Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 124 of 198
Found at i:39809826 original size:18 final size:18
Alignment explanation
Indices: 39809803--39809871 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
39809793 AGCTCTCAGG
39809803 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
39809821 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ** *
39809839 CA-GCAAGCTCCATTCATC
1 CATTC-TTCTCCCTTCATC
39809857 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
39809872 CTTCATTCCT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 1 0.02
18 39 0.95
19 1 0.02
ACGTcount: A:0.14, C:0.43, G:0.03, T:0.39
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:39812853 original size:14 final size:15
Alignment explanation
Indices: 39812831--39812907 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
39812821 CAATCAAACA
39812831 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
39812845 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
39812860 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
39812880 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
39812894 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
39812908 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:39812872 original size:20 final size:20
Alignment explanation
Indices: 39812847--39812886 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39812837 AATATTTTCC
*
39812847 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
39812867 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
39812887 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:39812892 original size:34 final size:35
Alignment explanation
Indices: 39812835--39812901 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
39812825 CAAACACCAG
*
39812835 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
39812870 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
39812902 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:39813061 original size:21 final size:21
Alignment explanation
Indices: 39813037--39813078 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39813027 ATATATAATT
39813037 TTTTATAATATAAAA-TAAATA
1 TTTTAT-ATATAAAATTAAATA
*
39813058 TTTTATATTTAAAATTAAATA
1 TTTTATATATAAAATTAAATA
39813079 AAATGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTATATATAAAATTAAATA
Found at i:39819484 original size:37 final size:37
Alignment explanation
Indices: 39819412--39819484 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
39819402 AGATAATCAC
*
39819412 TTTAATATTAAATTAATAAAATACTACTAAGATAAGT
1 TTTAATATTAAATTAATAAAATACTACTAAAATAAGT
* *
39819449 TTTAA-ATTAAATTTAATATTAAT-CTATTAAAATAAG
1 TTTAATATTAAA-TTAATA-AAATACTACTAAAATAAG
39819485 ATTATTATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 6 0.19
37 22 0.71
38 3 0.10
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (37 bp):
TTTAATATTAAATTAATAAAATACTACTAAAATAAGT
Found at i:39820718 original size:15 final size:15
Alignment explanation
Indices: 39820698--39820728 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39820688 GCTATGCATG
*
39820698 AAAAATATAAAAGAC
1 AAAAATACAAAAGAC
39820713 AAAAATACAAAAGAC
1 AAAAATACAAAAGAC
39820728 A
1 A
39820729 TAATATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAAATACAAAAGAC
Found at i:39822757 original size:6 final size:6
Alignment explanation
Indices: 39822746--39822772 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39822736 TTAGTCTAAT
39822746 TGAAAA TGAAAA TGAAAA TGAAAA TGA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGA
39822773 TAAAATGAAT
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:0.63, C:0.00, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAAAA
Found at i:39825780 original size:16 final size:18
Alignment explanation
Indices: 39825754--39825787 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39825744 TTAGAATTGG
39825754 ATTGAGAAAATT-ATTTA
1 ATTGAGAAAATTAATTTA
39825771 ATTG-GAAAATTAATTTA
1 ATTGAGAAAATTAATTTA
39825788 TCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
ATTGAGAAAATTAATTTA
Found at i:39832953 original size:2 final size:2
Alignment explanation
Indices: 39832946--39832976 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39832936 CTTGCTCTTC
39832946 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
39832977 CAAGTCAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:39842200 original size:28 final size:28
Alignment explanation
Indices: 39842160--39842215 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
39842150 TCAACTCTAA
* *
39842160 ACAAATTAGTCCACCTAGAGTCATATGC
1 ACAAATCAGTCCACCTAGAGCCATATGC
39842188 ACAAATCAGTCCACCTAGAGCCATATGC
1 ACAAATCAGTCCACCTAGAGCCATATGC
39842216 TCACAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (28 bp):
ACAAATCAGTCCACCTAGAGCCATATGC
Found at i:39859417 original size:15 final size:16
Alignment explanation
Indices: 39859384--39859425 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
39859374 ATAAATTGAG
*
39859384 AAATAATAAA-TTCAT
1 AAATTATAAATTTCAT
39859399 AAATTATAAATTTCA-
1 AAATTATAAATTTCAT
39859414 AAATT-TAAATTT
1 AAATTATAAATTT
39859426 TGAAATCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 14 0.56
16 4 0.16
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTATAAATTTCAT
Found at i:39865139 original size:2 final size:2
Alignment explanation
Indices: 39865067--39865131 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
39865057 ATTAAGCCTT
*
39865067 TA TA TA TA TA TA TA TA TA TA TA TA TA TT 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 TA TA
*
39865109 TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
39865132 CAATATATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39865422 original size:17 final size:19
Alignment explanation
Indices: 39865388--39865435 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
39865378 TTAATAATAT
*
39865388 TATATTTTTTGCACTTTTA
1 TATATTTTATGCACTTTTA
*
39865407 TATATTTTATG-ATTTTCTA
1 TATATTTTATGCACTTT-TA
*
39865426 TAAATTTTAT
1 TATATTTTAT
39865436 CTTTTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.62
Consensus pattern (19 bp):
TATATTTTATGCACTTTTA
Found at i:39866445 original size:18 final size:18
Alignment explanation
Indices: 39866400--39866454 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
39866390 AGGAATGTTG
*
39866400 ATATGATTAATATTT-TTA
1 ATATAATTAA-ATTTATTA
*
39866418 ATCATCATTAAATTTATTA
1 AT-ATAATTAAATTTATTA
*
39866437 ATATAATTATATTTATTA
1 ATATAATTAAATTTATTA
39866455 TGAATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
ATATAATTAAATTTATTA
Found at i:39868722 original size:14 final size:14
Alignment explanation
Indices: 39868703--39868742 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39868693 TTGATTGCCA
39868703 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
39868717 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
39868731 GGAAAATGTTTT
1 GTAAAATGTTTT
39868743 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:39868751 original size:20 final size:20
Alignment explanation
Indices: 39868726--39868765 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39868716 CGTAAAATGA
*
39868726 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
39868746 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
39868766 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:39868755 original size:34 final size:35
Alignment explanation
Indices: 39868711--39868777 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
39868701 CAGTAAAATG
*
39868711 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
39868745 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
39868778 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:39868781 original size:14 final size:15
Alignment explanation
Indices: 39868705--39868781 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
39868695 GATTGCCAGT
* *
39868705 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
39868719 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
39868733 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
39868753 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
39868768 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
39868782 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:39873284 original size:2 final size:2
Alignment explanation
Indices: 39873277--39873317 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39873267 AATGCTTTGG
39873277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39873318 GATTACCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39895142 original size:50 final size:50
Alignment explanation
Indices: 39895067--39895308 Score: 324
Period size: 50 Copynumber: 4.8 Consensus size: 50
39895057 ATTTGGGTAA
*
39895067 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
39895117 AGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTTGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* ** *
39895167 AGAGGCCCCCCGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * * *
39895217 AGAGGCCCCCTGTAAGACCATGTCTGGGACATGGCATAGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *
39895267 AGAACATCCCATGTAAGACCATGT-TTGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
39895309 TGTTATTATC
Statistics
Matches: 170, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
50 153 0.90
51 17 0.10
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:39895863 original size:19 final size:19
Alignment explanation
Indices: 39895839--39895876 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39895829 GTAAGTATTT
39895839 GATGATGAATGGTTGTTAA
1 GATGATGAATGGTTGTTAA
39895858 GATGATGAATGGTTGTTAA
1 GATGATGAATGGTTGTTAA
39895877 AATGGCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.37
Consensus pattern (19 bp):
GATGATGAATGGTTGTTAA
Found at i:39912870 original size:27 final size:27
Alignment explanation
Indices: 39912840--39912911 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
39912830 AACGTCCCTG
* * *
39912840 TGGCAAACTTTAAAGGAATGGTACT-TA
1 TGGCAAACTATAAAGGAACGGT-CTACA
* *
39912867 TGGCAAACTCTGAAGGAACGGTCTACA
1 TGGCAAACTATAAAGGAACGGTCTACA
*
39912894 TGGCGAACTATAAAGGAA
1 TGGCAAACTATAAAGGAA
39912912 ATGCCCTTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
26 2 0.05
27 35 0.95
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (27 bp):
TGGCAAACTATAAAGGAACGGTCTACA
Found at i:39917151 original size:152 final size:151
Alignment explanation
Indices: 39916826--39917293 Score: 554
Period size: 151 Copynumber: 3.1 Consensus size: 151
39916816 AAAGTTTTAT
* *
39916826 TTTTTTTC-AAAAAAGAGAAAGTTTAGATTTT-AACAAATAAAAATATGATTTTTTTTTAGTTAT
1 TTTTTTTCTAAAAAGGAGAAAGTTTAGATTTTGAA-AAATAAAAATAT-A-TTTTTTTTAGTCAT
* *
39916889 TTTAAAGGAAAGTTTAAATTTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCAAACTAAAA
63 TTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGA-TTTTTTTCAACTATTTCAAAATAAAA
* *
39916954 GC-TTAAACCTTCAAGAAAAATAGTG
127 GCTTTAATCATT-AAGAAAAATAGTG
39916979 TGTTTTTT-TAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATATATTTTTTTTAGTCATTT
1 T-TTTTTTCTAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATATATTTTTTTTAGTCATTT
*
39917043 TAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGGTTTTTTTCAACTATTTCAAAATAAAAGCT
65 TAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGCT
*
39917108 TTCATCATTAAGAAAAATAGTG
130 TTAATCATTAAGAAAAATAGTG
* * * * *
39917130 TTTTTTTCTAAAAAGGGAGAAATTTTAGACTTTGAAAAATAAAAATAT-GTTTTTTAAATCATTT
1 TTTTTTTCTAAAAA-GGAGAAAGTTTAGATTTTGAAAAATAAAAATATATTTTTTTTAGTCATTT
** * * * * * * * *
39917194 TAAAAAAAAGTCT-AAATATTTCAAATAAATTTTTGATTTTCTTAAACTATTTCAAAAT-AAGGT
