Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 128 of 325
Found at i:38622846 original size:96 final size:97
Alignment explanation
Indices: 38622722--38622955 Score: 285
Period size: 96 Copynumber: 2.4 Consensus size: 97
38622712 TACGAAGTCT
* * * *
38622722 CATATC-GGTGCCGA-GTCCATGTCCCAGACATGGTCTTTCACCAGCACACATATCATCACCGAT
1 CATATCAGATGCCGATG-CCATGTCCCAGACATGGTCTTACACCAGCACACATATCAACACCAAT
*
38622785 ACCATGTCCCAGACATGGTCTTACATTGGCACA
65 ACCATGTCCCAGACATGGTCTTACACTGGCACA
* ** * *
38622818 CATATCA-ATGTCGATGCCATGTCCCAGACATGGTCTTACATTAGCACACATATCAACGCCAATG
1 CATATCAGATGCCGATGCCATGTCCCAGACATGGTCTTACACCAGCACACATATCAACACCAATA
* * * *
38622882 CCATGTTCCAGATATGGTCTTACACTGGCTCT
66 CCATGTCCCAGACATGGTCTTACACTGGCACA
* * *
38622914 CATCTCAGATGCCGATGCCATGTCCCAGACAAGGTTTTACAC
1 CATATCAGATGCCGATGCCATGTCCCAGACATGGTCTTACAC
38622956 GGGATCTCAT
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
96 85 0.73
97 31 0.27
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (97 bp):
CATATCAGATGCCGATGCCATGTCCCAGACATGGTCTTACACCAGCACACATATCAACACCAATA
CCATGTCCCAGACATGGTCTTACACTGGCACA
Found at i:38624564 original size:66 final size:66
Alignment explanation
Indices: 38624482--38624614 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
38624472 CTCAAACATG
38624482 ATTGAATACCATTTCATTAAAATTTCTCAATGTAGTACTTGAATAGGTTCCGTACATACCCGTAT
1 ATTGAATACCATTTCATTAAAATTTCTCAATGTAGTACTTGAATAGGTTCCGTACATACCCGTAT
38624547 C
66 C
* *
38624548 ATTGAATACCATTTCATTAAACTTTCTTAATGTAGTACTTGAATAGGTTCCGTACATACCCGTAT
1 ATTGAATACCATTTCATTAAAATTTCTCAATGTAGTACTTGAATAGGTTCCGTACATACCCGTAT
38624613 C
66 C
38624614 A
1 A
38624615 CCTCGTAAAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (66 bp):
ATTGAATACCATTTCATTAAAATTTCTCAATGTAGTACTTGAATAGGTTCCGTACATACCCGTAT
C
Found at i:38628919 original size:29 final size:29
Alignment explanation
Indices: 38628875--38629025 Score: 171
Period size: 29 Copynumber: 5.2 Consensus size: 29
38628865 GTATCGAAGC
*
38628875 CCATCAAATATGAAAAGGGATGGCTTTGA
1 CCATCGAATATGAAAAGGGATGGCTTTGA
* * *
38628904 CCATCAAATATTAAAAAGGATGGCTTTGA
1 CCATCGAATATGAAAAGGGATGGCTTTGA
* * *
38628933 CCATTGAATATGGAAAA-GGTTGGCTTCGA
1 CCATCGAATAT-GAAAAGGGATGGCTTTGA
* *
38628962 CCATCGAATATGAAAAGGGATGACTTCGA
1 CCATCGAATATGAAAAGGGATGGCTTTGA
* *
38628991 CCATTGAATATGGAAAGGGATGG-TTTCGA
1 CCATCGAATATGAAAAGGGATGGCTTT-GA
38629020 CCATCG
1 CCATCG
38629026 TTTAGCACAC
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
28 7 0.07
29 93 0.89
30 4 0.04
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGCTTTGA
Found at i:38628972 original size:58 final size:58
Alignment explanation
Indices: 38628881--38629025 Score: 193
Period size: 58 Copynumber: 2.5 Consensus size: 58
38628871 AAGCCCATCA
* * * * *
38628881 AATAT-GAAAAGGGATGGCTTTGACCATCAAATATTAAAAAGGATGGCTTTGACCATTG
1 AATATGGAAAA-GGATGGCTTCGACCATCGAATATGAAAAAGGATGACTTCGACCATTG
* *
38628939 AATATGGAAAAGGTTGGCTTCGACCATCGAATATGAAAAGGGATGACTTCGACCATTG
1 AATATGGAAAAGGATGGCTTCGACCATCGAATATGAAAAAGGATGACTTCGACCATTG
* *
38628997 AATATGGAAAGGGATGGTTTCGACCATCG
1 AATATGGAAAAGGATGGCTTCGACCATCG
38629026 TTTAGCACAC
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
58 71 0.93
59 5 0.07
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.26
Consensus pattern (58 bp):
AATATGGAAAAGGATGGCTTCGACCATCGAATATGAAAAAGGATGACTTCGACCATTG
Found at i:38635084 original size:40 final size:40
Alignment explanation
Indices: 38635020--38635251 Score: 383
Period size: 40 Copynumber: 5.8 Consensus size: 40
38635010 CCAGCATGAT
* * *
38635020 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* *
38635060 TGCTCTTCTGAACTTAGTCTGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
38635100 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * *
38635140 TGCTCCTCAGAACTTAGTCCGGATACGTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
38635180 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
38635220 TGCTCTTCGGAACTTAGTCCGGATATATCACT
1 TGCTCTTCGGAACTTAGTCCGGATACATCACT
38635252 CTCAATTCTC
Statistics
Matches: 178, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 178 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:38637130 original size:37 final size:37
Alignment explanation
Indices: 38637080--38637170 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
38637070 TTATTACGAA
38637080 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
38637117 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
38637154 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
38637171 TTTCCAAGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 47 0.90
38 5 0.10
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:38637268 original size:48 final size:48
Alignment explanation
Indices: 38637210--38637409 Score: 328
Period size: 48 Copynumber: 4.2 Consensus size: 48
38637200 TGTTACAACA
38637210 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
38637258 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACTCATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* ** * *
38637306 TTCACATTAGCCCTTCGGCTTTACCACATATACATATCTTATATATGT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
38637354 TTCACATTAGCCCTTCGGCTTTACCACATATACACATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
38637402 TTCACATT
1 TTCACATT
38637410 CATCACATCG
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 140 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:38637468 original size:96 final size:96
Alignment explanation
Indices: 38637380--38637585 Score: 290
Period size: 96 Copynumber: 2.1 Consensus size: 96
38637370 GGCTTTACCA
*
38637380 CATATACACATCACACATATA-TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 CATAT-CACAT-ACACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
*
38637444 -ACACTTTCACATTCATCACATCGGCCATTAGGC
64 AACACTTTCACATTCATCACATCGG-CATTAGCC
* * *
38637477 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CATATCACATACACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA-
*
38637542 ACACTTTCACATTCATCACATCGGCCATTAGGC
65 ACACTTTCACATTCATCACATCGG-CATTAGCC
*
38637575 CTTATCACATA
1 CATATCACATA
38637586 TATACATCTC
Statistics
Matches: 102, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
95 6 0.06
96 48 0.47
97 4 0.04
98 44 0.43
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.31
Consensus pattern (96 bp):
CATATCACATACACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAA
CACTTTCACATTCATCACATCGGCATTAGCC
Found at i:38637587 original size:96 final size:95
Alignment explanation
Indices: 38637401--38637591 Score: 348
Period size: 96 Copynumber: 2.0 Consensus size: 95
38637391 CACACATATA
38637401 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
