATAAAAATAAATAATAATGAGATAATAATGACAATATAAAAAAATGT
1 ATAAAATAACACAAAAAAATAAAAATAAATAATAATGAGATAATAATGACAATAGAAAAAAATGT
30441956 ACAAATATGAACAATATAAATTTTAAAATAAAAAAC
66 ACAAATATGAACAATATAAATTTTAAAATAAAAAAC
*
30441992 ATAAAATAACAC-AAAAAATAAAAATAAATAATAATGAGATAATAATGACAATAGAACAAAATGT
1 ATAAAATAACACAAAAAAATAAAAATAAATAATAATGAGATAATAATGACAATAGAAAAAAATGT
30442056 ACAAATATGAACAATATAAATTTTAAAATAAAAA
66 ACAAATATGAACAATATAAATTTTAAAATAAAAA
30442090 GCAAGGGAAT
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
100 84 0.88
101 12 0.12
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (101 bp):
ATAAAATAACACAAAAAAATAAAAATAAATAATAATGAGATAATAATGACAATAGAAAAAAATGT
ACAAATATGAACAATATAAATTTTAAAATAAAAAAC
Found at i:30442881 original size:18 final size:19
Alignment explanation
Indices: 30442845--30442890 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
30442835 CTTTTTGTAA
*
30442845 TTGGACTTGTAATTTTTAT
1 TTGGGCTTGTAATTTTTAT
30442864 TTGGGCTTGTAA-TTTTAT
1 TTGGGCTTGTAATTTTTAT
30442882 TTGGG-TTGT
1 TTGGGCTTGT
30442891 TTGTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 11 0.42
19 11 0.42
ACGTcount: A:0.15, C:0.04, G:0.24, T:0.57
Consensus pattern (19 bp):
TTGGGCTTGTAATTTTTAT
Found at i:30444062 original size:19 final size:19
Alignment explanation
Indices: 30444025--30444063 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
30444015 TTATAAAGGC
*
30444025 TTAAAAATATATACATATA
1 TTAAAAATATACACATATA
* *
30444044 TTAAAAATATGCACCTATA
1 TTAAAAATATACACATATA
30444063 T
1 T
30444064 ATTATATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (19 bp):
TTAAAAATATACACATATA
Found at i:30445963 original size:44 final size:44
Alignment explanation
Indices: 30445738--30446438 Score: 584
Period size: 44 Copynumber: 15.8 Consensus size: 44
30445728 TGCTGCGCTT
* *
30445738 GATCTACTTCACGCC---A-ATGAAAACAAGGTCTG-TTCTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT-TCTTC
* * * * * * *
30445778 GATCTACTCCCCCACCAGTATAGGGAGACAAGATCTG-TTGTCTTT
1 GATCTACT-TCACGCCAGTACATGAAGACAAGATCTGCTT-TCTTC
* * *
30445823 GATCTATTTCACGCCAATACATGAAGACAAGATCTACTTTTTCCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGC--TTT-CTTC
* *** * *
30445870 GATCTACTTTGC-CACCAGTATGGGAAGACAAGATCT-ATTATCTTT
1 GATCTAC-TT-CACGCCAGTACATGAAGACAAGATCTGCTT-TCTTC
* * * *
30445915 GATCTACTTCAAGCTAGTACATGAAGACAATATTTGCTTTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
** * * *** * *
30445959 GATCTTTTTCGCCACCAGTATGGGAAGACAAGATCTG-TTACCTTT
1 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT-TCTTC
30446004 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
** * * *** *
30446048 GATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTG-TTATCTTT
1 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT-TCTTC
* * *
30446093 GATTTACTTCACGCCAGTACATGAAGACAATATTTGCTTTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
*
30446137 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
*
30446181 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* *
30446225 GATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
* * * *** *
30446269 GATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTG-TTATCTTT
1 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT-TCTTC
* *
30446314 GATCTACTCCACGCCAGTACATGAAGACAAGATCTACTTTCTTC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
** * * *
30446358 GATCTGTTTCGCCACCAGT--ATGGAAAGACAAGATCTG-TTATCTTT
1 GATCTACTTC-ACGCCAGTACAT-G-AAGACAAGATCTGCTT-TCTTC
*
30446403 GATCTACTTCACGCTAGTACATGAAGACAAGATCTG
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTG
30446439 TTATCTTTCA
Statistics
Matches: 519, Mismatches: 113, Indels: 54
0.76 0.16 0.08
Matches are distributed among these distances:
40 8 0.02
41 4 0.01
43 3 0.01
44 300 0.58
45 167 0.32
46 4 0.01
47 11 0.02
48 21 0.04
49 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (44 bp):
GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
Found at i:30445994 original size:89 final size:89
Alignment explanation