65 TAAAGGAAAGTTTAAAAT-TTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGC
* ** * *
39917257 TTTGATTTTTAAGAAAAGTAATG
129 TTTAATCATTAAGAAAAATAGTG
*
39917280 GTTTTTTCTAAAAA
1 TTTTTTTCTAAAAA
39917294 AAAAACTTTT
Statistics
Matches: 278, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
150 44 0.16
151 104 0.37
152 86 0.31
153 2 0.01
154 40 0.14
155 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (151 bp):
TTTTTTTCTAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATATATTTTTTTTAGTCATTTT
AAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGCTT
TAATCATTAAGAAAAATAGTG
Found at i:39917247 original size:31 final size:31
Alignment explanation
Indices: 39917206--39917265 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
39917196 AAAAAAAGTC
*
39917206 TAAATATTTC-AAATAAATTTTTGATTTTCT
1 TAAATATTTCAAAATAAAGTTTTGATTTTCT
*
39917236 TAAACTATTTCAAAATAAGGTTTTGATTTT
1 TAAA-TATTTCAAAATAAAGTTTTGATTTT
39917266 TAAGAAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 4 0.15
31 6 0.23
32 16 0.62
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (31 bp):
TAAATATTTCAAAATAAAGTTTTGATTTTCT
Found at i:39917959 original size:2 final size:2
Alignment explanation
Indices: 39917952--39917982 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39917942 NNNNNNNNNN
39917952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39917983 TACACATTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39918884 original size:81 final size:80
Alignment explanation
Indices: 39918749--39918905 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 80
39918739 AAAATAAGCA
* *
39918749 TTAGCGGCGTTTTTATAAAAGCGCCGCAAAAAGCCAAAGACAAATGGCACCGTTTTCTGATTTTT
1 TTAGCGGCGTTTTTATAAAAGCGCCGCAAAAAGCCAAAGACAAACGGCACCGTTTTCTGA-GTTT
39918814 TGGGGTCTTTAGGTCT
65 TGGGGTCTTTAGGTCT
* * * *
39918830 TTAGCGGCGTTGTTT-TAAAAGCGCCGCAAAAAGTCTAAA-CCCAACGGCATCGTTTTCTGAGTT
1 TTAGCGGCGTT-TTTATAAAAGCGCCGCAAAAAG-CCAAAGACAAACGGCACCGTTTTCTGAGTT
39918893 TTGGGGTCTTTAG
64 TTGGGGTCTTTAG
39918906 TGGCGTTTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
80 15 0.22
81 46 0.68
82 7 0.10
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (80 bp):
TTAGCGGCGTTTTTATAAAAGCGCCGCAAAAAGCCAAAGACAAACGGCACCGTTTTCTGAGTTTT
GGGGTCTTTAGGTCT
Found at i:39919367 original size:112 final size:113
Alignment explanation
Indices: 39918824--39919539 Score: 1034
Period size: 113 Copynumber: 6.3 Consensus size: 113
39918814 TGGGGTCTTT
* * * * *
39918824 AGGTCTTTAGCGGCGTTGTTTTAAAAGCGCCGCAAAAAGTCTAAACCCAACGGCATCGTTTTCTG
1 AGGTCTTTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTG
* *
39918889 AG-TTTTGGGGTCTTTAGTGGCGTTTATGTAAAGTGCCGCTAATGCTC
66 AGTTTTTGGGGTCTTTAGCGGCGTTTATGTAAAGCGCCGCTAATGCTC
* *
39918936 ATGTCTTTAGCGGCGTTTTTTTAAA-GCGCCGCAAAAAAGCCTAAGCTCAACGGCACCGTTTTCT
1 AGGTCTTTAGCGGCGTTTTTTTAAATGCGCCGC-AAAAAGCCTAAGCCCAACGGCACCGTTTTCT
* *
39919000 GAGTTTTTGGGGTCTTTCGCGGCGTTTATGTAAAGCGCCGCTAATGTTC
65 GAGTTTTTGGGGTCTTTAGCGGCGTTTATGTAAAGCGCCGCTAATGCTC
* * *
39919049 AAGTCTTTAGTGGCATTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTG
1 AGGTCTTTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTG
*
39919114 AGTTTTTGAGGGTCTTTAGCGGCGCATTTA--TAAAGCGCCGCTAATGCTG
66 AGTTTTTG-GGGTCTTTAGCGGCG--TTTATGTAAAGCGCCGCTAATGCTC
* * * *
39919163 AGGTCTTTAGCGGCGTTTTCTCAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTG
1 AGGTCTTTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTG
*
39919228 AGTTTTTGGGGTCTTTAGTGGCGTTTTATGTAAAGCGCCGCTAATGCTC
66 AGTTTTTGGGGTCTTTAGCGGCG-TTTATGTAAAGCGCCGCTAATGCTC
* *
39919277 AGGTCTTTAGCGGCGTTTTTTTAAATGCGCCGC-AAAAGCCTAAGCCCAGC-GCACCGTTTTTTG
1 AGGTCTTTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTG
*
39919340 AGTTTTTGGGGTCTTTAGTGGCGTTTTATGTAAAGCGCCGCTAATGCTC
66 AGTTTTTGGGGTCTTTAGCGGCG-TTTATGTAAAGCGCCGCTAATGCTC
* *
39919389 AGGTCTTTAGCGGCGTTTTTTTAAATGCGCAGC-AAAAGCCTAAGCCCAACGGCACCGTTCTCTG
1 AGGTCTTTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTG
* * *
39919453 AGTTTTTGGGGTCTTTAGCGGCGTTTCTGAATAAGCGCCGCTAATGCTG
66 AGTTTTTGGGGTCTTTAGCGGCGTTTATGTA-AAGCGCCGCTAATGCTC
* *
39919502 ATGCCTTTAGCGGCGTTTTTTGTAAA-GCGCCGCAAAAA
1 AGGTCTTTAGCGGCGTTTTTT-TAAATGCGCCGCAAAAA
39919540 CATTTTATCT
Statistics
Matches: 548, Mismatches: 44, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
111 7 0.01
112 172 0.31
113 205 0.37
114 160 0.29
116 4 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (113 bp):
AGGTCTTTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTG
AGTTTTTGGGGTCTTTAGCGGCGTTTATGTAAAGCGCCGCTAATGCTC
Found at i:39922731 original size:21 final size:22
Alignment explanation
Indices: 39922687--39922731 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
39922677 TATAAAAAAA
39922687 TTAATATTATACATAACTTGATTAT
1 TTAATATTATACATAA--T-ATTAT
39922712 TTAATATTATACATAA-ATTA
1 TTAATATTATACATAATATTA
39922732 CATAACTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
25 16 0.80
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAATATTATACATAATATTAT
Found at i:39922739 original size:34 final size:33
Alignment explanation
Indices: 39922696--39923026 Score: 245
Period size: 34 Copynumber: 10.3 Consensus size: 33
39922686 ATTAATATTA
*
39922696 TACATAACTTGATTATTTAATATTATACATAAAT
1 TACATAACTT-ATTAATTAATATTATACATAAAT
39922730 TACATAACTTAATTAATTAATATTATAC----A-
1 TACATAACTT-ATTAATTAATATTATACATAAAT
**
39922759 T--ATAAC-T-TGCATTAATATTATACATAAAT
1 TACATAACTTATTAATTAATATTATACATAAAT
* *
39922788 TACATGACTTAATTAATTAATATTATACATTAAT
1 TACATAACTT-ATTAATTAATATTATACATAAAT
* *
39922822 TACATAACTTA--CATTAATATTATACTTAAAT
1 TACATAACTTATTAATTAATATTATACATAAAT
* *
39922853 TACATAAGTTAGTTAATTAATATTATACATAACT
1 TACATAACTTA-TTAATTAATATTATACATAAAT
* * *
39922887 TACATAACTTA-CAACTTACATAACT-TAC--AACT
1 TACATAACTTATTAA-TTA-AT-ATTATACATAAAT
* * *
39922919 TACATAACTTA-CAATCTACATAACT-TAC-T-ACT
1 TACATAACTTATTAAT-TA-AT-ATTATACATAAAT
* *
39922951 TACATAACTTA--CATTAATATTATACTTAAAT
1 TACATAACTTATTAATTAATATTATACATAAAT
* *
39922982 TACATAAGTTAGTTAATTAATATTATACATAACT
1 TACATAACTTA-TTAATTAATATTATACATAAAT
39923016 TACATAACTTA
1 TACATAACTTA
39923027 CAACTTACAT
Statistics
Matches: 246, Mismatches: 27, Indels: 48
0.77 0.08 0.15
Matches are distributed among these distances:
24 14 0.06
26 1 0.00
27 5 0.02
28 3 0.01
29 7 0.03
30 4 0.02
31 46 0.19
32 47 0.19
33 4 0.02
34 113 0.46
35 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (33 bp):
TACATAACTTATTAATTAATATTATACATAAAT
Found at i:39922837 original size:65 final size:65
Alignment explanation
Indices: 39922760--39923225 Score: 330
Period size: 65 Copynumber: 7.2 Consensus size: 65
39922750 TATTATACAT
* * *
39922760 ATAACTTGCATTAATATTATACATAAATTACATGACTTAATTAATTAATATTATACATTAA-TTA
1 ATAACTTACATTAATATTATACTTAAATTACATAACTTAATTAATTAATATTATACA-TAACTTA
39922824 C
65 C
* *
39922825 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
1 ATAACTTACATTAATATTATACTTAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
* * *
39922890 ATAACTTACAACTT-ACA-TA-ACTTACAACTTACATAACTT-A-CAATCTACATAACT-TAC-T
1 ATAACTTAC-A-TTAATATTATACTTA-AA-TTACATAACTTAATTAAT-TA-AT-ATTATACAT
39922948 -ACTTAC
59 AACTTAC
* *
39922954 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
1 ATAACTTACATTAATATTATACTTAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
* * *
39923019 ATAACTTACAACTT-ACA-TA-ACTTACAATCTACATAACTTACA--ACTTACATAACT-TACAT
1 ATAACTTAC-A-TTAATATTATACTTA-AAT-TACATAACTTA-ATTAATTA-AT-ATTATACA-
***
39923078 TTTTTTA-
58 TAACTTAC
* * * * * * *
39923085 ATTATTCGTAAATTACATAACT-TACTTAATTTTCATAA--TACA-TAACTTACATAACT-TAC-
1 A-TA-ACTTACATTA-AT-ATTATACTTAAATTACATAACTTA-ATTAA-TTA-AT-ATTATACA
39923144 -AACTTAC
58 TAACTTAC
* *
39923151 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
1 ATAACTTACATTAATATTATACTTAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
39923216 ATAACTTACA
1 ATAACTTACA
39923226 ACTTACATAA
Statistics
Matches: 319, Mismatches: 41, Indels: 82
0.72 0.09 0.19
Matches are distributed among these distances:
62 8 0.03
63 39 0.12
64 48 0.15
65 131 0.41
66 45 0.14
67 16 0.05
68 23 0.07
69 3 0.01
70 6 0.02
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.39
Consensus pattern (65 bp):
ATAACTTACATTAATATTATACTTAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
Found at i:39922892 original size:9 final size:9
Alignment explanation
Indices: 39922878--39923258 Score: 212
Period size: 9 Copynumber: 44.6 Consensus size: 9
39922868 ATTAATATTA
39922878 TACATAACT
1 TACATAACT
39922887 TACATAACT
1 TACATAACT
39922896 TAC--AACT
1 TACATAACT
39922903 TACATAACT
1 TACATAACT
39922912 TAC--AACT
1 TACATAACT
39922919 TACATAACT
1 TACATAACT
*
39922928 TACA-ATC-
1 TACATAACT
39922935 TACATAACT
1 TACATAACT
39922944 TAC-T-ACT
1 TACATAACT
39922951 TACATAACT
1 TACATAACT
*
39922960 TACATTAATATT
1 TACA-T-A-ACT
* *
39922972 ATACTTAAAT
1 -TACATAACT
*
39922982 TACATAAGT
1 TACATAACT
**
39922991 TAGTTAA-T
1 TACATAACT
*
39922999 TA-AT-ATT
1 TACATAACT
39923006 ATACATAACT
1 -TACATAACT
39923016 TACATAACT
1 TACATAACT
39923025 TAC--AACT
1 TACATAACT
39923032 TACATAACT
1 TACATAACT
*
39923041 TACA-ATC-
1 TACATAACT
39923048 TACATAACT
1 TACATAACT
39923057 TAC--AACT
1 TACATAACT
39923064 TACATAACT
1 TACATAACT
***
39923073 TACATTTTTT
1 TACA-TAACT
*
39923083 TA-ATTA-T
1 TACATAACT
* *
39923090 T-CGTAAAT
1 TACATAACT
39923098 TACATAACT
1 TACATAACT
* *
39923107 TACTTAATT
1 TACATAACT
*
39923116 TTCATAA--
1 TACATAACT
39923123 TACATAACT
1 TACATAACT
39923132 TACATAACT
1 TACATAACT
39923141 TAC--AACT
1 TACATAACT
39923148 TACATAACT
1 TACATAACT
*
39923157 TACATTAATATT
1 TACA-T-A-ACT
* *
39923169 ATACTTAAAT
1 -TACATAACT
*
39923179 TACATAAGT
1 TACATAACT
**
39923188 TAGTTAA-T
1 TACATAACT
*
39923196 TA-AT-ATT
1 TACATAACT
39923203 ATACATAACT
1 -TACATAACT
39923213 TACATAACT
1 TACATAACT
39923222 TAC--AACT
1 TACATAACT
39923229 TACATAACT
1 TACATAACT
*
39923238 TACA-ATC-
1 TACATAACT
39923245 TACATAACT
1 TACATAACT
39923254 TACAT
1 TACAT
39923259 TTTTTTAATT
Statistics
Matches: 293, Mismatches: 37, Indels: 84
0.71 0.09 0.20
Matches are distributed among these distances:
6 2 0.01
7 74 0.25
8 28 0.10
9 159 0.54
10 14 0.05
11 4 0.01
12 6 0.02
13 6 0.02
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:39922904 original size:16 final size:16
Alignment explanation
Indices: 39922883--39923257 Score: 216
Period size: 16 Copynumber: 23.1 Consensus size: 16
39922873 TATTATACAT
39922883 AACTTACATAACTTAC
1 AACTTACATAACTTAC
39922899 AACTTACATAACTTAC
1 AACTTACATAACTTAC
39922915 AACTTACATAACTTAC
1 AACTTACATAACTTAC
39922931 AA-TCTACATAACTTAC
1 AACT-TACATAACTTAC
*
39922947 TACTTACATAACTTAC
1 AACTTACATAACTTAC
*
39922963 -A-TTAATATTATACTTA-
1 AACTT-ACA-TA-ACTTAC
* *
39922979 AA-TTACATAAGTTAGTT
1 AACTTACATAACTTA--C
*
39922996 AA-TTA-AT-ATTATAC
1 AACTTACATAACT-TAC
39923010 ATAACTTACATAACTTAC
1 --AACTTACATAACTTAC
39923028 AACTTACATAACTTAC
1 AACTTACATAACTTAC
39923044 AA-TCTACATAACTTAC
1 AACT-TACATAACTTAC
39923060 AACTTACATAACTTAC
1 AACTTACATAACTTAC
* ***
39923076 -ATTTTTTTAA-TTATTC
1 AACTTACATAACTTA--C
*
39923092 GTAAATTACATAACTTAC
1 --AACTTACATAACTTAC
* *
39923110 TTAATTTTCATAA--TAC
1 --AACTTACATAACTTAC
39923126 ATAACTTACATAACTTAC
1 --AACTTACATAACTTAC
39923144 AACTTACATAACTTAC
1 AACTTACATAACTTAC
*
39923160 -A-TTAATATTATACTTA-
1 AACTT-ACA-TA-ACTTAC
* *
39923176 AA-TTACATAAGTTAGTT
1 AACTTACATAACTTA--C
*
39923193 AA-TTA-AT-ATTATAC
1 AACTTACATAACT-TAC
39923207 ATAACTTACATAACTTAC
1 --AACTTACATAACTTAC
39923225 AACTTACATAACTTAC
1 AACTTACATAACTTAC
39923241 AA-TCTACATAACTTAC
1 AACT-TACATAACTTAC
39923257 A
1 A
39923258 TTTTTTTAAT
Statistics
Matches: 293, Mismatches: 27, Indels: 78
0.74 0.07 0.20
Matches are distributed among these distances:
14 15 0.05
15 23 0.08
16 184 0.63
17 34 0.12
18 24 0.08
19 10 0.03
20 3 0.01
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.38
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:39922980 original size:129 final size:127
Alignment explanation
Indices: 39922820--39923160 Score: 485
Period size: 129 Copynumber: 2.8 Consensus size: 127
39922810 TTATACATTA
39922820 ATTACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAA
1 ATTACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAA
39922885 CTTACATAACTTACAACTTACATAACTTACAA-CTTACATAACTTACAA-TCTACATAACTTAC
66 CTTACATAACTTACAACTTACATAACTTACAATC-TACATAACTTACAACT-TACATAACTTAC
39922947 TACTTACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACAT
1 -A-TTACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACAT
39923012 AACTTACATAACTTACAACTTACATAACTTACAATCTACATAACTTACAACTTACATAACTTAC
64 AACTTACATAACTTACAACTTACATAACTTACAATCTACATAACTTACAACTTACATAACTTAC
* * * * * *
39923076 ATT---T---TT---TT-A-ATTATTCGTAAATTACATAACTTACTTAATT-TTCATAATACATA
1 ATTACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAAT-ATTATACATA
39923129 ACTTACATAACTTACAACTTACATAACTTACA
65 ACTTACATAACTTACAACTTACATAACTTACA
39923161 TTAATATTAT
Statistics
Matches: 203, Mismatches: 6, Indels: 20
0.89 0.03 0.09
Matches are distributed among these distances:
115 1 0.00
116 68 0.33
117 1 0.00
118 2 0.01
121 2 0.01
124 1 0.00
127 2 0.01
128 2 0.01
129 122 0.60
130 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.01, T:0.38
Consensus pattern (127 bp):
ATTACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAA
CTTACATAACTTACAACTTACATAACTTACAATCTACATAACTTACAACTTACATAACTTAC
Found at i:39923106 original size:34 final size:35
Alignment explanation
Indices: 39923063--39923144 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 35
39923053 AACTTACAAC
* * * *
39923063 TTACATAACTTACATT-TTTTTAATTATTCGTAAA
1 TTACATAACTTACATTAATTTTAATAATACATAAA
* *
39923097 TTACATAACTTAC-TTAATTTTCATAATACATAAC
1 TTACATAACTTACATTAATTTTAATAATACATAAA
39923131 TTACATAACTTACA
1 TTACATAACTTACA
39923145 ACTTACATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.05
34 38 0.95
ACGTcount: A:0.39, C:0.16, G:0.01, T:0.44
Consensus pattern (35 bp):
TTACATAACTTACATTAATTTTAATAATACATAAA
Found at i:39929010 original size:65 final size:66
Alignment explanation
Indices: 39928906--39929051 Score: 224
Period size: 65 Copynumber: 2.2 Consensus size: 66
39928896 GAGGCAACAT
*
39928906 CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCAGCAGCTTAGAGCAGAT-CAGCA
1 CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCAACAGCTTAGAGCAGATGCAGCA
39928970 G
66 G
* *
39928971 CGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAGCAACAGCTTAGAGCAGATGCGGC
1 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCAACAGCTTAGAGCAGATGCAGC
39929035 AG
65 AG
* *
39929037 CAAGAGAAGCAGAGG
1 CGAGAGAAGCTGAGG
39929052 CGGCAGCAAG
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
65 52 0.70
66 22 0.30
ACGTcount: A:0.39, C:0.18, G:0.30, T:0.12
Consensus pattern (66 bp):
CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCAACAGCTTAGAGCAGATGCAGCA
G
Found at i:39929047 original size:21 final size:21
Alignment explanation
Indices: 39929023--39929134 Score: 91
Period size: 21 Copynumber: 5.3 Consensus size: 21
39929013 AACAGCTTAG
*
39929023 AGCAGATGCGGCAGCAAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
39929044 AGCAGAGGCGGCAGCAAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
* * * * *
39929065 AGTACAGGCTGCAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
* * *
39929086 AGCAGAGGCTGTAGCGAG-GCA
1 AGCAGAGGCGGCAGCAAGAG-A
* * * *
39929107 AGTAGAGGCTGCAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
39929128 AGCAGAG
1 AGCAGAG
39929135 TAGCGTCAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
20 1 0.01
21 75 0.97
22 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.43, T:0.06
Consensus pattern (21 bp):
AGCAGAGGCGGCAGCAAGAGA
Found at i:39929088 original size:42 final size:42
Alignment explanation
Indices: 39929033--39929134 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 42
39929023 AGCAGATGCG
* *
39929033 GCAGCAAGAGAAGCAGAGGCGGCAGCAAGAG-AAGTACAGGCT
1 GCAGCGAGGGAAGCAGAGGCGGCAGCAAG-GCAAGTACAGGCT
* * * *
39929075 GCAGCGAGGGAAGCAGAGGCTGTAGCGAGGCAAGTAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCGGCAGCAAGGCAAGTACAGGCT
39929117 GCAGCGAGGGAAGCAGAG
1 GCAGCGAGGGAAGCAGAG
39929135 TAGCGTCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.33, C:0.18, G:0.43, T:0.06
Consensus pattern (42 bp):
GCAGCGAGGGAAGCAGAGGCGGCAGCAAGGCAAGTACAGGCT
Found at i:39929616 original size:43 final size:43
Alignment explanation
Indices: 39929484--39929838 Score: 171
Period size: 43 Copynumber: 8.3 Consensus size: 43
39929474 AGGTGTTGGC
* * * ** * *
39929484 CTTTAGTGGCATTTTTGGTAAAAGCGCCGCTAAAGAGAAGGTT
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGACCATGAT
* * * * * *
39929527 ATTTACCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGACCATGAT
* *
39929570 CTTTAGCGGCGTTTTCGGGAAAAGCGCCGCTAAAGACCATGAT
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGACCATGAT
* ***** * * * *
39929613 CTTTAGTGGCGTTTTTATCCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGACCATGAT
* * * * * ** *
39929656 CTACT-GCGGCGTTTTTTGTAAAAGCGCCGCTATAGATCGGGGT
1 CT-TTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGACCATGAT
* ** * * * **
39929699 CTATT-GAGGCGTTTGCGGGAGAAGCGCCGCTATAGATCGGTG-T
1 CT-TTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGA-CCATGAT
* ***
39929742 CTATT-GCGGCGTTTTTAGAAAAAGCGCCGCTAAAGACCCCAAT
1 CT-TTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGACCATGAT
*** * * *
39929785 CTTTAGCGGCG-TTTCCCACAAAAACGCCGATAAAGACCCTGAT
1 CTTTAGCGGCGTTTTTGGA-AAAAGCGCCGCTAAAGACCATGAT
39929828 CTTTAGCGGCG
1 CTTTAGCGGCG
39929839 CTTCCACTAA
Statistics
Matches: 241, Mismatches: 66, Indels: 10
0.76 0.21 0.03
Matches are distributed among these distances:
42 7 0.03
43 231 0.96
44 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGACCATGAT
Found at i:39929624 original size:86 final size:87
Alignment explanation
Indices: 39929440--39929626 Score: 196
Period size: 86 Copynumber: 2.2 Consensus size: 87
39929430 AATCTGCCAA
* * ** * * *
39929440 ATTTAGTGGCGTTTTTCAAAAAAAACGCCACTAAAGGTGTTGGCCTTTAGTGGCATTTTTGGTAA
1 ATTTAGTGGCGTTTGTCAAAAAAAACGCCACTAAAGATCATGGCCTTTAGCGGCATTTTCGGGAA
* *
39929505 AAGCGCCGCTAAAGAGAAGGTT
66 AAGCGCCGCTAAAGACAAGGAT
** ** * * *
39929527 ATTTACCGGCGTTTGT-GGAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCGGGAA
1 ATTTAGTGGCGTTTGTCAAAAAAAACGCCACTAAAGATCATGGCCTTTAGCGGCATTTTCGGGAA
* *
39929591 AAGCGCCGCTAAAGACCATGAT
66 AAGCGCCGCTAAAGACAAGGAT
*
39929613 CTTTAGTGGCGTTT
1 ATTTAGTGGCGTTT
39929627 TTATCCGAAG
Statistics
Matches: 79, Mismatches: 21, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
86 66 0.84
87 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (87 bp):
ATTTAGTGGCGTTTGTCAAAAAAAACGCCACTAAAGATCATGGCCTTTAGCGGCATTTTCGGGAA
AAGCGCCGCTAAAGACAAGGAT
Found at i:39930047 original size:22 final size:22
Alignment explanation
Indices: 39930021--39930062 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
39930011 TACGGCGCTT
*
39930021 AAAAGCGCCGCTAAAGGCCTAA
1 AAAAGCGCCGCTAAAAGCCTAA
39930043 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCCGCTAAAAGCCT
39930063 GTTCTGCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGCGCCGCTAAAAGCCTAA
Found at i:39940176 original size:17 final size:16
Alignment explanation
Indices: 39940129--39940201 Score: 53
Period size: 17 Copynumber: 4.6 Consensus size: 16
39940119 TTATATCAAG
39940129 AAAAA-AAAAAG--AA
1 AAAAATAAAAAGAAAA
* *
39940142 AAAAACACAAAGACAAA
1 AAAAATAAAAAGA-AAA
* *
39940159 AATAATAAAACGAAAA
1 AAAAATAAAAAGAAAA
*
39940175 AAAGAAAAAAAAGAAACA
1 AAA-AATAAAAAGAAA-A
39940193 AAAAATAAA
1 AAAAATAAA
39940202 GAGATAGCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
16 5 0.11
17 26 0.58
18 4 0.09
ACGTcount: A:0.82, C:0.07, G:0.07, T:0.04
Consensus pattern (16 bp):
AAAAATAAAAAGAAAA
Found at i:39940677 original size:42 final size:42
Alignment explanation
Indices: 39940603--39941107 Score: 654
Period size: 42 Copynumber: 12.1 Consensus size: 42
39940593 AAGGAAAACA
* * *
39940603 TTCATTGCATTTAGAGGCCCAGGTCTGGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * *
39940645 TTCATTGCATTTAGAGACCCAAGTGTGAAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * * * *
39940687 TTCATTACATTTAGAAACTCAGGTTTGGAGGTCCACTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * *
39940729 TTCATTGCATTTAGAGGCCCGGGTATGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* ** *
39940771 TTCATTGCATTTAGAGGCTTAGGTATGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
**
39940813 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCTGTTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
39940855 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* ** * ** *
39940897 TTTATTGCATTTA-A-ACTTAAGACTGGAGATCCATTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* *
39940937 TTCATTGCATTTAGAGACCCAGGTTTGGAGGTCAATTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * * *
39940979 TTTATTGCATTTAGAGGCCCAGGTGTGGAGGTCAATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * *
39941021 TTCATTGCATTTAAAGACCCAGGTGTGGAGGTTCATTAACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* *
39941063 TTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
39941105 TTC
1 TTC
39941108 TAGTTTACTT
Statistics
Matches: 401, Mismatches: 60, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
40 32 0.08
41 2 0.00
42 367 0.92
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
Found at i:39941445 original size:16 final size:16
Alignment explanation
Indices: 39941424--39941458 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
39941414 GAGACCTATA
*
39941424 TTTCTCTTTTCTTTCT
1 TTTCTCTCTTCTTTCT
39941440 TTTCTCTCTTCTTTCT
1 TTTCTCTCTTCTTTCT
39941456 TTT
1 TTT
39941459 TTGGGCTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTCTCTTCTTTCT
Found at i:39942408 original size:154 final size:150
Alignment explanation
Indices: 39941885--39942603 Score: 879
Period size: 153 Copynumber: 4.8 Consensus size: 150
39941875 TTTAAAAAAA
* * *
39941885 AAAAAGG-GAAAGTTTAGATTTT-AACAAATAAAAATCTA-TTTTTTTTACTTATTTCAAAGGAA
1 AAAAAGGAGAAAGTTTAGATTTTGAA-AAATAAAAATCTATTTTTTTTTAGTCATTTTAAAGGAA
* * * **
39941947 AGTTTAAAATTTTAAAAC--A--TT--TTTTTTTTCAATTATTTCAGAGTGCAAGCTTTAATCTT
65 AGTTTAAAATTTTAAAACAAAGTTTGATTTTTTTTCAACTATTTCAAAATAAAAGCTTTAATCTT
39942006 TAAGAAAAATAGTGTTTTTTT
130 TAAGAAAAATAGTGTTTTTTT
39942027 AAAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTTAGTCATTTTAAAG
1 ----AAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTTAGTCATTTTAAAG
* * *
39942092 GAAAGTTTAAAATTTTTAAACAAAGTTTTAATTTTTTTTCAACTATTTCAAAATAAAATCTTTAA
62 GAAAGTTTAAAATTTTAAAACAAAG-TTTGATTTTTTTTCAACTATTTCAAAATAAAAGCTTTAA
39942157 TCTTTAAGAAAAATAGTGTTTTTCTT
126 TCTTTAAGAAAAATAGTGTTTTT-TT
* *
39942183 AAAAAGGAAGAAAGTTTAGATTTTGAAAAATAAAAAATCTA-TTTTTTTAAATCATTTTAAAGGA
1 AAAAAGG-AGAAAGTTTAGATTTTGAAAAAT-AAAAATCTATTTTTTTTTAGTCATTTTAAAGGA
* * * * * *
39942247 AAATTTAAATTTTTAAAATAAAGTTTCGATTTTTTTTTCAACTATTTCAAAGTAAAAAACGTTAA
64 AAGTTTAAAATTTTAAAACAAAGTTT-GA-TTTTTTTTCAACTATTTCAAAAT-AAAAGCTTTAA
39942312 TCTTTAAGAAAAATAGTGTTTTTTT
126 TCTTTAAGAAAAATAGTGTTTTTTT
*** *
39942337 TTTAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCCATTTTTGTTTTAGTCATTTTAAAGGAA
1 AAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTT-TTTTAGTCATTTTAAAGGAA
* *
39942402 ACTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCAAAATAAAAGTTTTAATCT
65 AGTTTAAAATTTTAAAACAAAG-TTTGATTTTTTTTCAACTATTTCAAAATAAAAGCTTTAATCT
39942467 TTAAGAAAAATAGTGTTTTTTT
129 TTAAGAAAAATAGTGTTTTTTT
* * * * * * *
39942489 TAAAGGGAGAAAGTTTAGATTTTAAAAAATAAAAAT-T-TGTTTCTTTAAGCCATTTTAAAGAAA
1 AAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTAT-TTTTTTTTAGTCATTTTAAAGGAA
* * * *
39942552 AGTTTAAACTTTTAAAATAAAATTTTGATTTTTTTT-AACTATTTCGAAATAA
65 AGTTTAAAATTTTAAAA-CAAAGTTTGATTTTTTTTCAACTATTTCAAAATAA
39942604 GTTTTTGATT
Statistics
Matches: 505, Mismatches: 47, Indels: 39
0.85 0.08 0.07
Matches are distributed among these distances:
146 7 0.01
147 28 0.06
148 40 0.08
149 15 0.03
150 47 0.09
151 6 0.01
152 83 0.16
153 115 0.23
154 76 0.15
155 86 0.17
156 2 0.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (150 bp):
AAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTTAGTCATTTTAAAGGAAA
GTTTAAAATTTTAAAACAAAGTTTGATTTTTTTTCAACTATTTCAAAATAAAAGCTTTAATCTTT
AAGAAAAATAGTGTTTTTTT
Found at i:39942589 original size:31 final size:32
Alignment explanation
Indices: 39942558--39942616 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
39942548 GAAAAGTTTA
39942558 AACT-TTT-AAAATAAAATTTTGATTTTTTTT
1 AACTATTTCAAAATAAAATTTTGATTTTTTTT
* **
39942588 AACTATTTCGAAATAAGTTTTTGATTTTT
1 AACTATTTCAAAATAAAATTTTGATTTTT
39942617 AAGAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 3 0.12
32 17 0.71
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (32 bp):
AACTATTTCAAAATAAAATTTTGATTTTTTTT
Found at i:39943157 original size:25 final size:24
Alignment explanation
Indices: 39943129--39943175 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
39943119 TCACTTGCAT
39943129 TTATACA-TTATATATTTAATGTTAA
1 TTATACACTT-TAT-TTTAATGTTAA
*
39943154 TTATGCACTTTATTTTAATGTT
1 TTATACACTTTATTTTAATGTT
39943176 TTATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 9 0.45
26 2 0.10
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TTATACACTTTATTTTAATGTTAA
Found at i:39943351 original size:3 final size:3
Alignment explanation
Indices: 39943334--39943375 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
39943324 GAATAAGGTA
* *
39943334 TAT TAT TGT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39943376 CATCATGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39944747 original size:43 final size:43
Alignment explanation
Indices: 39944646--39944747 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 43
39944636 AGGCTGTGTT
* *
39944646 CTTTAGCGACGCATTTATAACAATCGCCGCTAAAAAACATGGC
1 CTTTAGCGACGCTTTTATAACAATCGCCGCTAAAAAACATGAC
* * * * *
39944689 ATTTAGCGACACTTTTCTAACAATTGCCGCTAAAGAACATGAC
1 CTTTAGCGACGCTTTTATAACAATCGCCGCTAAAAAACATGAC
*
39944732 CTTTAGCAACGCTTTT
1 CTTTAGCGACGCTTTT
39944748 TATCACAAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (43 bp):
CTTTAGCGACGCTTTTATAACAATCGCCGCTAAAAAACATGAC
Found at i:39944802 original size:22 final size:22
Alignment explanation
Indices: 39944776--39944824 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
39944766 TTAAAAACAT
*
39944776 TTAAA-AATATTAAATATTAAAA
1 TTAAACAATATT-AATATCAAAA
*
39944798 TTAAACATTATTAATATCAAAA
1 TTAAACAATATTAATATCAAAA
*
39944820 ATAAA
1 TTAAA
39944825 TTAATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
TTAAACAATATTAATATCAAAA
Found at i:39947094 original size:14 final size:14
Alignment explanation
Indices: 39947059--39947101 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
39947049 TTCTGATTTG
39947059 ATCAATATGTAT--
1 ATCAATATGTATAA
*
39947071 A-CACTATGTATAA
1 ATCAATATGTATAA
39947084 ATCAATATGTATAA
1 ATCAATATGTATAA
39947098 ATCA
1 ATCA
39947102 TAAACAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 9 0.35
12 1 0.04
13 1 0.04
14 15 0.58
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (14 bp):
ATCAATATGTATAA
Found at i:39948404 original size:14 final size:14
Alignment explanation
Indices: 39948386--39948425 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
39948376 AATCCCAACC
39948386 CTTAAATCATAATT
1 CTTAAATCATAATT
* *
39948400 TTTAATTCATAATT
1 CTTAAATCATAATT
39948414 CTTAAATTCATA
1 CTTAAA-TCATA
39948426 TATAATCCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
CTTAAATCATAATT
Found at i:39948423 original size:15 final size:15
Alignment explanation
Indices: 39948386--39948425 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
39948376 AATCCCAACC
39948386 CTTAAA-TCATAATT
1 CTTAAATTCATAATT
*
39948400 -TTTAATTCATAATT
1 CTTAAATTCATAATT
39948414 CTTAAATTCATA
1 CTTAAATTCATA
39948426 TATAATCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 10 0.45
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (15 bp):
CTTAAATTCATAATT
Found at i:39948963 original size:40 final size:40
Alignment explanation
Indices: 39948918--39949007 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 40
39948908 TAATTTTTTT
** *
39948918 GCGGCGCTTTTCGAAAAA-CGCTGCTAATGCTTGATCTCTA
1 GCGGCG-TTTTCGAAAAAGCGCCACTAATGCTTGATCTATA
39948958 GCGGCGTTTT-GCAAAAAGCGCCACTAATGCTTGATCTATA
1 GCGGCGTTTTCG-AAAAAGCGCCACTAATGCTTGATCTATA
39948998 GCGGCGTTTT
1 GCGGCGTTTT
39949008 TCAGAAAGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 9 0.20
40 35 0.78
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.30
Consensus pattern (40 bp):
GCGGCGTTTTCGAAAAAGCGCCACTAATGCTTGATCTATA
Found at i:39949016 original size:40 final size:40
Alignment explanation
Indices: 39948941--39949027 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
39948931 AAAAACGCTG
*
39948941 CTAATGCTTGATCTCTAGCGGCGTTTTGCAAAAAGCGCCA
1 CTAATGCTTGATCTATAGCGGCGTTTTGCAAAAAGCGCCA
* * * *
39948981 CTAATGCTTGATCTATAGCGGCGTTTTTCAGAAAGCGTCG
1 CTAATGCTTGATCTATAGCGGCGTTTTGCAAAAAGCGCCA
39949021 CTAATGC
1 CTAATGC
39949028 CACCAAAGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (40 bp):
CTAATGCTTGATCTATAGCGGCGTTTTGCAAAAAGCGCCA
Found at i:39949115 original size:155 final size:154
Alignment explanation
Indices: 39948802--39949182 Score: 473
Period size: 155 Copynumber: 2.4 Consensus size: 154
39948792 AATATTTTTT
* * * *
39948802 GCGGCGTTTTTAAAATAAGCGCCACTAATGCTCGATCTATAACGGCGTTTTTCAAAAAGCACCAC
1 GCGGCG-TTTTGAAA-AAGCGCCACTAATGCTTGATCTATAGCGGCGTTTTTCAAAAAGCGCCAC
* * * *
39948867 TAATACCATCAAAGCTCAACATAAAACGATGGCGTTGTGCTTAATTTTTTTGCGGCGCTTTTCGA
64 TAATGCCACCAAAGCTCAACATAAAACGATGGAGTTGTGCTTAATTTTTTTGCGGCACTTTTCGA
* * *
39948932 AAAACGCTGCTAATGCTTGATCTCTA
129 AAAACGCCGCTAATGCTCGAGCTCTA
* * *
39948958 GCGGCGTTTTGCAAAAAGCGCCACTAATGCTTGATCTATAGCGGCGTTTTTCAGAAAGCGTCGCT
1 GCGGCGTTTTG-AAAAAGCGCCACTAATGCTTGATCTATAGCGGCGTTTTTCAAAAAGCGCCACT
* * *
39949023 AATGCCACCAAAGCTTAACATAAAATGATGGAGTTGTGCTTAATTTTTTTGCGGCATTTTTC-AA
65 AATGCCACCAAAGCTCAACATAAAACGATGGAGTTGTGCTTAATTTTTTTGCGGCACTTTTCGAA
* *
39949087 GAAGCGCCGCT-ATAGGTCGAGCAT-TA
130 -AAACGCCGCTAAT-GCTCGAGC-TCTA
* *
39949113 GCGGCGCTTTTTGAAAAA-CGCCGCTAATGCTTGATCTATAGCGGCTTTTTTCAAAAAGCGCCAC
1 GCGGCG--TTTTGAAAAAGCGCCACTAATGCTTGATCTATAGCGGCGTTTTTCAAAAAGCGCCAC
39949177 TAATGC
64 TAATGC
39949183 TCGAACTATA
Statistics
Matches: 195, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
154 4 0.02
155 171 0.88
156 15 0.08
157 5 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (154 bp):
GCGGCGTTTTGAAAAAGCGCCACTAATGCTTGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTA
ATGCCACCAAAGCTCAACATAAAACGATGGAGTTGTGCTTAATTTTTTTGCGGCACTTTTCGAAA
AACGCCGCTAATGCTCGAGCTCTA
Found at i:39949155 original size:40 final size:40
Alignment explanation
Indices: 39949111--39949211 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 40
39949101 GGTCGAGCAT
* * * *
39949111 TAGCGGCGCTTTTTGAAAAA-CGCCGCTAATGCTTGATCTA
1 TAGCGGC-CTTTTTCAAAAAGCGCCACTAATGCTCGAACTA
*
39949151 TAGCGGCTTTTTTCAAAAAGCGCCACTAATGCTCGAACTA
1 TAGCGGCCTTTTTCAAAAAGCGCCACTAATGCTCGAACTA
39949191 TAGC-GCCATTTTTCAAAAAGC
1 TAGCGGCC-TTTTTCAAAAAGC
39949212 ACTGCTAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 12 0.23
40 41 0.77
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (40 bp):
TAGCGGCCTTTTTCAAAAAGCGCCACTAATGCTCGAACTA
Found at i:39949170 original size:195 final size:186
Alignment explanation
Indices: 39948918--39949367 Score: 521
Period size: 195 Copynumber: 2.4 Consensus size: 186
39948908 TAATTTTTTT
* * * *
39948918 GCGGCGCTTTTCGAAAAACGCTGCTAATGCTTGATCTCTAGCGGCGTTTTGCAAAAAGCGCCACT
1 GCGGCGCTTTTTGAAAAACGCCGCTAATGCTTGATCTATAGCGGCGTTTTTCAAAAAGCGCCACT
* * * * * * *
39948983 AATGCTTGATCTATAGCGGCGTTTTTCAGAAAGC-GTCGCTAATGCCACCAAAGCTTAACATAAA
66 AATGCTCGAACTATAGCGCCATTTTTCAAAAAGCACT-GCTAATGCCACCAAAGCTCAACATAAA
* * * * * *
39949047 ATGATGGAGTTGTGCTTAATTTTTTTGCGGC-ATTTTTCAAGAAGCGCCGCT-ATAGGTCGAGC-
130 ACGATGGAG-T-TG--T-A----CTTGCGGCGA-TTTTCAAAAAGCGCCACTAAT-GCTCAAGCT
39949109 ATTA
184 A-TA
*
39949113 GCGGCGCTTTTTGAAAAACGCCGCTAATGCTTGATCTATAGCGGCTTTTTTCAAAAAGCGCCACT
1 GCGGCGCTTTTTGAAAAACGCCGCTAATGCTTGATCTATAGCGGCGTTTTTCAAAAAGCGCCACT
*
39949178 AATGCTCGAACTATAGCGCCATTTTTCAAAAAGCACTGCTAATGCCACCGAAGCTCAACATAAAA
66 AATGCTCGAACTATAGCGCCATTTTTCAAAAAGCACTGCTAATGCCACCAAAGCTCAACATAAAA
* *
39949243 CGATGGCGTTGTACTTGCGGCGATTTTCAAAAAGCGCCACTAATGCTCAATCTATA
131 CGATGGAGTTGTACTTGCGGCGATTTTCAAAAAGCGCCACTAATGCTCAAGCTATA
* * * * *
39949299 GCGGCGCTTTTTGAAAAATGCCGCTAATGCTCGATCTATAGTGGCGTTTTTCAAAAAGCACCGCT
1 GCGGCGCTTTTTGAAAAACGCCGCTAATGCTTGATCTATAGCGGCGTTTTTCAAAAAGCGCCACT
39949364 AATG
66 AATG
39949368 TGCGATCTAC
Statistics
Matches: 224, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
186 93 0.42
187 4 0.02
190 1 0.00
191 1 0.00
193 2 0.01
194 1 0.00
195 121 0.54
196 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (186 bp):
GCGGCGCTTTTTGAAAAACGCCGCTAATGCTTGATCTATAGCGGCGTTTTTCAAAAAGCGCCACT
AATGCTCGAACTATAGCGCCATTTTTCAAAAAGCACTGCTAATGCCACCAAAGCTCAACATAAAA
CGATGGAGTTGTACTTGCGGCGATTTTCAAAAAGCGCCACTAATGCTCAAGCTATA
Found at i:39949220 original size:40 final size:40
Alignment explanation
Indices: 39949120--39949222 Score: 118
Period size: 40 Copynumber: 2.6 Consensus size: 40
39949110 TTAGCGGCGC
* * * * * *
39949120 TTTTTGAAAAA-CGCCGCTAATGCTTGATCTATAGCGGCT
1 TTTTTCAAAAAGCACCGCTAATGCTCGAACTATAGCGCCA
* *
39949159 TTTTTCAAAAAGCGCCACTAATGCTCGAACTATAGCGCCA
1 TTTTTCAAAAAGCACCGCTAATGCTCGAACTATAGCGCCA
*
39949199 TTTTTCAAAAAGCACTGCTAATGC
1 TTTTTCAAAAAGCACCGCTAATGC
39949223 CACCGAAGCT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 10 0.19
40 44 0.81
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (40 bp):
TTTTTCAAAAAGCACCGCTAATGCTCGAACTATAGCGCCA
Found at i:39949363 original size:40 final size:39
Alignment explanation
Indices: 39949259--39949381 Score: 133
Period size: 40 Copynumber: 3.1 Consensus size: 39
39949249 CGTTGTACTT
* * *
39949259 GCGGCGATTTTCAAAAAGCGCCACTAATGCTCAATCTATA
1 GCGGCGTTTTTCAAAAAGC-CCGCTAATGCTCGATCTATA
*
39949299 GCGGCGCTTTTTGAAAAATG-CCGCTAATGCTCGATCTATA
1 GCGGCG-TTTTTCAAAAA-GCCCGCTAATGCTCGATCTATA
* *
39949339 GTGGCGTTTTTCAAAAAGCACCGCTAATG-TGCGATCTACA
1 GCGGCGTTTTTCAAAAAGC-CCGCTAATGCT-CGATCTATA
39949379 GCG
1 GCG
39949382 AAGTTTCTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
38 1 0.01
39 11 0.16
40 48 0.69
41 9 0.13
42 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (39 bp):
GCGGCGTTTTTCAAAAAGCCCGCTAATGCTCGATCTATA
Found at i:39955760 original size:162 final size:162
Alignment explanation
Indices: 39955493--39955820 Score: 647
Period size: 162 Copynumber: 2.0 Consensus size: 162
39955483 TTTTCTTAGC
*
39955493 AAGTTCTACAAGGAATAGGAGTAACATACTCAACCACTAATGGACAACAAGATTGGAAAACATGG
1 AAGTTCTACAAGGAATAGGAGTAACATACTCAACCACTAATGGACAACAAGATTGGAAAAAATGG
39955558 TTAGTAACACTACAGGAAATTAAGCTTTTAGTGACATTTGGACCGAAAATGCCGGAAATGTTATA
66 TTAGTAACACTACAGGAAATTAAGCTTTTAGTGACATTTGGACCGAAAATGCCGGAAATGTTATA
39955623 CATTAGTGGCGCTAACCGAAAAATTTCGCAAT
131 CATTAGTGGCGCTAACCGAAAAATTTCGCAAT