38637466 GGCCATTAGGCCTTATCACATATATATACAC
66 GGCCATTAGGCCTTATCACA-ATATATACAC
38637497 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT--ACACTTTCACATTCATCACA
38637562 TCGGCCATTAGGCCTTATCAC-ATATATACA
64 TCGGCCATTAGGCCTTATCACAATATATACA
38637592 TCTCATACAT
Statistics
Matches: 93, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
96 52 0.56
98 41 0.44
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (95 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACAATATATACAC
Found at i:38637588 original size:49 final size:49
Alignment explanation
Indices: 38637401--38637591 Score: 359
Period size: 49 Copynumber: 3.9 Consensus size: 49
38637391 CACACATATA
38637401 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT--ACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACAC
*
38637448 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACAC
38637497 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACAC
38637546 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
38637592 TCTCATACAT
Statistics
Matches: 141, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
47 43 0.30
49 98 0.70
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.32
Consensus pattern (49 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACAC
Found at i:38661219 original size:20 final size:19
Alignment explanation
Indices: 38661178--38661222 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
38661168 GAATTAAGAA
*
38661178 CAAATATTTAAGAACAAGT
1 CAAATATTTAACAACAAGT
* *
38661197 CAAATATTTATCATACAATT
1 CAAATATTTAACA-ACAAGT
38661217 CAAATA
1 CAAATA
38661223 AAAATAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.31
Consensus pattern (19 bp):
CAAATATTTAACAACAAGT
Found at i:38667596 original size:20 final size:20
Alignment explanation
Indices: 38667571--38667608 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38667561 GTCTAAACTG
*
38667571 AAAACTCAGGGAATTTTTAT
1 AAAACTCAGGAAATTTTTAT
*
38667591 AAAACTTAGGAAATTTTT
1 AAAACTCAGGAAATTTTT
38667609 GTTAGAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
AAAACTCAGGAAATTTTTAT
Found at i:38669735 original size:42 final size:44
Alignment explanation
Indices: 38669623--38669770 Score: 142
Period size: 42 Copynumber: 3.5 Consensus size: 44
38669613 TGAATTTTCA
* ** **
38669623 TGTAAGACCATGTCTGGGACGTTGGCATCAATATGAGATTTACG
1 TGTAAGACCATGTATGGGACACTGGCATCAATATTTGATTTACG
* * *
38669667 TTTAAGACCATGTTTGGGACACTGGCATC-GTATTTGATTT-CG
1 TGTAAGACCATGTATGGGACACTGGCATCAATATTTGATTTACG
* * * *
38669709 TGTAAGACCCTGTATGGGATAGTGGCATCAATATTTGA--TACA
1 TGTAAGACCATGTATGGGACACTGGCATCAATATTTGATTTACG
* *
38669751 TGTAAGACCACGTTTGGGAC
1 TGTAAGACCATGTATGGGAC
38669771 GTTGGCATTG
Statistics
Matches: 84, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
41 1 0.01
42 43 0.51
43 15 0.18
44 25 0.30
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (44 bp):
TGTAAGACCATGTATGGGACACTGGCATCAATATTTGATTTACG
Found at i:38678614 original size:40 final size:40
Alignment explanation
Indices: 38678569--38678735 Score: 180
Period size: 40 Copynumber: 4.2 Consensus size: 40
38678559 CGGAATATAA
38678569 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
38678609 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
38678649 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
38678689 CCGGATATAAATTC-C-AGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATAT-AA-TCACTAGCACAAATGCCTTCGGGTCTTAGC
38678728 CCGGATAT
1 CCGGATAT
38678736 CATTCAATTT
Statistics
Matches: 108, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
39 14 0.13
40 91 0.84
41 2 0.02
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38679791 original size:42 final size:42
Alignment explanation
Indices: 38679682--38679847 Score: 158
Period size: 42 Copynumber: 3.9 Consensus size: 42
38679672 CGATATGTGT
* *
38679682 TTTCGTGTAAGACCATGTCTAGGA-AGTTGGCATC-AATTTGAGA
1 TTTCGTGTAAGACCATGTCTGGGACA-TTGGCATCGTATTT--GA
* *
38679725 TTTATGTGTAAGACCATGTTTGGGACATTGGCATCGTATTTGA
1 TTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGA
* * * *
38679768 TTTCGTGTAAGACCCTATCTGGGACAGTGGCATCAATATTTGA
1 TTTCGTGTAAGACCATGTCTGGGACATTGGCATC-GTATTTGA
* * * *
38679811 -TACATGTAAGACCATGTCTGGGACGTTGGCATTGTAT
1 TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTAT
38679848 GAGCTTTTCG
Statistics
Matches: 101, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.03
42 52 0.51
43 15 0.15
44 26 0.26
45 5 0.05
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (42 bp):
TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGA
Found at i:38685850 original size:40 final size:40
Alignment explanation
Indices: 38685727--38685876 Score: 137
Period size: 40 Copynumber: 3.8 Consensus size: 40
38685717 GAATGATGTT
* *
38685727 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGACCATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGCT-ACCAAATC
* * *
38685767 CGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAATC
1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGCTACCAAATC
* **
38685807 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAA-C
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCA-AATC
* * *
38685847 CGGGCTATGTCCCGAAGGCTTTTGAGCGAG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAG
38685877 TCACTATATC
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
39 1 0.01
40 79 0.87
41 11 0.12
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCAAATC
Found at i:38693811 original size:40 final size:40
Alignment explanation
Indices: 38693728--38693839 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
38693718 TCGAATGATG
* *
38693728 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAA
* **
38693768 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAA
*
38693808 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
38693840 CTATTATAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
39 1 0.02
40 53 0.85
41 8 0.13
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:38695302 original size:29 final size:29
Alignment explanation
Indices: 38695267--38695325 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
38695257 TTGACTATCA
*
38695267 AATATGGAAAGGGATGGGTTCGATCATCG
1 AATATGGAAAGGGATGGGTTCGACCATCG
* *
38695296 AATATGGAAAGGGGTGGTTTCGACCATCG
1 AATATGGAAAGGGATGGGTTCGACCATCG
38695325 A
1 A
38695326 TTAAAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.34, T:0.24
Consensus pattern (29 bp):
AATATGGAAAGGGATGGGTTCGACCATCG
Found at i:38695334 original size:29 final size:29
Alignment explanation
Indices: 38695273--38695334 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
38695263 ATCAAATATG
* **