Indices: 30445736--30446230 Score: 603
Period size: 89 Copynumber: 5.6 Consensus size: 89
30445726 TCTGCTGCGC
* * * * *
30445736 TTGATCTACTTCACGCC---A-ATGAAAACAAGGTCTG-TTCTCTTCGATCTACTCCCCCACCAG
1 TTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT-TCTTCGATCTATTTCGCCACCAG
*
30445796 TATAGGG-AGACAAGATCTGTTGTCT
65 TAT-GGGAAGACAAGATCTGTTATCT
* * *
30445821 TTGATCTATTTCACGCCAATACATGAAGACAAGATCTACTTTTTCCTTCGATCTACTTT-GCCAC
1 TTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC--TTT-CTTCGATCTA-TTTCGCCAC
*
30445885 CAGTATGGGAAGACAAGATCTATTATCT
62 CAGTATGGGAAGACAAGATCTGTTATCT
* * * * *
30445913 TTGATCTACTTCAAGCTAGTACATGAAGACAATATTTGCTTTCTTCGATCTTTTTCGCCACCAGT
1 TTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTATTTCGCCACCAGT
*
30445978 ATGGGAAGACAAGATCTGTTACCT
66 ATGGGAAGACAAGATCTGTTATCT
*
30446002 TTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGT
1 TTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTATTTCGCCACCAGT
30446067 ATGGGAAGACAAGATCTGTTATCT
66 ATGGGAAGACAAGATCTGTTATCT
* * * * * * *
30446091 TTGATTTACTTCACGCCAGTACATGAAGACAATATTTGCTTTCTTCGATCTACTTC-ACGCCAAT
1 TTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTATTTCGCCACCAGT
***
30446155 ACATGAAGACAAGATCTGCTT-TCT
66 ATGGGAAGACAAGATCTG-TTATCT
* *
30446179 TCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTA
1 TTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
30446231 CTTCACGCCA
Statistics
Matches: 357, Mismatches: 41, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
85 16 0.04
88 74 0.21
89 189 0.53
90 3 0.01
91 4 0.01
92 70 0.20
93 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (89 bp):
TTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTATTTCGCCACCAGT
ATGGGAAGACAAGATCTGTTATCT
Found at i:30446286 original size:310 final size:313
Alignment explanation
Indices: 30445818--30446432 Score: 952
Period size: 310 Copynumber: 2.0 Consensus size: 313
30445808 AGATCTGTTG
* *
30445818 TCTTTGATCTATTTCACGCCAATACATGAAGACAAGATCTACTTTTTCCTTCGATCTACTTTGCC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTAC-TTTTCCTTCGATCTACTTTGCC
* ** * * * *
30445883 ACCAGTATGGGAAGACAAGATCTATTATCTTTGATCTACTTCAAGCTAGTACATGAAGACAATAT
65 ACCAATACAGGAAGACAAGATCTATTATCTTCGATCTACTTCAAGCCAATACATGAAGACAAGAT
* * ** *
30445948 TTGCTTTCTTCGATCTTTTTCGCCACCAGTATGGGAAGACAAGATCTGTTACCTTTGATCTACTT
130 CTACTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTACCTTTGATCTACTC
* *
30446013 CACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACA
195 CACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTGTTTCGCCACCAGTATGGAAAGACA
*
30446078 AGATCTGTTATCTTTGATTTACTTCACGCCAGTACATGAAGACAATATTTGCTT
260 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAATATTTGCTT
*
30446132 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC-TTT-CTTCGATCTAC-TT-CAC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTTCCTTCGATCTACTTTGC-C
* * * *
30446193 GCCAATACATGAAGACAAGATCTGCTT-TCTTCGATCTACTTCACGCCAATACATGAAGACAAGA
65 ACCAATACAGGAAGACAAGATCT-ATTATCTTCGATCTACTTCAAGCCAATACATGAAGACAAGA
*
30446257 TCTACTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACT
129 TCTACTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTACCTTTGATCTACT
30446322 CCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTGTTTCGCCACCAGTATGGAAAGAC
194 CCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTGTTTCGCCACCAGTATGGAAAGAC
*
30446387 AAGATCTGTTATCTTTGATCTACTTCACGCTAGTACATGAAGACAA
259 AAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAA
30446433 GATCTGTTAT
Statistics
Matches: 275, Mismatches: 24, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
309 1 0.00
310 219 0.80
311 13 0.05
312 3 0.01
314 39 0.14
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (313 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTTCCTTCGATCTACTTTGCCA
CCAATACAGGAAGACAAGATCTATTATCTTCGATCTACTTCAAGCCAATACATGAAGACAAGATC
TACTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTACCTTTGATCTACTCC
ACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTGTTTCGCCACCAGTATGGAAAGACAA
GATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAATATTTGCTT
Found at i:30446347 original size:89 final size:89
Alignment explanation
Indices: 30446115--30446437 Score: 445
Period size: 89 Copynumber: 3.6 Consensus size: 89
30446105 GCCAGTACAT
* * *
30446115 GAAGACAATATTTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTT
* * * * ***
30446180 CGATCTACTTC-ACGCCAATACAT
66 CGATCTGCTTCGCCACCAGTATGG
30446203 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTT
30446268 CGATCTGCTTCGCCACCAGTATGG
66 CGATCTGCTTCGCCACCAGTATGG
* * *
30446292 GAAGACAAGATCTG-TTATCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATCTACTTTCT
1 GAAGACAAGATCTGCTT-TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCT
*
30446356 TCGATCTGTTTCGCCACCAGTATGG
65 TCGATCTGCTTCGCCACCAGTATGG
* * * *
30446381 AAAGACAAGATCTG-TTATCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATCT
1 GAAGACAAGATCTGCTT-TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
30446438 GTTATCTTTC
Statistics
Matches: 216, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
88 74 0.34
89 142 0.66
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (89 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTT
CGATCTGCTTCGCCACCAGTATGG
Found at i:30448741 original size:19 final size:20
Alignment explanation
Indices: 30448713--30448754 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
30448703 ATAGTTTGGC
30448713 AAAAAGAATC-TGAAAGAATG
1 AAAAAGAATCGT-AAAGAATG
30448733 AAAAA-AATCGTAAAGAATG
1 AAAAAGAATCGTAAAGAATG
30448752 AAA
1 AAA
30448755 GAACATTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.64, C:0.05, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAAAGAATCGTAAAGAATG
Found at i:30450646 original size:19 final size:19
Alignment explanation
Indices: 30450622--30450667 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
30450612 AACGATGTCT
* *
30450622 AATGCATATG-ATGTAATG
1 AATGCAAATGCATGAAATG
30450640 AAATGCAAATGCATGAAATG
1 -AATGCAAATGCATGAAATG
30450660 AATGCAAA
1 AATGCAAA
30450668 AAAGAGATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (19 bp):
AATGCAAATGCATGAAATG
Found at i:30452407 original size:14 final size:14
Alignment explanation
Indices: 30452378--30452423 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
30452368 AATTTACAAC
*
30452378 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
30452392 ATTTACAAATATAT
1 ATATACAAATAAAT
30452406 ATATACAAATACAAT
1 ATATACAAATA-AAT
30452421 ATA
1 ATA
30452424 ACAGTAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:30452749 original size:19 final size:19
Alignment explanation
Indices: 30452712--30452750 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
30452702 TTATAAAGGC
*
30452712 TTAAAAATATATACATATA
1 TTAAAAATATACACATATA
* *
30452731 TTAAAAATATGCACCTATA
1 TTAAAAATATACACATATA
30452750 T
1 T
30452751 ATTATATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (19 bp):
TTAAAAATATACACATATA
Found at i:30463721 original size:21 final size:21
Alignment explanation
Indices: 30463696--30463766 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
30463686 CAGCAACTTA
* *
30463696 AAGCAGAGGCGGCAGCGAGTG
1 AAGCAGAGGCCGCAGCGAGAG
** *
30463717 AAGCAGAGGCTACAGCGAGAC
1 AAGCAGAGGCCGCAGCGAGAG
30463738 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
30463759 AAGCAGAG
1 AAGCAGAG
30463767 AGAGAAGCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.35, C:0.21, G:0.41, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:30463769 original size:12 final size:12
Alignment explanation
Indices: 30463749--30463790 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
30463739 AGCAGAGGCC
*
30463749 GCAGCGAGAGAA
1 GCAGAGAGAGAA
30463761 GCAGAGAGAGAA
1 GCAGAGAGAGAA
*
30463773 GCAGCA-ATAGAA
1 GCAG-AGAGAGAA
30463785 GCAGAG
1 GCAGAG
30463791 GTTCAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 24 0.92
13 1 0.04
ACGTcount: A:0.45, C:0.14, G:0.38, T:0.02
Consensus pattern (12 bp):
GCAGAGAGAGAA
Done.