39955655 AAGTTCTACAAGGAATAGGAGTAACATACTCAACCACTAATGGACAACAAGATTGGAAAAAATGG
1 AAGTTCTACAAGGAATAGGAGTAACATACTCAACCACTAATGGACAACAAGATTGGAAAAAATGG
39955720 TTAGTAACACTACAGGAAATTAAGCTTTTAGTGACATTTGGACCGAAAATGCCGGAAATGTTATA
66 TTAGTAACACTACAGGAAATTAAGCTTTTAGTGACATTTGGACCGAAAATGCCGGAAATGTTATA
39955785 CATTAGTGGCGCTAACCGAAAAATTTCGCAAT
131 CATTAGTGGCGCTAACCGAAAAATTTCGCAAT
39955817 AAGT
1 AAGT
39955821 AAAGCAATAG
Statistics
Matches: 165, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 165 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (162 bp):
AAGTTCTACAAGGAATAGGAGTAACATACTCAACCACTAATGGACAACAAGATTGGAAAAAATGG
TTAGTAACACTACAGGAAATTAAGCTTTTAGTGACATTTGGACCGAAAATGCCGGAAATGTTATA
CATTAGTGGCGCTAACCGAAAAATTTCGCAAT
Found at i:39956012 original size:21 final size:20
Alignment explanation
Indices: 39955988--39956027 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39955978 TTATTTTTTC
39955988 CCCTAAAAATTTTCCCCAAAT
1 CCCT-AAAATTTTCCCCAAAT
* *
39956009 CCCTTAGATTTTCCCCAAA
1 CCCTAAAATTTTCCCCAAA
39956028 CGTCTGCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.30
Consensus pattern (20 bp):
CCCTAAAATTTTCCCCAAAT
Found at i:39956064 original size:25 final size:25
Alignment explanation
Indices: 39956030--39956091 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
39956020 TCCCCAAACG
39956030 TCTGCTGCATCACCGTCAACAATCC
1 TCTGCTGCATCACCGTCAACAATCC
* * *
39956055 TCTGCTGCATCGCCGTCGACAGTCC
1 TCTGCTGCATCACCGTCAACAATCC
*
39956080 TCTGCTACATCA
1 TCTGCTGCATCA
39956092 TCGTGTAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.39, G:0.16, T:0.26
Consensus pattern (25 bp):
TCTGCTGCATCACCGTCAACAATCC
Found at i:39956589 original size:21 final size:21
Alignment explanation
Indices: 39956563--39956605 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
39956553 ATGTTATGTG
39956563 TTTGAACAGAATCAATTCCAA
1 TTTGAACAGAATCAATTCCAA
39956584 TTTGAACAGAATCAATTCCAA
1 TTTGAACAGAATCAATTCCAA
39956605 T
1 T
39956606 GAACTTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (21 bp):
TTTGAACAGAATCAATTCCAA
Found at i:39958335 original size:59 final size:58
Alignment explanation
Indices: 39958263--39958794 Score: 803
Period size: 59 Copynumber: 9.0 Consensus size: 58
39958253 AAACGCTAGG
* *
39958263 TCATATTTCATAATAATTTAATGAATAATTAATTAATTTCTGATTAATTATATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTT-TGATTAATTAAATAAATAA
* *
39958322 TCATATTTCATAATAATTTTATAAATAATTAATTAATTTTCAATTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTT-GATTAATTAAATAAATAA
*
39958381 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTTATTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAA-TTTTGATTAATTAAATAAATAA
* * *
39958440 TCATATTTCATAATAATTCTACGAATAATTAATTAATTTTCGGTTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTT-GATTAATTAAATAAATAA
* *
39958499 TCATATGTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATTAATTAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTT-GATTAATTAAATAAATAA
* ** *
39958558 TCATATTTCATAATAATTCTACAAATAATTAATTAATTTTTGGTTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAA-TTTTGATTAATTAAATAAATAA
39958617 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAA-TTTTGATTAATTAAATAAATAA
* *
39958676 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAAAAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTT-GATTAATTAAATAAATAA
* * * *
39958735 TCATATTTCCTTATAATTCTATGAATAATTAATTAATTTTTGATTAATTAAATAATTAA
1 TCATATTTCATAATAATTTTATGAATAATTAATTAA-TTTTGATTAATTAAATAAATAA
39958794 T
1 T
39958795 TAAATAAATA
Statistics
Matches: 434, Mismatches: 33, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
58 9 0.02
59 413 0.95
60 12 0.03
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (58 bp):
TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTGATTAATTAAATAAATAA
Found at i:39958559 original size:177 final size:176
Alignment explanation
Indices: 39958263--39958879 Score: 875
Period size: 177 Copynumber: 3.4 Consensus size: 176
39958253 AAACGCTAGG
*
39958263 TCATATTTCATAATAATTTAATGAATAATTAATTAA-TTTCTGATTAATTATATAAATAATCATA
1 TCATATTTCATAATAATTT-ATGAATAATTAATTAATTTTC-GATTAATTAAATAAATAATCATA
*
39958327 TTTCATAATAATTTTATAAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCAT
64 TTTCATAATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCAT
* *
39958392 AATAATTTTATGAATAATTAATTAATTTTTTATTAATTAAATAAATAA
129 AATAATTCTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
* *
39958440 TCATATTTCATAATAATTCTACGAATAATTAATTAATTTTCGGTTAATTAAATAAATAATCATAT
1 TCATATTTCATAATAATT-TATGAATAATTAATTAATTTTCGATTAATTAAATAAATAATCATAT
* * *
39958505 GTCATAATAATTTTATGAATAATTAATTAATTTTCGATTAATTAATTAAATAATCATATTTCATA
65 TTCATAATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCATA
** *
39958570 ATAATTCTACAAATAATTAATTAATTTTTGGTTAATTAAATAAATAA
130 ATAATTCTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
*
39958617 TCATATTTCATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAATCATAT
1 TCATATTTCATAATAA-TTTATGAATAATTAATTAATTTTCGATTAATTAAATAAATAATCATAT
* * *
39958682 TTCATAATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAAAAATCATATTTCCTT
65 TTCATAATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCATA
39958747 ATAATTCTATGAATAATTAATTAATTTTTGATTAATTAAATAATTAATTAAATAAATAA
130 ATAATTCTATGAATAATTAATTAATTTTTG------------ATTAATTAAATAAATAA
* *
39958806 TCATATTTCATAATAATTCTATG---AA-TAATTAATTTTCGATTAAATAAATAAATAATCGTAT
1 TCATATTTCATAATAATT-TATGAATAATTAATTAATTTTCGATTAATTAAATAAATAATCATAT
39958867 TTCATAATTAATT
65 TTCATAA-TAATT
39958880 AATTTTCGAT
Statistics
Matches: 396, Mismatches: 27, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
177 304 0.77
178 7 0.02
185 40 0.10
186 7 0.02
188 2 0.01
189 36 0.09
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (176 bp):
TCATATTTCATAATAATTTATGAATAATTAATTAATTTTCGATTAATTAAATAAATAATCATATT
TCATAATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCATAA
TAATTCTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAA
Found at i:39958655 original size:20 final size:20
Alignment explanation
Indices: 39958628--39958715 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
39958618 CATATTTCAT
39958628 AATAATTTTATGAATAATTA
1 AATAATTTTATGAATAATTA
* *
39958648 ATTAATTTT-TGATTAATTA
1 AATAATTTTATGAATAATTA
* * * *
39958667 AATAA-ATAAT-CATATTTCA
1 AATAATTTTATGAATAATT-A
39958686 TAATAATTTTATGAATAATTA
1 -AATAATTTTATGAATAATTA
*
39958707 ATTAATTTT
1 AATAATTTT
39958716 CAATTAATTA
Statistics
Matches: 50, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
18 5 0.10
19 15 0.30
20 21 0.42
21 4 0.08
22 5 0.10
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (20 bp):
AATAATTTTATGAATAATTA
Found at i:39958794 original size:12 final size:12
Alignment explanation
Indices: 39958777--39958806 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39958767 TTAATTTTTG
39958777 ATTAATTAAATA
1 ATTAATTAAATA
39958789 ATTAATTAAATA
1 ATTAATTAAATA
*
39958801 AATAAT
1 ATTAAT
39958807 CATATTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAATTAAATA
Found at i:39958847 original size:67 final size:69
Alignment explanation
Indices: 39958717--39958861 Score: 204
Period size: 71 Copynumber: 2.1 Consensus size: 69
39958707 ATTAATTTTC
* * *
39958717 AATTAATTAAATAAAAAATCATATTTCCTTATAATTCTATGAATAATTAATTAATTTTTGATTAA
1 AATTAATTAAATAAAAAATCATATTTCATAATAATTCTATG-A-AATTAATTAATTTTCGATTAA
*
39958782 TTAAAT
64 ATAAAT
*
39958788 AATTAATTAAATAAATAATCATATTTCATAATAATTCTATG-AA-TAATTAATTTTCGATTAAAT
1 AATTAATTAAATAAAAAATCATATTTCATAATAATTCTATGAAATTAATTAATTTTCGATTAAAT
39958851 AAAT
66 AAAT
*
39958855 AAATAAT
1 AATTAAT
39958862 CGTATTTCAT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
67 28 0.41
68 2 0.03
71 38 0.56
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (69 bp):
AATTAATTAAATAAAAAATCATATTTCATAATAATTCTATGAAATTAATTAATTTTCGATTAAAT
AAAT
Found at i:39958892 original size:55 final size:54
Alignment explanation
Indices: 39958759--39958893 Score: 132
Period size: 55 Copynumber: 2.4 Consensus size: 54
39958749 AATTCTATGA
*
39958759 ATAATTAATTAATTTTTGATTAATTAAATAATTAATTAAATAAATAATCATATTTC
1 ATAATTAATTAA-TTTTGATTAATT-AATAATTAAATAAATAAATAATCATATTTC
* * * * *
39958815 ATAA-TAATT--CTATGAATAATTAATTTTCGATTAAATAAATAAATAATCGTATTTC
1 ATAATTAATTAATTTTGATTAATTAA---T-AATTAAATAAATAAATAATCATATTTC
39958870 ATAATTAATTAATTTTCGATTAAT
1 ATAATTAATTAATTTT-GATTAAT
39958894 CATTCATTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
51 2 0.03
52 9 0.15
54 1 0.02
55 33 0.53
56 9 0.15
58 2 0.03
59 6 0.10
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (54 bp):
ATAATTAATTAATTTTGATTAATTAATAATTAAATAAATAAATAATCATATTTC
Found at i:39959348 original size:7 final size:7
Alignment explanation
Indices: 39959336--39959360 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39959326 TAAATAATTA
39959336 GATACTT
1 GATACTT
39959343 GATACTT
1 GATACTT
39959350 GATACTT
1 GATACTT
39959357 GATA
1 GATA
39959361 TATATTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (7 bp):
GATACTT
Found at i:39966813 original size:27 final size:27
Alignment explanation
Indices: 39966776--39966848 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
39966766 GGTGGAGGGC
*
39966776 CTGCCACAGGCGGCACCAGTGGTGCCA
1 CTGCCACAGGCGGCACCAGTGATGCCA
* * * * *
39966803 GTGGCAGAGGCGACACCAATGATGCCA
1 CTGCCACAGGCGGCACCAGTGATGCCA
39966830 CTGCCACAGGCGGCACCAG
1 CTGCCACAGGCGGCACCAG
39966849 CCCTTATATT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.23, C:0.34, G:0.33, T:0.10
Consensus pattern (27 bp):
CTGCCACAGGCGGCACCAGTGATGCCA
Found at i:39966933 original size:20 final size:20
Alignment explanation
Indices: 39966908--39966961 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
39966898 AAAAACAAAA
39966908 AAGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
*
39966928 AAGAAAGGAAAGGAAAGGAG
1 AAGAAAGAAAAGGAAAGGAG
39966948 AAG-AAGAAGAAGGA
1 AAGAAAGAA-AAGGA
39966962 GGAGGGAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAAAGGAAAGGAG
Found at i:39968106 original size:457 final size:462
Alignment explanation
Indices: 39967362--39968426 Score: 1464
Period size: 457 Copynumber: 2.3 Consensus size: 462
39967352 AGGGTTTTTT
** *
39967362 ACTAAATTAATGTATTTCAAACATAATGTACTAAAATAACGTTAAATAATAAAA-TACGAAAATA
1 ACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATG-TAAATAATAAAATTA-GAAAATA
* *** * *
39967426 ATATA-TTTTTTGAAA-CAATGAGGCTTCGATA-AAAAAATACGAACAAATGACCGAAA-AAGGG
64 ATATATTTTTTTGAAAGTAAT-A-AAATCCA-AGAAAAAATACGAACAAAGGACCGAAATAAGGG
* *
39967487 TTTTTTACTAAATTTATTTAAAACACACACTAAATTAATACATTTCAAACAGAATGTACTAAAAA
126 TTTTTTA-TAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACAGAATGTACTAAAAA
* **
39967552 AATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTAAAAGTAATAAAATTCGGGAAAAAA
190 AATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTAAAAGTAATAAAATCCAAGAAAAAA
* *
39967617 TACGAACAAAGGGCCGGAATAAGGGTTAATTTTTGAAATTTATTT-AAAAACACACTAAATTAAT
255 TACGAACAAAGGGCCGAAATAAGGGTTAATTTTTAAAATTTATTTAAAAAACACACTAAATTAAT
*
39967681 AAATTTCAAATATAATGTACT-AAA-AATGT-AA-AAT-AA-T-AAAATAATATATTATTATTGA
320 AAATTTCAAACATAATGTACTAAAATAATGTAAACAATAAATTAAAAATAATATATTATTATTGA
39967739 AAAT-ATAAAATTCAGGAAAAAAATACGAACAAA-ATGCCGAAATAAGGGTTAATTTTTGAAATT
385 AAATAATAAAA-TCAGGAAAAAAATACGAACAAAGA-GCCGAAATAAGGGTTAATTTTTGAAATT
39967802 TATTTAAAAA-ACAC
448 TATTTAAAAAGACAC
39967816 ACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAACTAATAAAATTAGAAAATAA
1 ACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAA-TAATAAAATTAGAAAATAA
*
39967881 TATATTTTTATTGAAAGTAATAAAATCCAAGAAAAAATACGAACAAAGGGCCGAAATAAGGGTTA
65 TATATTTTT-TTGAAAGTAATAAAATCCAAGAAAAAATACGAACAAAGGACCGAAATAAGGGTT-