38695273 GAAAGGGATGGGTTCGATCATCGAATATG
1 GAAAGGGATGGGTTCGACCATCGAATAAA
* * *
38695302 GAAAGGGGTGGTTTCGACCATCGATTAAA
1 GAAAGGGATGGGTTCGACCATCGAATAAA
38695331 GAAA
1 GAAA
38695335 ATGGATGGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.23
Consensus pattern (29 bp):
GAAAGGGATGGGTTCGACCATCGAATAAA
Found at i:38696920 original size:93 final size:93
Alignment explanation
Indices: 38696760--38696932 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
38696750 CGGATATTTG
** * *
38696760 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGATTGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTAAG
*
38696825 TTGAGTCCGAGTTCGTGAGACGTAACTA
66 TTGAGTCCAAGTTCGTGAGACGTAACTA
* * * *
38696853 GGCATCTGAGCTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTAAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTAAG
38696918 TTGAGTCCAAGTTCG
66 TTGAGTCCAAGTTCG
38696933 CTTGTGGGTG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTAAG
TTGAGTCCAAGTTCGTGAGACGTAACTA
Found at i:38702686 original size:40 final size:40
Alignment explanation
Indices: 38702641--38702807 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
38702631 CGGAATATAA
38702641 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
38702681 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
38702721 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
38702761 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
38702800 CCGGATAT
1 CCGGATAT
38702808 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38702791 original size:80 final size:79
Alignment explanation
Indices: 38702641--38702807 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
38702631 CGGAATATAA
* *
38702641 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
38702706 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
38702721 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
38702783 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
38702800 CCGGATAT
1 CCGGATAT
38702808 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:38703655 original size:17 final size:19
Alignment explanation
Indices: 38703632--38703677 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
38703622 AAGAAGCATG
38703632 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
38703650 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
38703668 AATCATGCTC
1 AATCATGCTC
38703678 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:38710687 original size:40 final size:40
Alignment explanation
Indices: 38710642--38710807 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
38710632 CGGAATATAA
38710642 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
38710682 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
38710722 CCGGATAT-ACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
38710761 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
38710800 CCGGATAT
1 CCGGATAT
38710808 CATTCAATTG
Statistics
Matches: 105, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 46 0.44
40 59 0.56
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38710764 original size:39 final size:38
Alignment explanation
Indices: 38710658--38710769 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 38
38710648 ATAATCACGT
* * *
38710658 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATA-TACAACTA
* *
38710698 GCACGAATGCCTTCGGGCCTTAGCCCGGATATACCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATACAACTA
*
38710737 GCACAATTGCCTTCGGGTCTTAACCCGGATATA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATA
38710770 ATTTCCAGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 2 0.03
39 32 0.51
40 29 0.46
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATATACAACTA
Found at i:38710791 original size:79 final size:78
Alignment explanation
Indices: 38710658--38710807 Score: 196
Period size: 79 Copynumber: 1.9 Consensus size: 78
38710648 ATAATCACGT
*
38710658 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
38710723 CGGATATACCACTA
65 CGGATATACCACTA
* * ** * *
38710737 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
38710800 CCGGATAT
64 CCGGATAT
38710808 CATTCAATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
78 17 0.27
79 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (78 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATACCACTA
Found at i:38715824 original size:17 final size:17
Alignment explanation
Indices: 38715802--38715842 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
38715792 AGGATGAAAC
*
38715802 TTTTTCTTTCTTTTTTT
1 TTTTTCTTTCTTGTTTT
38715819 TTTTTCTTTCTTGTTTT
1 TTTTTCTTTCTTGTTTT
*
38715836 TGTTTCT
1 TTTTTCT
38715843 CTCATGTACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTGTTTT
Found at i:38742637 original size:245 final size:245
Alignment explanation
Indices: 38742207--38742653 Score: 867
Period size: 245 Copynumber: 1.8 Consensus size: 245
38742197 TTTGCTCAAA
38742207 GTACAGTCAAGGTCATCCATTACTCACTCAGTAGCCTCTAACCAATATTCTTCCATATTCAGGGC
1 GTACAGTCAAGGTCATCCATTACTCACTCAGTAGCCTCTAACCAATATTCTTCCATATTCAGGGC
38742272 TACACCCGAAACACCCTTGAAGATTTCCACTCCATTAGATCGGAGTCACTCCGAAATTGACCCCC
66 TACACCCGAAACACCCTTGAAGATTTCCACTCCATTAGATCGGAGTCACTCCGAAATTGACCCCC
38742337 AGCCTACAGATCCAGTACTTCTCCAGCAACCCTTTCAAGAACTCGTAGCATTGCTTGAGATAAAG
131 AGCCTACAGATCCAGTACTTCTCCAGCAACCCTTTCAAGAACTCGTAGCATTGCTTGAGATAAAG
38742402 CATCATCCCCAACTGCTCGATCATAAGACCCTGACTCAGTTACTGGTGAG
196 CATCATCCCCAACTGCTCGATCATAAGACCCTGACTCAGTTACTGGTGAG
*
38742452 GTACAGTCAAGGTCATCCATTACTCTCTCAGTAGCCTCTAACCAATATTCTTCCATATTCAGGGC
1 GTACAGTCAAGGTCATCCATTACTCACTCAGTAGCCTCTAACCAATATTCTTCCATATTCAGGGC
*
38742517 TACACCCGAAACACCCTTGAATATTTCCACTCCATTAGATCGGAGTCACTCCGAAATTGACCCCC
66 TACACCCGAAACACCCTTGAAGATTTCCACTCCATTAGATCGGAGTCACTCCGAAATTGACCCCC
*
38742582 AGCCTACAGATCCAGTACTTCTCCAGTAACCCTTTCAAGAACTCGTAGCATTGCTTGAGATAAAG
131 AGCCTACAGATCCAGTACTTCTCCAGCAACCCTTTCAAGAACTCGTAGCATTGCTTGAGATAAAG
38742647 CATCATC
196 CATCATC
38742654 TCAGTTACTG
Statistics
Matches: 199, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
245 199 1.00
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.26
Consensus pattern (245 bp):
GTACAGTCAAGGTCATCCATTACTCACTCAGTAGCCTCTAACCAATATTCTTCCATATTCAGGGC
TACACCCGAAACACCCTTGAAGATTTCCACTCCATTAGATCGGAGTCACTCCGAAATTGACCCCC
AGCCTACAGATCCAGTACTTCTCCAGCAACCCTTTCAAGAACTCGTAGCATTGCTTGAGATAAAG
CATCATCCCCAACTGCTCGATCATAAGACCCTGACTCAGTTACTGGTGAG
Found at i:38755659 original size:7 final size:7
Alignment explanation
Indices: 38755647--38755679 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
38755637 CTCTAATTTC
38755647 AGTTTGT
1 AGTTTGT
38755654 AGTTTGT
1 AGTTTGT
38755661 AGTTTGT
1 AGTTTGT