* *
39967946 ATTTT-TGAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATA
128 -TTTTAT-AAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACAGAATGTACTAAAAAA
* * * *
39968010 ATGTAAACTAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCAAGAAAAAAT
191 ATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTAAAAGTAATAAAATCCAAGAAAAAAT
*
39968075 ACGAACAAAGGGCCGAAATAAGGGTTAATTTTTAAAATTTATTTAAAAAATACACTAAATTAATA
256 ACGAACAAAGGGCCGAAATAAGGGTTAATTTTTAAAATTTATTTAAAAAACACACTAAATTAATA
* *
39968140 AATTTCAAACATAATGTACTAAAATAATTTAAACTAATAAAATTAGAAAATAATATATTTTTATT
321 AATTTCAAACATAATGTACTAAAATAATGTAAAC-AAT-AAATTA-AAAATAATATATTATTATT
* * * *
39968205 GAAAGTAATAAAATCTGGGAAAAAATACGAATAAAGAGCCGAAATAAGGGTTAATTTTTGAAATT
383 GAAAATAATAAAATCAGGAAAAAAATACGAACAAAGAGCCGAAATAAGGGTTAATTTTTGAAATT
39968270 TATTTAAAAAGACAC
448 TATTTAAAAAGACAC
* * * * *
39968285 ACTAAATTAATACATTTCAAACATAATGTATTGAAATAATGTAAAATAATAAAATTGGAAAATAG
1 ACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGT-AAATAATAAAATTAGAAAATAA
** * *
39968350 TATATTTTTTT-AAAGTAATAAAATCCGGGGAAAAAAATACGAACAAAGGTCCGAAATAACGGTT
65 TATATTTTTTTGAAAGTAATAAAATCC-AAG-AAAAAATACGAACAAAGGACCGAAATAAGGGTT
39968414 TTTTACTAAATTT
128 TTTTA-TAAATTT
39968427 TTTTTGAAGT
Statistics
Matches: 542, Mismatches: 40, Indels: 44
0.87 0.06 0.07
Matches are distributed among these distances:
453 4 0.01
454 59 0.11
455 32 0.06
456 15 0.03
457 156 0.29
458 42 0.08
459 3 0.01
460 4 0.01
461 2 0.00
463 3 0.01
465 2 0.00
466 1 0.00
467 19 0.04
468 89 0.16
469 108 0.20
470 3 0.01
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (462 bp):
ACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAATAATAAAATTAGAAAATAAT
ATATTTTTTTGAAAGTAATAAAATCCAAGAAAAAATACGAACAAAGGACCGAAATAAGGGTTTTT
TATAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACAGAATGTACTAAAAAAATGTA
AAATAATAAAATAAAAAAATAATATATTTTTATTAAAAGTAATAAAATCCAAGAAAAAATACGAA
CAAAGGGCCGAAATAAGGGTTAATTTTTAAAATTTATTTAAAAAACACACTAAATTAATAAATTT
CAAACATAATGTACTAAAATAATGTAAACAATAAATTAAAAATAATATATTATTATTGAAAATAA
TAAAATCAGGAAAAAAATACGAACAAAGAGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAA
AAGACAC
Found at i:39968357 original size:157 final size:156
Alignment explanation
Indices: 39967709--39968413 Score: 1105
Period size: 156 Copynumber: 4.5 Consensus size: 156
39967699 ACTAAAAATG
* * * * * *
39967709 TAAAATAATAAAATAATATATTATTATTGAAAAT-ATAAAATTCAGGAAAAAAATACGAACAAA-
1 TAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAA-TCCGGGAAAAAATACGAACAAAG
39967772 ATGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAA
65 A-GCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAA
39967837 CATAATGTACTAAAATAATGTAAACTAA
129 CATAATGTACTAAAATAATGTAAACTAA
** *
39967865 TAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCAAGAAAAAATACGAACAAAGG
1 TAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGA
39967930 GCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACA
66 GCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACA
39967995 TAATGTACTAAAATAATGTAAACTAA
131 TAATGTACTAAAATAATGTAAACTAA
** *
39968021 TAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCAAGAAAAAATACGAACAAAGG
1 TAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGA
* *
39968086 GCCGAAATAAGGGTTAATTTTTAAAATTTATTTAAAAAATACACTAAATTAATAAATTTCAAACA
66 GCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACA
*
39968151 TAATGTACTAAAATAATTTAAACTAA
131 TAATGTACTAAAATAATGTAAACTAA
* *
39968177 TAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCTGGGAAAAAATACGAATAAAGA
1 TAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGA
*
39968242 GCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAGACACACTAAATTAATACATTTCAAAC
66 GCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAA-ACACACTAAATTAATAAATTTCAAAC
* * *
39968307 ATAATGTATTGAAATAATGTAAAATAA
130 ATAATGTACTAAAATAATGTAAACTAA
* *
39968334 TAAAATTGGAAAATAGTATATTTTT-TT-AAAGTAATAAAATCCGGGGAAAAAAATACGAACAAA
1 TAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCC-GGG-AAAAAATACGAACAAA
*
39968397 G-GTCCGAAATAACGGTT
64 GAG-CCGAAATAAGGGTT
39968414 TTTTACTAAA
Statistics
Matches: 514, Mismatches: 29, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
155 14 0.03
156 395 0.77
157 105 0.20
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (156 bp):
TAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGA
GCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAAATTAATAAATTTCAAACA
TAATGTACTAAAATAATGTAAACTAA
Found at i:39970492 original size:6 final size:6
Alignment explanation
Indices: 39970481--39970539 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
39970471 GGATACAATT
39970481 TAAGCA TAAGCA TAAGCA TAAGCA TAAGCA TAAGCA TAAGCA TAAGCA
1 TAAGCA TAAGCA TAAGCA TAAGCA TAAGCA TAAGCA TAAGCA TAAGCA
39970529 TAAGCA TAAGC
1 TAAGCA TAAGC
39970540 TGAATTTTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
TAAGCA
Found at i:39973570 original size:37 final size:39
Alignment explanation
Indices: 39973485--39973571 Score: 117
Period size: 37 Copynumber: 2.3 Consensus size: 39
39973475 ACTAACACAA
**
39973485 TAACAATAATAATAGTTTTTTACTCAAAATAATACTAAC
1 TAACAATAATAATAGGGTTTTACTCAAAATAATACTAAC
*
39973524 TAACAATAATAATTAGGGTTTTACTTAAAAT-A-A-TAAC
1 TAACAATAATAA-TAGGGTTTTACTCAAAATAATACTAAC
39973561 TAACAATAATA
1 TAACAATAATA
39973572 TAATGTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 15 0.34
38 1 0.02
39 13 0.30
40 15 0.34
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (39 bp):
TAACAATAATAATAGGGTTTTACTCAAAATAATACTAAC
Found at i:39973570 original size:76 final size:77
Alignment explanation
Indices: 39973485--39973693 Score: 230
Period size: 76 Copynumber: 2.7 Consensus size: 77
39973475 ACTAACACAA
39973485 TAACAATAATAATAGTTTTTTACTCAA-AATAATACTAACTAACAATAATAATTAGGG-TTTTAC
1 TAACAATAATAATAGTTTTTTACT-AACAATAATACTAACTAACAATAATAATTAGGGTTTTTAC
39973548 TTAA-AATAATAAC
65 -TAATAATAATAAC
* **** *
39973561 TAACAATAAT-ATAATGTAAAAACTAACAATCATACTAACTAA-AATAATAATTAGGGTTTTTAC
1 TAACAATAATAATAGT-TTTTTACTAACAATAATACTAACTAACAATAATAATTAGGGTTTTTAC
**
39973624 TAATCCTAATAAC
65 TAATAATAATAAC
* * *
39973637 TAACCATAATAATCTTAGTTTTTTACTAACAATAATACTAAGTAACAATAATTATTA
1 TAACAATAATAA---TAGTTTTTTACTAACAATAATACTAACTAACAATAATAATTA
39973694 ATAACTAAAC
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
75 23 0.21
76 50 0.47
77 1 0.01
79 20 0.19
80 13 0.12
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (77 bp):
TAACAATAATAATAGTTTTTTACTAACAATAATACTAACTAACAATAATAATTAGGGTTTTTACT
AATAATAATAAC
Found at i:39973603 original size:23 final size:23
Alignment explanation
Indices: 39973558--39973604 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
39973548 TTAAAATAAT
*
39973558 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
39973581 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
39973604 A
1 A
39973605 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:39973907 original size:3 final size:3
Alignment explanation
Indices: 39973901--39973957 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
39973891 CCGGCACCAC
* * **
39973901 CTT CTT CTC CTT CTT CTT CTT CTT CTC CTT CAG CTCT CTCT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CT-T CTT CTT
*
39973948 CTT CTC CTT C
1 CTT CTT CTT C
39973958 AGTTGGGCTG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.02, C:0.42, G:0.02, T:0.54
Consensus pattern (3 bp):
CTT
Found at i:39973914 original size:9 final size:9
Alignment explanation
Indices: 39973900--39973957 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
39973890 TCCGGCACCA
39973900 CCTTCTTCT
1 CCTTCTTCT
39973909 CCTTCTTCT
1 CCTTCTTCT
*
39973918 TCTTCTTCT
1 CCTTCTTCT
**
39973927 CCTTCAGCT
1 CCTTCTTCT
39973936 -C-TCTCTCT
1 CCTTCT-TCT
*
39973944 TCTTCTTCT
1 CCTTCTTCT
39973953 CCTTC
1 CCTTC
39973958 AGTTGGGCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
9 31 0.79
10 3 0.08
ACGTcount: A:0.02, C:0.43, G:0.02, T:0.53
Consensus pattern (9 bp):
CCTTCTTCT
Found at i:39975272 original size:3 final size:3
Alignment explanation
Indices: 39975264--39975335 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
39975254 TCAATTATTC
39975264 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
39975312 CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT
39975336 TCTTGTTAGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:39977774 original size:102 final size:102
Alignment explanation
Indices: 39977652--39977853 Score: 336
Period size: 102 Copynumber: 2.0 Consensus size: 102
39977642 CCAATGAGTT
* *
39977652 GGGGAATCAGCACTTAGCAA-CCCCTTTCACATTTAAGATACGGTGCG-ATCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGCAACCCCCTTT-ACATTTAAGATACGATG-GAATCAGCAATTAGCAAC
*
39977715 CACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTCG
64 CACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTCG
*
39977754 GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGATGGAATCAGCAATTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGATACGATGGAATCAGCAATTAGCAACCA
39977819 CCAATAATTCGGGGAATCAGCACTTAGCAACCCCT
66 CCAATAATTCGGGGAATCAGCACTTAGCAACCCCT
39977854 TTCACATTTA
Statistics
Matches: 94, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
101 1 0.01
102 86 0.91
103 7 0.07
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGATACGATGGAATCAGCAATTAGCAACCA
CCAATAATTCGGGGAATCAGCACTTAGCAACCCCTCG
Found at i:39977815 original size:42 final size:40
Alignment explanation
Indices: 39977756--39977892 Score: 137
Period size: 42 Copynumber: 3.5 Consensus size: 40
39977746 ACCCCTCGGG
39977756 GGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGAT
1 GGAATCAGCACTTAGCAACCCCCTTTACATTTAA-GTACG-T
* * * *
39977798 GGAATCAGCAATTAGCAACCACC---A-A--TAA-TTCGG
1 GGAATCAGCACTTAGCAACCCCCTTTACATTTAAGTACGT
39977831 GGAATCAGCACTTAGCAA-CCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTT-ACATTTAAG-TAC-GT
39977873 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
39977893 ACCAATGAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
32 3 0.04
33 17 0.22
34 3 0.04
36 4 0.05
37 1 0.01
38 1 0.01
39 4 0.05
41 2 0.03
42 40 0.53
43 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (40 bp):
GGAATCAGCACTTAGCAACCCCCTTTACATTTAAGTACGT
Found at i:39977847 original size:75 final size:76
Alignment explanation
Indices: 39977754--39977927 Score: 282
Period size: 75 Copynumber: 2.3 Consensus size: 76
39977744 CAACCCCTCG
*
39977754 GGGGAATCAGCACTTAGCAACCCCCTTT-ACATTTAAGGTACGATGGAATCAGCAATTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAGATACGATGGAATCAGCAATTAGCAACC
39977818 ACCAAT-AATTC
66 ACCAATGAA-TC
* *
39977829 GGGGAATCAGCACTTAGCAA-CCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAGATACGATGGAATCAGCAATTAGCAACC
39977893 ACCAATGAATC
66 ACCAATGAATC
*
39977904 GAGGAATCAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
39977928 TTGGGGGAAT
Statistics
Matches: 92, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
74 7 0.08
75 80 0.87
76 5 0.05
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (76 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAGATACGATGGAATCAGCAATTAGCAACC
ACCAATGAATC
Found at i:39977928 original size:177 final size:177
Alignment explanation
Indices: 39977620--39977959 Score: 594
Period size: 177 Copynumber: 1.9 Consensus size: 177
39977610 CCGTTATCGG
* * *
39977620 TGGATTCAGCACTTAGCAACCACCAATGAGTTGGGGAATCAGCACTTAGCAACCCCTTTCACATT
1 TGGAATCAGCAATTAGCAACCACCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTTCACATT
* *
39977685 TAAGATACGGTGCGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCC
66 TAAGATACGGTGCGATCAGCACTTAGCAACCACCAATGAATCGAGGAATCAGCACTTAGCAACCC