38755668 AGTTTGT
1 AGTTTGT
38755675 AGTTT
1 AGTTT
38755680 TTAGGCTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (7 bp):
AGTTTGT
Found at i:38755957 original size:32 final size:32
Alignment explanation
Indices: 38755916--38755978 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
38755906 TGAGTGGAGG
38755916 TGTGATTAATTAATTCTTATATAGGGTTTTCA
1 TGTGATTAATTAATTCTTATATAGGGTTTTCA
38755948 TGTGATTAATTAATTCTTATATAGGGTTTTC
1 TGTGATTAATTAATTCTTATATAGGGTTTTC
38755979 TTAGCGGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (32 bp):
TGTGATTAATTAATTCTTATATAGGGTTTTCA
Found at i:38762726 original size:25 final size:23
Alignment explanation
Indices: 38762695--38762762 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
38762685 ATACAGTAAA
38762695 AATATATAATAAAATATAAATGGAAT
1 AATATATAATAAAATATAAAT---AT
* * *
38762721 AA-ATATCATATAATAAAAATAT
1 AATATATAATAAAATATAAATAT
*
38762743 AATATATAATAAAATTTAAA
1 AATATATAATAAAATATAAA
38762763 AAATGTATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 4 0.12
23 13 0.38
25 15 0.44
26 2 0.06
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (23 bp):
AATATATAATAAAATATAAATAT
Found at i:38762882 original size:24 final size:23
Alignment explanation
Indices: 38762849--38762893 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
38762839 TATAGTATTT
38762849 AAAATAAATTGAATTTATAAAAAA
1 AAAATAAATTGAATTT-TAAAAAA
* *
38762873 AAAATTAATTTAATTTTAAAA
1 AAAATAAATTGAATTTTAAAA
38762894 TTTTAGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATAAATTGAATTTTAAAAAA
Found at i:38763293 original size:13 final size:13
Alignment explanation
Indices: 38763277--38763301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38763267 AAAAAAAAAC
38763277 TTTAAACATTCAT
1 TTTAAACATTCAT
38763290 TTTAAACATTCA
1 TTTAAACATTCA
38763302 ACAGAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTAAACATTCAT
Found at i:38764123 original size:17 final size:18
Alignment explanation
Indices: 38764101--38764139 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
38764091 CTTAAATGGA
*
38764101 TTGTTTAA-TTTTATTTT
1 TTGTTTAATTTTTAATTT
38764118 TTGTTTAATTTTTAATTT
1 TTGTTTAATTTTTAATTT
38764136 TTGT
1 TTGT
38764140 AAGCCAGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (18 bp):
TTGTTTAATTTTTAATTT
Found at i:38765993 original size:27 final size:27
Alignment explanation
Indices: 38765963--38766103 Score: 155
Period size: 27 Copynumber: 5.2 Consensus size: 27
38765953 GTGATGAAGT
* *
38765963 CACCAGATACAGATATTGTAGCAAAGC
1 CACCAGATACAGATATTGTGGCAGAGC
*
38765990 CACCA-AAACAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
38766017 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
*
38766044 CACCA-AGACAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
* *
38766071 CACCAGAT-CAGATAATTGTGGTATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
38766098 CACCAG
1 CACCAG
38766104 GACGCTTCCT
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
26 12 0.12
27 79 0.81
28 6 0.06
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (27 bp):
CACCAGATACAGATATTGTGGCAGAGC
Found at i:38766090 original size:54 final size:54
Alignment explanation
Indices: 38765963--38766102 Score: 228
Period size: 54 Copynumber: 2.6 Consensus size: 54
38765953 GTGATGAAGT
* *
38765963 CACCAGATACAGAT-ATTGTAGCAAAGCCACCAAAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAAAACAGATATATGTGGCAGAGC
*
38766017 CACCAGATCAGATAATTGTGGCATAGCCACCAAGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAAAACAGATATATGTGGCAGAGC
*
38766071 CACCAGATCAGATAATTGTGGTATAGCCACCA
1 CACCAGATCAGATAATTGTGGCATAGCCACCA
38766103 GGACGCTTCC
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 5 0.06
54 76 0.94
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAAAACAGATATATGTGGCAGAGC
Found at i:38766271 original size:28 final size:26
Alignment explanation
Indices: 38766209--38766271 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
38766199 AAAGTAACCC
** *
38766209 TAGGGGTATAATGGTAATTTTACACC
1 TAGGGGTATAACAGTAATTTTACACA
*
38766235 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATAACAGTAATTTT--ACACA
38766263 TAGGGGTAT
1 TAGGGGTAT
38766272 TCAAGTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 19 0.61
28 12 0.39
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (26 bp):
TAGGGGTATAACAGTAATTTTACACA
Found at i:38767720 original size:26 final size:26
Alignment explanation
Indices: 38767689--38767744 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
38767679 TGAAATTTCC
38767689 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
38767715 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
38767741 ATCA
1 ATCA
38767745 ATTTGTACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:38771356 original size:16 final size:16
Alignment explanation
Indices: 38771335--38771369 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
38771325 CAGTCCAAGT
38771335 TGTCCATAATCCGTTC
1 TGTCCATAATCCGTTC
38771351 TGTCCATAATCCGTTC
1 TGTCCATAATCCGTTC
38771367 TGT
1 TGT
38771370 GGCCTAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.29, G:0.14, T:0.40
Consensus pattern (16 bp):
TGTCCATAATCCGTTC
Found at i:38773004 original size:26 final size:25
Alignment explanation
Indices: 38772968--38773122 Score: 127
Period size: 26 Copynumber: 5.9 Consensus size: 25
38772958 GCGAGGCTGC
*
38772968 CAGATATTGTGACAAAGTCACCA-ATA
1 CAGATATTGTGAC-AAGCCACCAGA-A
*
38772994 CAGATATTGTGGCAAGCCACCAGAA
1 CAGATATTGTGACAAGCCACCAGAA
* *
38773019 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGACA-AGCCACCAGAA
*
38773046 CA-ATAATTGTGGCATAGCCACCAG-A
1 CAGAT-ATTGTGACA-AGCCACCAGAA
* *
38773071 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGACA-AGCCACCAGAA
*
38773098 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGACA-AGCCACCAG
38773123 GACGAATCAG
Statistics
Matches: 113, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
25 20 0.18
26 56 0.50
27 35 0.31
28 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (25 bp):
CAGATATTGTGACAAGCCACCAGAA
Found at i:38773106 original size:53 final size:54
Alignment explanation
Indices: 38772968--38773122 Score: 232
Period size: 52 Copynumber: 3.0 Consensus size: 54
38772958 GCGAGGCTGC
* * *
38772968 CAGATAT-TGTGACAAAGTCACCA-ATACAGAT-ATTGTGGCA-AGCCACCAGAA
1 CAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAGAA
38773019 CAGATATATGTGGCAGAGCCACCAGATCA-ATAATTGTGGCATAGCCACCAG-A
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAA
38773071 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAG
38773123 GACGAATCAG
Statistics
Matches: 96, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
51 9 0.09
52 54 0.56
53 33 0.34
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (54 bp):
CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAA
Found at i:38774638 original size:26 final size:26
Alignment explanation
Indices: 38774608--38774715 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
38774598 TGAAATTCCC
38774608 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
38774634 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
38774660 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
38774686 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
38774712 ATCA
1 ATCA
38774716 ATTTGTACCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:38776350 original size:13 final size:13
Alignment explanation
Indices: 38776332--38776361 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38776322 TTCAGAAAGT
*
38776332 ACACTCTCGAGCC
1 ACACTCTCAAGCC
38776345 ACACTCTCAAGCC
1 ACACTCTCAAGCC
38776358 ACAC
1 ACAC
38776362 ATGTGTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.47, G:0.10, T:0.13
Consensus pattern (13 bp):
ACACTCTCAAGCC
Found at i:38784230 original size:39 final size:40
Alignment explanation
Indices: 38784172--38784272 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
38784162 AAATTGAATG
* *
38784172 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
38784211 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
38784251 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
38784273 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:38784265 original size:40 final size:40
Alignment explanation
Indices: 38784172--38784354 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
38784162 AAATTGAATG
* * * * *
38784172 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
38784211 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
38784251 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
38784291 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
38784331 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
38784355 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.26
40 87 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:38792313 original size:39 final size:40
Alignment explanation
Indices: 38792255--38792355 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
38792245 AAATTGAATG
* *
38792255 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
38792294 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
38792334 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
38792356 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:38792348 original size:40 final size:40
Alignment explanation
Indices: 38792255--38792437 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
38792245 AAATTGAATG
* * * * *
38792255 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
38792294 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
38792334 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
38792374 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
38792414 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
38792438 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.26
40 87 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:38798078 original size:40 final size:41
Alignment explanation
Indices: 38797994--38798135 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 41
38797984 ACATTCAAAT
* * * * *
38797994 GCCTTCGGGACATAGCCCGG-TTACAGTAAC-TCGCACGAAT
1 GCCTTCGGGACTTAGCCCGGATT-TAGTCACTTAGCACGAAA
* * *
38798034 GCCTTCGGGACTCAACCCGGATTTAGT-AGCTT-GCTCGAAA
1 GCCTTCGGGACTTAGCCCGGATTTAGTCA-CTTAGCACGAAA
*
38798074 GCCTTC-GGATCTTAGTCCGGATTTAGTCACTTAGCAC-AAA
1 GCCTTCGGGA-CTTAGCCCGGATTTAGTCACTTAGCACGAAA
38798114 GCCTTCGGGACTTAGCCCGGAT
1 GCCTTCGGGACTTAGCCCGGAT
38798136 ATCATTCGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
39 4 0.05
40 70 0.83
41 10 0.12
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATTTAGTCACTTAGCACGAAA
Found at i:38806072 original size:40 final size:41
Alignment explanation
Indices: 38805988--38806129 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 41
38805978 ACATTCAAAT
* * * * *
38805988 GCCTTCGGGACATAGCCCGG-TTACAGTAAC-TCGCACGAAT
1 GCCTTCGGGACTTAGCCCGGATT-TAGTCACTTAGCACGAAA
* * *
38806028 GCCTTCGGGACTCAACCCGGATTTAGT-AGCTT-GCTCGAAA
1 GCCTTCGGGACTTAGCCCGGATTTAGTCA-CTTAGCACGAAA
*
38806068 GCCTTC-GGATCTTAGTCCGGATTTAGTCACTTAGCAC-AAA
1 GCCTTCGGGA-CTTAGCCCGGATTTAGTCACTTAGCACGAAA
38806108 GCCTTCGGGACTTAGCCCGGAT
1 GCCTTCGGGACTTAGCCCGGAT
38806130 ATCATTCGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
39 4 0.05
40 70 0.83
41 10 0.12
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATTTAGTCACTTAGCACGAAA
Found at i:38808745 original size:64 final size:64
Alignment explanation
Indices: 38808664--38808847 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
38808654 AGACATTATG
* *
38808664 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
** * * * * *
38808728 ATGTAGCTAGGTCGCATGCATGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
38808793 AA
63 AA
* * * *
38808795 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
38808848 CGAACTATAT
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 20 0.21
65 8 0.08
66 15 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:38811166 original size:18 final size:18
Alignment explanation
Indices: 38811143--38811193 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
38811133 TTTGGAGAGT
38811143 CACACGCCCGTGTGGTCA
1 CACACGCCCGTGTGGTCA
*
38811161 CACACGCTCGTGTGGTCA
1 CACACGCCCGTGTGGTCA
*
38811179 CACACGCCCATGTGG
1 CACACGCCCGTGTGG
38811194 CTCGGACACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.18, C:0.37, G:0.27, T:0.18
Consensus pattern (18 bp):
CACACGCCCGTGTGGTCA
Found at i:38813069 original size:48 final size:48
Alignment explanation
Indices: 38812993--38813198 Score: 222
Period size: 48 Copynumber: 4.3 Consensus size: 48
38812983 ATGCCAACAG
* * * *
38812993 CCCAGTTATGGTCTTACAC-GAAGTCTCATAACGGTGTCGATGCCATGT
1 CCCAGATATGGTCTTACACGGGA-TCTCATAACGATGTCGATGCCATAT
* * * * *
38813041 CCCAAACATGGTCTTATACGGGACCTCATATA-GATGTCAATGCCATAT
1 CCCAGATATGGTCTTACACGGGATCTCATA-ACGATGTCGATGCCATAT
* *
38813089 -CCAGATATGGTCTTACATGGGATCTCAT-ACTGATGCCGATGCCATAT
1 CCCAGATATGGTCTTACACGGGATCTCATAAC-GATGTCGATGCCATAT
**
38813136 CCCAGATATGGTCTTACACGGGATCTCATCTCGATGTCGATGCCATAT
1 CCCAGATATGGTCTTACACGGGATCTCATAACGATGTCGATGCCATAT
* *
38813184 CCAAGATATAGTCTT
1 CCCAGATATGGTCTT
38813199 GTACGAGATC
Statistics
Matches: 131, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
45 1 0.01
47 37 0.28
48 89 0.68
49 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (48 bp):
CCCAGATATGGTCTTACACGGGATCTCATAACGATGTCGATGCCATAT