39977750 CTCGGGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGA
131 CTCGGGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGA
39977797 TGGAATCAGCAATTAGCAACCACCAAT-AATTCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
1 TGGAATCAGCAATTAGCAACCACCAATGAATT-GGGGAATCAGCACTTAGCAACCCCTTTCACAT
39977861 TTAAGATACGGTG-GAATCAGCACTTAGCAACCACCAATGAATCGAGGAATCAGCACTTAGCAAC
65 TTAAGATACGGTGCG-ATCAGCACTTAGCAACCACCAATGAATCGAGGAATCAGCACTTAGCAAC
*
39977925 CCCTTGGGGGAATCAGCACTTAGCAACCCCCTTTA
129 CCCTCGGGGGAATCAGCACTTAGCAACCCCCTTTA
39977960 TATTCAATGT
Statistics
Matches: 155, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
176 4 0.03
177 151 0.97
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.21
Consensus pattern (177 bp):
TGGAATCAGCAATTAGCAACCACCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTTCACATT
TAAGATACGGTGCGATCAGCACTTAGCAACCACCAATGAATCGAGGAATCAGCACTTAGCAACCC
CTCGGGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGA
Found at i:39985358 original size:102 final size:102
Alignment explanation
Indices: 39985236--39985434 Score: 330
Period size: 102 Copynumber: 2.0 Consensus size: 102
39985226 CCAATGAGTC
*
39985236 GGGGAATCAGCACTTAGCAA-CCCCTTTCACATTTAAGATACGATGCG-ATCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGCAACCCCCTTT-ACATTTAAGATACGATG-GAATCAGCAATTAGCAAC
*
39985299 CACCAATGATTCGGGGAATCAGCACTTAGCAACCTCTCG
64 CACCAATAATTCGGGGAATCAGCACTTAGCAACCTCTCG
* *
39985338 GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGATGGAATCAGCAATTAGCAGCCA
1 GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGATACGATGGAATCAGCAATTAGCAACCA
39985403 CCAATAATTCGGGGAATCAGCACTTAGCAACC
66 CCAATAATTCGGGGAATCAGCACTTAGCAACC
39985435 CCTTTCACAT
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
101 1 0.01
102 83 0.91
103 7 0.08
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGATACGATGGAATCAGCAATTAGCAACCA
CCAATAATTCGGGGAATCAGCACTTAGCAACCTCTCG
Found at i:39985512 original size:75 final size:74
Alignment explanation
Indices: 39985338--39985513 Score: 282
Period size: 75 Copynumber: 2.4 Consensus size: 74
39985328 CAACCTCTCG
* *
39985338 GGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGATGGAATCAGCAATTAGCAGCCA
1 GGGGAATCAGCACTTAGCAA-CCCCTTTACATTTAAGATACGATGGAATCAGCAATTAGCAACCA
39985403 CCAATAATTC
65 CCAATAATTC
* *
39985413 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCTTT-ACATTTAAGATACGATGGAATCAGCAATTAGCAACCA
39985478 CCAATGAA-TC
65 CCAAT-AATTC
39985488 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
39985514 GGGGGAATCA
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
74 7 0.07
75 86 0.91
76 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (74 bp):
GGGGAATCAGCACTTAGCAACCCCTTTACATTTAAGATACGATGGAATCAGCAATTAGCAACCAC
CAATAATTC
Found at i:39985520 original size:177 final size:177
Alignment explanation
Indices: 39985204--39985543 Score: 583
Period size: 177 Copynumber: 1.9 Consensus size: 177
39985194 CCGTTATCGG
* * *
39985204 TGGATTCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
1 TGGAATCAGCAATTAGCAACCACCAATAAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
* *
39985269 TAAGATACGATGCGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCT
66 TAAGATACGATGCGATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCC
39985334 CTCGGGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGA
131 CTCGGGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGA
* *
39985381 TGGAATCAGCAATTAGCAGCCACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
1 TGGAATCAGCAATTAGCAACCACCAATAAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
*
39985446 TAAGATACGGTG-GAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACC
66 TAAGATACGATGCG-ATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACC
*
39985510 CCTTGGGGGAATCAGCACTTAGCAACCCCCTTTA
130 CCTCGGGGGAATCAGCACTTAGCAACCCCCTTTA
39985544 TATTCAATGT
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
176 1 0.01
177 152 0.99
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (177 bp):
TGGAATCAGCAATTAGCAACCACCAATAAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
TAAGATACGATGCGATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCC
CTCGGGGGAATCAGCACTTAGCAACCCCCTTTACATTTAAGGTACGA
Found at i:39992582 original size:32 final size:32
Alignment explanation
Indices: 39992546--39992608 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
39992536 TCATAAACCT
*
39992546 ATAAATTAATTACTTAAATTTAATAACTCATG
1 ATAAATTAATTAATTAAATTTAATAACTCATG
* **
39992578 ATAAATTAATTAATTTAATTTTGTAACTCAT
1 ATAAATTAATTAATTAAATTTAATAACTCAT
39992609 ATTGATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (32 bp):
ATAAATTAATTAATTAAATTTAATAACTCATG
Found at i:39993220 original size:15 final size:16
Alignment explanation
Indices: 39993191--39993220 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39993181 ATGTTCTACA
39993191 TCAATTGTATATAATT
1 TCAATTGTATATAATT
39993207 TCAATTGT-TATAAT
1 TCAATTGTATATAAT
39993221 AACAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
TCAATTGTATATAATT
Found at i:40003140 original size:32 final size:32
Alignment explanation
Indices: 40003102--40003164 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
40003092 CCATAAACTT
*
40003102 ATAAATTAATTACTTGAATTTAATAACTCATG
1 ATAAATTAATTAATTGAATTTAATAACTCATG
* * *
40003134 ATAAATTAATTAATTTAATTTTATAATTCAT
1 ATAAATTAATTAATTGAATTTAATAACTCAT
40003165 ATCGGTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAACTCATG
Found at i:40004825 original size:6 final size:6
Alignment explanation
Indices: 40004814--40004839 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40004804 AAAAATTATA
40004814 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
40004840 TATAAAAAAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:40012866 original size:18 final size:18
Alignment explanation
Indices: 40012837--40012884 Score: 87
Period size: 18 Copynumber: 2.6 Consensus size: 18
40012827 GGAAACGAAA
40012837 AACTCAAAAAGAATTTATT
1 AACTC-AAAAGAATTTATT
40012856 AACTCAAAAGAATTTATT
1 AACTCAAAAGAATTTATT
40012874 AACTCAAAAGA
1 AACTCAAAAGA
40012885 GAAGTTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.27
Consensus pattern (18 bp):
AACTCAAAAGAATTTATT
Found at i:40014941 original size:22 final size:22
Alignment explanation
Indices: 40014908--40014968 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
40014898 GCCCGGCCCG
* *
40014908 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
40014931 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
40014953 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
40014969 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:40014981 original size:16 final size:16
Alignment explanation
Indices: 40014944--40014983 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
40014934 TTAATAAAAT
* *
40014944 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
40014960 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
40014976 TAAAATTA
1 TAAAATTA
40014984 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:40015042 original size:66 final size:67
Alignment explanation
Indices: 40014972--40015113 Score: 250
Period size: 68 Copynumber: 2.1 Consensus size: 67
40014962 AAATTAATTG
*
40014972 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
40015036 GA
66 GA
*
40015038 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
40015103 TGA
65 TGA
40015106 TTAGTAAA
1 TTAGTAAA
40015114 GCAAACTTGA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 26 0.36
68 46 0.64
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:40015068 original size:9 final size:9
Alignment explanation
Indices: 40015056--40015083 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
40015046 TTTATCAAAT
40015056 TATTAATTG
1 TATTAATTG
40015065 TATTAATTG
1 TATTAATTG
40015074 TATTAATTG
1 TATTAATTG
40015083 T
1 T
40015084 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:40015208 original size:23 final size:22
Alignment explanation
Indices: 40015180--40015222 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
40015170 AAATAAACTT
40015180 AAAATAAAAAATATTATATTTTA
1 AAAATAAAAAATA-TATATTTTA
40015203 AAAATAAAAAATATATATTT
1 AAAATAAAAAATATATATTT
40015223 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATAAAAAATATATATTTTA
Found at i:40021606 original size:2 final size:2
Alignment explanation
Indices: 40021599--40021625 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40021589 AGCATAATGC
40021599 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
40021626 GAATAAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40021713 original size:3 final size:3
Alignment explanation
Indices: 40021705--40021738 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
40021695 GAAATAAAAC
*
40021705 TAA TAA TAA TAA TTAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
40021739 CATTGACGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:40023378 original size:25 final size:26
Alignment explanation
Indices: 40023349--40023400 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
40023339 AGTTTTAAAT
40023349 TAGAAAAATATC-TCTAGA-AATTTTC
1 TAGAAAAATATCTTC-AGAGAATTTTC
* *
40023374 TAGAATAATCTCTTCAGAGAATTTTC
1 TAGAAAAATATCTTCAGAGAATTTTC
40023400 T
1 T
40023401 CTCTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (26 bp):
TAGAAAAATATCTTCAGAGAATTTTC
Found at i:40023524 original size:17 final size:17
Alignment explanation
Indices: 40023502--40023647 Score: 71
Period size: 17 Copynumber: 8.8 Consensus size: 17
40023492 AAACTTAACT
40023502 AATTTAATATTAAATTA
1 AATTTAATATTAAATTA
40023519 AATTTAATATTAAATCT-
1 AATTTAATATTAAAT-TA
* *
40023536 TA-TTAA-AAT-AA-TA
1 AATTTAATATTAAATTA
*
40023549 GAATATT--TATAAAATTA
1 -AAT-TTAATATTAAATTA
40023566 AATTTAATATTAAGATAATA
1 AATTTAATATTAA-AT--TA
*
40023586 ACTTTAATATTAAATT-
1 AATTTAATATTAAATTA
** *
40023602 AATAAAATACT--ATTA
1 AATTTAATATTAAATTA
* *
40023617 AGA-TTAGTATTAAATTT
1 A-ATTTAATATTAAATTA
40023634 AATTTAATATTAAA
1 AATTTAATATTAAA
40023648 CTATTAAAAT
Statistics
Matches: 94, Mismatches: 17, Indels: 36
0.64 0.12 0.24
Matches are distributed among these distances:
12 1 0.01
14 6 0.06
15 10 0.11
16 20 0.21
17 38 0.40
18 3 0.03
19 2 0.02
20 14 0.15
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (17 bp):
AATTTAATATTAAATTA
Found at i:40030193 original size:21 final size:20
Alignment explanation
Indices: 40030150--40030194 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
40030140 TGAAGACTTG
*
40030150 AAGTTTGGTACTTACGGATC
1 AAGTTTGGTACTTACGGAAC
**
40030170 AAGTTTGGTTACTTGTGGAAC
1 AAGTTTGG-TACTTACGGAAC
40030191 AAGT
1 AAGT
40030195 AAAATCACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (20 bp):
AAGTTTGGTACTTACGGAAC
Found at i:40031928 original size:50 final size:50
Alignment explanation
Indices: 40031812--40032054 Score: 290
Period size: 50 Copynumber: 4.8 Consensus size: 50
40031802 GACAATAACA
** *
40031812 TGCCAA-AGCCATGTCCCAGACATGGTCTTACATGGGATGTCCTCATGTCGG
1 TGCCAACA-CCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* ** **
40031863 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
40031913 TGCCAACATCATGTCCCAGACATGGTCTTACATGGGATCTTTCATCCCGG
1 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** * *
40031963 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATTTCAG
1 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** *
40032013 TGCCAATGCCATGTCTCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCT
40032055 TTACCCAAAA
Statistics
Matches: 166, Mismatches: 25, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
50 133 0.80
51 33 0.20
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:40032000 original size:100 final size:101