Found at i:38813198 original size:143 final size:139
Alignment explanation
Indices: 38812933--38813203 Score: 307
Period size: 143 Copynumber: 1.9 Consensus size: 139
38812923 ACACATGAAA
* *
38812933 AGATGCCAATGCCATGTCCCAGATGTGGTCTTACATGAGATCTCACATCGATGCCAACAGCCCAG
1 AGATGCCAATGCCATATCCCAGATATGGTCTTACATGAGATCTCACATCGATGCCAACAGCCCAG
* * * *
38812998 TTATGGTCTTACACGAAGTCTCATAACGGTGTCGATGCCATGTCCCAAACATGGTCTTATACGGG
66 ATATGGTCTTACACGAAGTCTCATAACGATGTCGATGCCATATCCCAAACATAGTCTTATACGGG
38813063 ACCTCATAT
131 ACCTCATAT
* * *
38813072 AGATGTCAATGCCATAT-CCAGATATGGTCTTACATGGGATCTCATACTGATGCCGATGCC-ATA
1 AGATGCCAATGCCATATCCCAGATATGGTCTTACATGAGATCTC--AC--AT--CGATGCCAACA
* * ** *
38813135 TCCCAGATATGGTCTTACACG-GGATCTCATCTCGATGTCGATGCCATAT-CCAAGATATAGTCT
60 GCCCAGATATGGTCTTACACGAAG-TCTCATAACGATGTCGATGCCATATCCCAA-ACATAGTCT
*
38813198 TGTACG
123 TATACG
38813204 AGATCTCAAT
Statistics
Matches: 109, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
138 24 0.22
139 15 0.14
140 2 0.02
142 7 0.06
143 54 0.50
144 7 0.06
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (139 bp):
AGATGCCAATGCCATATCCCAGATATGGTCTTACATGAGATCTCACATCGATGCCAACAGCCCAG
ATATGGTCTTACACGAAGTCTCATAACGATGTCGATGCCATATCCCAAACATAGTCTTATACGGG
ACCTCATAT
Found at i:38821369 original size:22 final size:22
Alignment explanation
Indices: 38821327--38821369 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
38821317 TAATCTGTAA
*
38821327 AAAAAAAATAATAAAATAGAAT
1 AAAAAAAATAATAAAAAAGAAT
*
38821349 AAAATAAATAA-AAATAAAGAA
1 AAAAAAAATAATAAA-AAAGAA
38821370 CACATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (22 bp):
AAAAAAAATAATAAAAAAGAAT
Found at i:38825571 original size:10 final size:9
Alignment explanation
Indices: 38825531--38825575 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 9
38825521 TACCAATTTG
38825531 TAAAA-AAA
1 TAAAATAAA
38825539 T-AAATAAA
1 TAAAATAAA
38825547 TAAAATAGAA
1 TAAAATA-AA
38825557 TAAAATAAA
1 TAAAATAAA
38825566 TAAAAATAAA
1 T-AAAATAAA
38825576 GAACACATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 3 0.09
8 5 0.15
9 8 0.24
10 17 0.52
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (9 bp):
TAAAATAAA
Found at i:38826025 original size:15 final size:14
Alignment explanation
Indices: 38826001--38826035 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
38825991 TTGGTATGTG
38826001 ATGAATTTATTGAA
1 ATGAATTTATTGAA
38826015 ATGATATTTATTGAA
1 ATGA-ATTTATTGAA
*
38826030 TTGAAT
1 ATGAAT
38826036 ATGTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (14 bp):
ATGAATTTATTGAA
Found at i:38834807 original size:42 final size:42
Alignment explanation
Indices: 38834755--38834847 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
38834745 CTAAGACTAT
*
38834755 ATGTAAGACCATATCTGGGAAATGAAATCTATATGAGACTTC
1 ATGTAAGACCATATCTGGGAAATGAAATCGATATGAGACTTC
* *
38834797 ATGTAAGACCATATCTGGGATATGACATCGATATGAGACTTC
1 ATGTAAGACCATATCTGGGAAATGAAATCGATATGAGACTTC
*
38834839 GTGTAAGAC
1 ATGTAAGAC
38834848 TGTAGCTGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (42 bp):
ATGTAAGACCATATCTGGGAAATGAAATCGATATGAGACTTC
Found at i:38835107 original size:15 final size:16
Alignment explanation
Indices: 38835081--38835110 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38835071 ATGAACCCTC
38835081 AGTAAGGTTATGATTG
1 AGTAAGGTTATGATTG
38835097 AGTAA-GTTATGATT
1 AGTAAGGTTATGATT
38835111 ATAAGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (16 bp):
AGTAAGGTTATGATTG
Found at i:38837057 original size:37 final size:37
Alignment explanation
Indices: 38837007--38837081 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
38836997 CGTGTGGTCA
38837007 AAAATAAGGCTATCTACCAAGCCTCTTTGCCATCCTT
1 AAAATAAGGCTATCTACCAAGCCTCTTTGCCATCCTT
38837044 AAAATAAGGCTATCTACCAAGCCTCTTTGCCATCCTT
1 AAAATAAGGCTATCTACCAAGCCTCTTTGCCATCCTT
38837081 A
1 A
38837082 CTCACATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (37 bp):
AAAATAAGGCTATCTACCAAGCCTCTTTGCCATCCTT
Found at i:38839048 original size:40 final size:40
Alignment explanation
Indices: 38838979--38839203 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
38838969 AAACCAAGTA
* * * *
38838979 CCTTCGGGATTTAG-CCGGATATCGCAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
38839018 CCTTCGGGACTTAACCCGGATATAGTAACTCCCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
38839058 CCTTCGGGTCTTAGCCCGGAAATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
38839098 CCTTTGGGACTTAGCCCGGGTATAGCAACTACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACT-C--GCACAAATG
*
38839141 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
38839181 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
38839204 CATCCGAATA
Statistics
Matches: 157, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
39 12 0.08
40 109 0.69
43 36 0.23
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:38839166 original size:83 final size:80
Alignment explanation
Indices: 38838979--38839203 Score: 274
Period size: 83 Copynumber: 2.8 Consensus size: 80
38838969 AAACCAAGTA
* * * * *
38838979 CCTTCGGGATTTAG-CCGGATATCG-CAACTCGCACGAATGCCTTCGGGACTTAACCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
* *
38839042 GTAACTCCCACACATG
65 GCAACTCCCACAAATG
* * * *
38839058 CCTTCGGGTCTTAGCCCGGAAATAGTCACTAGCACAAATGCCTTTGGGACTTAGCCCGGGTATAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
38839123 CAACTACTTGCACAAATG
66 CAACT-C--CCACAAATG
* *
38839141 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
38839204 CATCCGAATA
Statistics
Matches: 123, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
79 12 0.10
80 45 0.37
81 2 0.02
83 64 0.52
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
CAACTCCCACAAATG
Found at i:38841471 original size:49 final size:47
Alignment explanation
Indices: 38841362--38841680 Score: 179
Period size: 46 Copynumber: 6.7 Consensus size: 47
38841352 GAATGTCGAT
* * *
38841362 GCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGAT
1 GCCATGTCCCAGACATAGTCTTACACTGGCTCATATCTCAAGGCGAC
** * * *
38841409 GCCATGTTTCAGACATATTCTTACCCTGGCT-ATCATCATCGAGGCTGAC
1 GCCATGTCCCAGACATAGTCTTACACTGGCTCAT-ATC-TCAAGGC-GAC
* * ** * *
38841458 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAATAT-TCGTGCCGAT
1 GCCATGTCCCAGACATAGTCTTACACT-G-GCTC--ATATCTCAAGGCGAC
* * * * * *
38841508 GCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTCGTAGTCGAT
1 GCCATGTCCCAGACATAGTCTTACACTGGCTCATATCTC-AAGGCGAC
* * ** * * *
38841554 G-CATGTCCCAGACAT-GTCTTACATTGGCTTACGTCTCCAGGCCAAT
1 GCCATGTCCCAGACATAGTCTTACACTGGCTCATATCTCAAGG-CGAC
* * * *
38841600 G-CATGTCCCAGACAT-GTCTTACACTAGCTC-TCGTCTCAATGCCGAT
1 GCCATGTCCCAGACATAGTCTTACACTGGCTCAT-ATCTCAA-GGCGAC
* *
38841646 GCCATGCCCCAGACATGGTCTTACACTGGCTCATA
1 GCCATGTCCCAGACATAGTCTTACACTGGCTCATA
38841681 ATAACCATTA
Statistics
Matches: 214, Mismatches: 40, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
44 12 0.06
45 19 0.09
46 55 0.26
47 43 0.20
48 19 0.09
49 25 0.12
50 30 0.14
51 7 0.03
53 2 0.01
54 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.28
Consensus pattern (47 bp):
GCCATGTCCCAGACATAGTCTTACACTGGCTCATATCTCAAGGCGAC
Found at i:38842415 original size:10 final size:10
Alignment explanation
Indices: 38842395--38842428 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
38842385 AATATAAGAA
38842395 ATTGTTATTAT
1 ATTG-TATTAT
38842406 ATTGTATTAT
1 ATTGTATTAT
*
38842416 ATTATATTAT
1 ATTGTATTAT
38842426 ATT
1 ATT
38842429 ATATATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (10 bp):
ATTGTATTAT
Found at i:38842439 original size:5 final size:5
Alignment explanation
Indices: 38842400--38842432 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
38842390 AAGAAATTGT
*
38842400 TATTA TATTG TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TAT
38842433 ATTATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:38844293 original size:45 final size:45
Alignment explanation
Indices: 38844194--38844296 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
38844184 CGACTACTGT
* * **
38844194 TACTGTTACCGTTACTATTACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACCATTACCGATTCAACACTTTGTGTGTCGAA
* * *
38844239 TACTGTTACTGTTACCGTTATCGATTCAACACTTTGTGTGTTGAA
1 TACTGTTACTGTTACCATTACCGATTCAACACTTTGTGTGTCGAA
38844284 TACTGTTACTGTT
1 TACTGTTACTGTT
38844297 CCGGATTTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACCATTACCGATTCAACACTTTGTGTGTCGAA
Found at i:38844730 original size:18 final size:18
Alignment explanation
Indices: 38844459--38844736 Score: 168
Period size: 18 Copynumber: 15.1 Consensus size: 18
38844449 AAAGGTATAA
* *
38844459 AATAACTGATTATTACTG
1 AATAATTGATTGTTACTG
*
38844477 AATAATTGACTGTTACTG
1 AATAATTGATTGTTACTG
* * *
38844495 GATAATAGACTGTTACTG
1 AATAATTGATTGTTACTG
* * *
38844513 AATAACTGAATATTACTG
1 AATAATTGATTGTTACTG
* **
38844531 AATAATTGGTCATTACTG
1 AATAATTGATTGTTACTG
* *
38844549 AATAACTGATTGTCACTG
1 AATAATTGATTGTTACTG
* *
38844567 AATAAATGACTGTTACTG
1 AATAATTGATTGTTACTG
* *
38844585 AATAACTTAATTGCTACTG
1 AATAA-TTGATTGTTACTG
*
38844604 AAT-ATCTGATT-TTACTA
1 AATAAT-TGATTGTTACTG
*
38844621 AATAATTGACTGTTACTGG
1 AATAATTGATTGTTACT-G
* *
38844640 ATAACCGATCAATTGATTGATACTA
1 ---A---AT-AATTGATTGTTACTG
* * *
38844665 AATAACT-AGTTATTAATG
1 AATAATTGA-TTGTTACTG
*
38844683 AATAATTGATTGTTACCG
1 AATAATTGATTGTTACTG
*
38844701 AATAAGTGATTGTTACTG
1 AATAATTGATTGTTACTG
* *
38844719 AATAAATAATTGTT-CTG
1 AATAATTGATTGTTACTG
38844736 A
1 A
38844737 TTGTTAATGA
Statistics
Matches: 199, Mismatches: 47, Indels: 29
0.72 0.17 0.11
Matches are distributed among these distances:
17 17 0.09
18 151 0.76
19 15 0.08
22 2 0.01
25 2 0.01
26 12 0.06
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (18 bp):
AATAATTGATTGTTACTG
Found at i:38846103 original size:7 final size:7
Alignment explanation
Indices: 38846088--38846117 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
38846078 TCTCCATCAA
38846088 CACATAT
1 CACATAT
*
38846095 CATATAT
1 CACATAT
38846102 CACATAT
1 CACATAT
38846109 CACATAT
1 CACATAT
38846116 CA
1 CA
38846118 TGTATCACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (7 bp):
CACATAT
Found at i:38846478 original size:19 final size:19
Alignment explanation
Indices: 38846456--38846492 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
38846446 TGCATGCATG
38846456 AATTGGTAACATGCAACCC
1 AATTGGTAACATGCAACCC
38846475 AATTGGTAACATGCAACC
1 AATTGGTAACATGCAACC
38846493 TAGAATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (19 bp):
AATTGGTAACATGCAACCC
Found at i:38846960 original size:16 final size:16
Alignment explanation
Indices: 38846932--38846993 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
38846922 CATGTTTATT
38846932 TTTTGTTTTTAG-TTG
1 TTTTGTTTTTAGTTTG
*
38846947 TTTTATTTTCTAGTTTG
1 TTTTGTTTT-TAGTTTG
*
38846964 TTTTGTTTTGA-TTTG
1 TTTTGTTTTTAGTTTG
38846979 TTTTTGTTTTT-GTTT
1 -TTTTGTTTTTAGTTT
38846994 TTGTGTGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 12 0.31
16 16 0.41
17 11 0.28
ACGTcount: A:0.06, C:0.02, G:0.16, T:0.76
Consensus pattern (16 bp):
TTTTGTTTTTAGTTTG
Found at i:38850764 original size:41 final size:41
Alignment explanation
Indices: 38850719--38850801 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
38850709 TAACTTTCCC
38850719 TTGAGAGTTATTTTTTAATAAATATGGAAATGTGATTCACA
1 TTGAGAGTTATTTTTTAATAAATATGGAAATGTGATTCACA
38850760 TTGAGAGTTATTTTTTAATAAATATGGAAATGTGATTCACA
1 TTGAGAGTTATTTTTTAATAAATATGGAAATGTGATTCACA
38850801 T
1 T
38850802 GATAAAAGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (41 bp):
TTGAGAGTTATTTTTTAATAAATATGGAAATGTGATTCACA
Found at i:38855689 original size:25 final size:25
Alignment explanation
Indices: 38855661--38855714 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
38855651 AGTTCAGTAT
*
38855661 TGTTCTACTCTGTTCCATCCTGTTC
1 TGTTCTACTCTATTCCATCCTGTTC
* * * *
38855686 TGTTTTGCTCTATTCGATTCTGTTC
1 TGTTCTACTCTATTCCATCCTGTTC
38855711 TGTT
1 TGTT
38855715 TGAATTGCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.07, C:0.24, G:0.15, T:0.54
Consensus pattern (25 bp):
TGTTCTACTCTATTCCATCCTGTTC
Found at i:38856566 original size:27 final size:28
Alignment explanation
Indices: 38856511--38856566 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
38856501 CGAGAAACAA
*
38856511 AAAAAAAATCAATTAAAATGATAATTTT
1 AAAAAAAATCAATTAAAATGATAAGTTT
* *
38856539 AAAAAATATCAATTAAAAT-ATTAGTTT
1 AAAAAAAATCAATTAAAATGATAAGTTT
38856566 A
1 A
38856567 TTAATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAAAAAATCAATTAAAATGATAAGTTT
Found at i:38865259 original size:21 final size:21
Alignment explanation
Indices: 38865230--38865280 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 21
38865220 AGCGCTGACA
*
38865230 TGGCAAGTTAACTAGTTGATG
1 TGGCCAGTTAACTAGTTGATG
38865251 TGGCCAG-T---TAGTTGATG
1 TGGCCAGTTAACTAGTTGATG
38865268 TGGCCAGTTAACT
1 TGGCCAGTTAACT
38865281 TGCCACGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
17 16 0.64
18 1 0.04
20 1 0.04
21 7 0.28
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (21 bp):
TGGCCAGTTAACTAGTTGATG
Found at i:38865264 original size:17 final size:17
Alignment explanation
Indices: 38865242--38865277 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
38865232 GCAAGTTAAC
38865242 TAGTTGATGTGGCCAGT
1 TAGTTGATGTGGCCAGT
38865259 TAGTTGATGTGGCCAGT
1 TAGTTGATGTGGCCAGT
38865276 TA