Alignment explanation
Indices: 40031812--40032049 Score: 336
Period size: 100 Copynumber: 2.4 Consensus size: 101
40031802 GACAATAACA
* ** *
40031812 TGCCAA-AGCCATGTCCCAGACATGGTCTTACATGGGATGTCCTCATGTCGGTGCCCATGCCATG
1 TGCCAACA-CCATGTCCCAGACATGGTCTTACATGGGATCTCCTCATCCCGGTGCCAATGCCATG
* *
40031876 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCATCTCAG
* *
40031913 TGCCAACATCATGTCCCAGACATGGTCTTACATGGGATCT-TTCATCCCGGTGCCAATGCCATGT
1 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGATCTCCTCATCCCGGTGCCAATGCCATGT
* *
40031977 CCCAGACATGGTCTTACATGGGACCTCTCATTTCAG
66 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCAG
** *
40032013 TGCCAATGCCATGTCTCAGACATGGTCTTACATGGGA
1 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGA
40032050 CCTCTTTACC
Statistics
Matches: 122, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
100 85 0.70
101 36 0.30
102 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.26
Consensus pattern (101 bp):
TGCCAACACCATGTCCCAGACATGGTCTTACATGGGATCTCCTCATCCCGGTGCCAATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCATCTCAG
Found at i:40035954 original size:39 final size:40
Alignment explanation
Indices: 40035922--40036079 Score: 146
Period size: 39 Copynumber: 4.0 Consensus size: 40
40035912 TATATCCTAT
*
40035922 TATACATATAATCACCTAACA-TCAAGGTATATATCACAA
1 TATACATATAATCACATAACATTCAAGGTATATATCACAA
* * * * *
40035961 TATTCATATAACCACATAACATTTAA-GCATATATCACAT
1 TATACATATAATCACATAACATTCAAGGTATATATCACAA
* * *
40036000 TACT-CGTATAATCACATAACATTCAAGCT-TATATCATAA
1 TA-TACATATAATCACATAACATTCAAGGTATATATCACAA
* * * * *
40036039 AATACATATAATCTCATAACATTTAA-GCATATATCATAA
1 TATACATATAATCACATAACATTCAAGGTATATATCACAA
40036078 TA
1 TA
40036080 CTCAAAACAT
Statistics
Matches: 94, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
38 1 0.01
39 89 0.95
40 4 0.04
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (40 bp):
TATACATATAATCACATAACATTCAAGGTATATATCACAA
Found at i:40035994 original size:78 final size:78
Alignment explanation
Indices: 40035904--40036083 Score: 222
Period size: 78 Copynumber: 2.3 Consensus size: 78
40035894 CATATTCACT
* * * *
40035904 TTTAAGCATATATC-CTATTA-TACATATAATCACCTAACA-TCAAGGTATATATCACAATATTC
1 TTTAAGCATATATCAC-ATTACT-CATATAATCACATAACATTCAAGCT-TATATCACAAAATAC
40035966 ATATAACCACATAACA
63 ATATAACCACATAACA
* *
40035982 TTTAAGCATATATCACATTACTCGTATAATCACATAACATTCAAGCTTATATCATAAAATACATA
1 TTTAAGCATATATCACATTACTCATATAATCACATAACATTCAAGCTTATATCACAAAATACATA
* *
40036047 TAATCTCATAACA
66 TAACCACATAACA
* *
40036060 TTTAAGCATATATCATAATACTCA
1 TTTAAGCATATATCACATTACTCA
40036084 AAACATGTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
78 80 0.91
79 8 0.09
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.33
Consensus pattern (78 bp):
TTTAAGCATATATCACATTACTCATATAATCACATAACATTCAAGCTTATATCACAAAATACATA
TAACCACATAACA
Found at i:40038686 original size:23 final size:24
Alignment explanation
Indices: 40038635--40038688 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
40038625 TTTGTTACAT
* * *
40038635 TATAAAT--AAAATTTTTAAACTC
1 TATAAATAAAAAATTTATAAAATA
40038657 TATAAATAAAAAATTTATAAAATA
1 TATAAATAAAAAATTTATAAAATA
40038681 TA-AAATAA
1 TATAAATAA
40038689 TGTGGGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.26
23 6 0.22
24 14 0.52
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
TATAAATAAAAAATTTATAAAATA
Found at i:40039568 original size:15 final size:16
Alignment explanation
Indices: 40039536--40039569 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
40039526 TAATGAGTAT
40039536 AATAAAATATTAAAAA
1 AATAAAATATTAAAAA
40039552 AATAAAA-ATTTAAAAA
1 AATAAAATA-TTAAAAA
40039568 AA
1 AA
40039570 GATATATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAAAATATTAAAAA
Found at i:40042888 original size:3 final size:3
Alignment explanation
Indices: 40042864--40042971 Score: 71
Period size: 3 Copynumber: 37.0 Consensus size: 3
40042854 TTTAATAATG
* * * * * *
40042864 TTA TCA TTA TTT TTA CTA TTA TTA TTA TGT- TTA ATA CTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * * * * *
40042909 CTA TTA CTA TTA TT- TT- TTA TTT TTA -TA TTT TTA CTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40042954 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
40042972 CTCTTATTTA
Statistics
Matches: 80, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
2 7 0.09
3 72 0.90
4 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:40043373 original size:9 final size:9
Alignment explanation
Indices: 40043359--40043390 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
40043349 TACATACTTA
40043359 TATATATTT
1 TATATATTT
40043368 TATATATTT
1 TATATATTT
40043377 TATA-A-TT
1 TATATATTT
40043384 TATATAT
1 TATATAT
40043391 ACATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.29
8 2 0.10
9 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TATATATTT
Found at i:40043391 original size:20 final size:19
Alignment explanation
Indices: 40043368--40043419 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
40043358 ATATATATTT
*
40043368 TATATATTTTATAATTTATA
1 TATATATTTTAT-ATCTATA
40043388 TATACATATATTTATATCTATA
1 TAT--ATAT-TTTATATCTATA
*
40043410 TACATATTTT
1 TATATATTTT
40043420 CTAAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
19 3 0.11
20 7 0.26
22 12 0.44
23 5 0.19
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATATTTTATATCTATA
Found at i:40043397 original size:53 final size:52
Alignment explanation
Indices: 40043337--40043509 Score: 131
Period size: 51 Copynumber: 3.3 Consensus size: 52
40043327 TTATGACAGG
40043337 TACATATATACATACATACTTATATATATTTTATATATTTTATAATTTATATA
1 TACATATATACATACATACTTATATATATTTT-TATATTTTATAATTTATATA
* * * * * *
40043390 TACATATAT--TTATAT-CTATATACATATTTTCTAAATTTTTATGA-GTATATA
1 TACATATATACATACATACT-TATATATATTTT-TATA-TTTTATAATTTATATA
* * ** * * * *
40043441 TATATTTATATGTACGTACTTATATAT-TTTTTATACTTTCTAATTTGTATA
1 TACATATATACATACATACTTATATATATTTTTATATTTTATAATTTATATA
* *
40043492 TACATATTTACATCCATA
1 TACATATATACATACATA
40043510 TTTTTTAATA
Statistics
Matches: 88, Mismatches: 26, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
50 7 0.08
51 50 0.57
52 11 0.12
53 18 0.20
54 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.51
Consensus pattern (52 bp):
TACATATATACATACATACTTATATATATTTTTATATTTTATAATTTATATA
Found at i:40046835 original size:5 final size:5
Alignment explanation
Indices: 40046825--40046852 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40046815 CAGTGGAGGC
40046825 AAACA AAACA AAACA AAACA AAACA AAA
1 AAACA AAACA AAACA AAACA AAACA AAA
40046853 AACCTCTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:40047324 original size:28 final size:26
Alignment explanation
Indices: 40047273--40047325 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 26
40047263 ACTTCACTTG
40047273 AAAAAAAGAAACGAAAAGAAAAAATA
1 AAAAAAAGAAACGAAAAGAAAAAATA
*
40047299 AAAAAAAG-AA-G-AACGAAAAAATA
1 AAAAAAAGAAACGAAAAGAAAAAATA
40047322 AAAA
1 AAAA
40047326 GGAGAGGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.58
24 1 0.04
25 2 0.08
26 8 0.31
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (26 bp):
AAAAAAAGAAACGAAAAGAAAAAATA
Found at i:40047324 original size:29 final size:26
Alignment explanation
Indices: 40047273--40047325 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
40047263 ACTTCACTTG
*
40047273 AAAAAAAGAAACGAAAAGAAAAAATA
1 AAAAAAAGAAACGAAAAAAAAAAATA
40047299 AAAAAAAGAAGAACGAAAAAATAAAAA
1 AAAAAAAG-A-AACGAAAAAA-AAAAA
40047326 GGAGAGGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 1 0.04
28 9 0.39
29 5 0.22
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (26 bp):
AAAAAAAGAAACGAAAAAAAAAAATA
Found at i:40047668 original size:45 final size:45
Alignment explanation
Indices: 40047605--40047691 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
40047595 TTTTATTTAT
* * *
40047605 TTTTGTATTTTGGAAAAATACG-TCATCTTGATTAATTTATTCTCA
1 TTTTGTATTCTAGAAAAATACGCT-ATCTTGATTAATTCATTCTCA
* **
40047650 TTTTGTATTCTAGCAAAATTTGCTATCTTGATTAATTCATTC
1 TTTTGTATTCTAGAAAAATACGCTATCTTGATTAATTCATTC
40047692 ATTTCGAGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 34 0.97
46 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (45 bp):
TTTTGTATTCTAGAAAAATACGCTATCTTGATTAATTCATTCTCA
Found at i:40048782 original size:50 final size:48
Alignment explanation
Indices: 40048726--40049166 Score: 332
Period size: 50 Copynumber: 8.8 Consensus size: 48
40048716 TTTGGCATTA
* **
40048726 CAGTGGAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCTGGTGATG
1 CAGT-GAACAGATTGAAGCTACAACAGCGAATCTTACTTCCC-GGACATG
* * *
40048776 TAGTGGAACAGATTGAAGCTACAACAACGAATCTTACTTCCCCGACATTG
1 CAGT-GAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCGGACA-TG
* * * ** *
40048826 CAGTTAAATAGATTGAAGCTACGACAGCGAATCTTACTTCTTTGG-CATTA
1 CAG-TGAACAGATTGAAGCTACAACAGCGAATCTTACTTC-CCGGACA-TG
* * *
40048876 CAGTAGAATAGATTGAAGCTACAACAGTGAATCTTACTTCCCTGG-CGGTG
1 CAGT-GAACAGATTGAAGCTACAACAGCGAATCTTACTTCCC-GGAC-ATG
* *
40048926 CAGTGGAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTG
1 CAGT-GAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCGGACA-TG
* * * * * * * *
40048976 CAGTTAAATAGATTAAAGCTACAACAACGAATCTTATTTCCTTGG-CGTTA
1 CAG-TGAACAGATTGAAGCTACAACAGCGAATCTTACTTCC-CGGAC-ATG
* * * * * *
40049026 CAGTGAAGCAGATTAAAGCTACAATAACAAATCTTACTTCCCCGACATTA
1 CAGTGAA-CAGATTGAAGCTACAACAGCGAATCTTACTTCCCGGACA-TG
* ** *
40049076 CAGTGAAGCAGATTAAAGCTACAACAGCGAATCTTACTTACCC-GATGTTA
1 CAGTGAA-CAGATTGAAGCTACAACAGCGAATCTTACTT-CCCGGA-CATG
* *
40049126 CAGTGAAGCAGATTAAAGCTACAATAGCGAATCTTACTTCC
1 CAGTGAA-CAGATTGAAGCTACAACAGCGAATCTTACTTCC
40049167 TCGAAGTTGT
Statistics
Matches: 327, Mismatches: 48, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
49 10 0.03
50 310 0.95
51 7 0.02
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (48 bp):
CAGTGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCGGACATG
Found at i:40048860 original size:100 final size:98
Alignment explanation
Indices: 40048723--40049166 Score: 422
Period size: 100 Copynumber: 4.4 Consensus size: 98
40048713 CTCTTTGGCA
* * **
40048723 TTACAGTGGAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCTGGTGATGT-AGTGGAACAG
1 TTACAGTGAAACAGATTGAAGCTACAATAGCGAATCTTACTTCCC-CGACAT-TAAGT-GAACAG
* *
40048787 ATTGAAGCTACAACAACGAATCTTACTTCCCCGACA
63 ATTAAAGCTACAACAACGAATCTTACTTCCCCGACG
* * * * * *** * *
40048823 TTGCAGTTAAATAGATTGAAGCTACGACAGCGAATCTTACTTCTTTGGCATTACAGTAGAATAGA
1 TTACAGTGAAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTA-AGT-GAACAGA
* ** * *
40048888 TTGAAGCTACAACAGTGAATCTTACTTCCCTGGCG
64 TTAAAGCTACAACAACGAATCTTACTTCCCCGACG
* * * * * * * *
40048923 GTGCAGTGGAATAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAATAGA
1 TTACAGTGAAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATT-AAG-TGAACAGA
* ** *
40048988 TTAAAGCTACAACAACGAATCTTATTTCCTTGGCG
64 TTAAAGCTACAACAACGAATCTTACTTCCCCGACG
* * * *
40049023 TTACAGTGAAGCAGATTAAAGCTACAATAACAAATCTTACTTCCCCGACATTACAGTGAAGCAGA
1 TTACAGTGAAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTA-AGTGAA-CAGA
* * *
40049088 TTAAAGCTACAACAGCGAATCTTACTTACCCGATG
64 TTAAAGCTACAACAACGAATCTTACTTCCCCGACG
* *
40049123 TTACAGTGAAGCAGATTAAAGCTACAATAGCGAATCTTACTTCC
1 TTACAGTGAAACAGATTGAAGCTACAATAGCGAATCTTACTTCC
40049167 TCGAAGTTGT
Statistics
Matches: 284, Mismatches: 54, Indels: 12
0.81 0.15 0.03
Matches are distributed among these distances:
98 1 0.00
99 6 0.02
100 276 0.97
101 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (98 bp):
TTACAGTGAAACAGATTGAAGCTACAATAGCGAATCTTACTTCCCCGACATTAAGTGAACAGATT
AAAGCTACAACAACGAATCTTACTTCCCCGACG
Done.