1 TA
38865278 ACTTGCCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.11, G:0.33, T:0.36
Consensus pattern (17 bp):
TAGTTGATGTGGCCAGT
Found at i:38866592 original size:3 final size:3
Alignment explanation
Indices: 38866579--38866653 Score: 50
Period size: 3 Copynumber: 26.0 Consensus size: 3
38866569 TTCCATTTTC
* * *
38866579 TCT TAT TCT TCT TCT TTT TCA TCT TCT TCT TCT TC- TCT GT-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT
* * * *
38866623 TCT T-T TAT TCT TTT TTT TC- TCT CCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
38866654 ACTGCCCAGG
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
2 7 0.12
3 48 0.86
4 1 0.02
ACGTcount: A:0.04, C:0.27, G:0.01, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:38867002 original size:7 final size:7
Alignment explanation
Indices: 38866990--38867015 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38866980 CACATATACA
38866990 CATATCT
1 CATATCT
38866997 CATATCT
1 CATATCT
38867004 CATATCT
1 CATATCT
38867011 CATAT
1 CATAT
38867016 TGTTTAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (7 bp):
CATATCT
Found at i:38867889 original size:85 final size:85
Alignment explanation
Indices: 38867746--38867917 Score: 247
Period size: 85 Copynumber: 2.0 Consensus size: 85
38867736 TTATAAAAAT
* * * * *
38867746 ATAGGGACGAATTTATGTTAAAAATTAGAATATAAAATTTAAATTTAAATTTTAGACATTTTAAA
1 ATAGGAACCAATTTATATTAAAAATTAGAATATAAAAATTAAATTTAAATTATAGACATTTTAAA
* **
38867811 CTGACCAAATTTGAAATTTA
66 CCGACCAAAACTGAAATTTA
*
38867831 ATAGGAACCAATTTATATTAAAAATTA-AAGTATAAAAATTAAATTTAAATTATAGACATTTTAG
1 ATAGGAACCAATTTATATTAAAAATTAGAA-TATAAAAATTAAATTTAAATTATAGACATTTTAA
38867895 ACCGACCAAAACTGAAATTTA
65 ACCGACCAAAACTGAAATTTA
38867916 AT
1 AT
38867918 CAAAATGCAC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 2 0.03
85 75 0.97
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.35
Consensus pattern (85 bp):
ATAGGAACCAATTTATATTAAAAATTAGAATATAAAAATTAAATTTAAATTATAGACATTTTAAA
CCGACCAAAACTGAAATTTA
Found at i:38868610 original size:19 final size:20
Alignment explanation
Indices: 38868578--38868615 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
38868568 TGACAAAAAT
* *
38868578 AATATTATATAAATTTTAAA
1 AATATTATACAAATATTAAA
38868598 AATA-TATACAAATATTAA
1 AATATTATACAAATATTAA
38868616 TCTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATTATACAAATATTAAA
Found at i:38869238 original size:30 final size:29
Alignment explanation
Indices: 38869204--38869267 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
38869194 AATAGTTATT
38869204 TTTATAAATTTTAA-AAGATTAAATTAAAAA
1 TTTATAAATTTTAAGAA-ATTAAATT-AAAA
* * *
38869234 TTTATTATTTTTAAGAAATTAAATTATAA
1 TTTATAAATTTTAAGAAATTAAATTAAAA
38869263 TTTAT
1 TTTAT
38869268 TTTACTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 8 0.27
30 20 0.67
31 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTATAAATTTTAAGAAATTAAATTAAAA
Found at i:38869264 original size:29 final size:30
Alignment explanation
Indices: 38869212--38869268 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
38869202 TTTTTATAAA
38869212 TTTTAAAAGATTAAATTAAAAATTTATTAT
1 TTTTAAAAGATTAAATTAAAAATTTATTAT
*
38869242 TTTTAAGAA-ATTAAATT-ATAATTTATT
1 TTTTAA-AAGATTAAATTAAAAATTTATT
38869269 TTACTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 14 0.56
31 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (30 bp):
TTTTAAAAGATTAAATTAAAAATTTATTAT
Found at i:38869841 original size:2 final size:2
Alignment explanation
Indices: 38869834--38869864 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38869824 TAAGTGCCTA
*
38869834 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38869865 ATTGAGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:38871432 original size:33 final size:32
Alignment explanation
Indices: 38871395--38871457 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
38871385 CGTTTTGCTA
38871395 ATATTCTATGTTCAACCAACAATACATATTTTT
1 ATATTCTATGTTCAACCAACAA-ACATATTTTT
* *
38871428 ATATTTTATGTTCAACCACCAAACATATTT
1 ATATTCTATGTTCAACCAACAAACATATTT
38871458 ATAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (32 bp):
ATATTCTATGTTCAACCAACAAACATATTTTT
Found at i:38873214 original size:13 final size:13
Alignment explanation
Indices: 38873187--38873258 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
38873177 CATGGAGCTG
* *
38873187 AGTGATACTAATA
1 AGTGATACCACTA
38873200 AGTGATACTC-CTA
1 AGTGATAC-CACTA
* *
38873213 AGTGCTACCATTA
1 AGTGATACCACTA
*
38873226 AGTGCTACCACTA
1 AGTGATACCACTA
* *
38873239 AATGATACCGCTA
1 AGTGATACCACTA
38873252 AGTGATA
1 AGTGATA
38873259 TTGCTAAGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
12 1 0.02
13 47 0.98
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (13 bp):
AGTGATACCACTA
Found at i:38873282 original size:13 final size:13
Alignment explanation
Indices: 38873266--38873320 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
38873256 ATATTGCTAA
38873266 GTGGTATCGCAAG
1 GTGGTATCGCAAG
* *
38873279 GTGGTATTGCGAG
1 GTGGTATCGCAAG
* * *
38873292 GTGATAACGCGAG
1 GTGGTATCGCAAG
*
38873305 GTGGTGTCGCAAG
1 GTGGTATCGCAAG
38873318 GTG
1 GTG
38873321 AGATCGTGAG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.20, C:0.13, G:0.44, T:0.24
Consensus pattern (13 bp):
GTGGTATCGCAAG
Found at i:38874180 original size:28 final size:29
Alignment explanation
Indices: 38874149--38874205 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
38874139 TAAAGTGATT
* *
38874149 TTTGACAAAAATGTCAATT-AGGGTTTAA
1 TTTGACAAAAATGTAAATTAAGGGGTTAA
* *
38874177 TTTGAGAAAAGTGTAAATTAAGGGGTTAA
1 TTTGACAAAAATGTAAATTAAGGGGTTAA
38874206 ATTGTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (29 bp):
TTTGACAAAAATGTAAATTAAGGGGTTAA
Found at i:38874733 original size:43 final size:43
Alignment explanation
Indices: 38874685--38874850 Score: 183
Period size: 43 Copynumber: 3.9 Consensus size: 43
38874675 GTTATCGAGA
* *
38874685 TGTGATTACATGTAAGACCATGTCTGGGACATTGACATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* *
38874728 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCATAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * * *
38874771 TATGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
** * * *
38874813 ATGTGACAACACGTAAGACCATATCTGGGATA-TGGCAT
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT
38874851 TGTACGAGCT
Statistics
Matches: 104, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
42 8 0.08
43 96 0.92
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:38876040 original size:42 final size:42
Alignment explanation
Indices: 38875972--38876059 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
38875962 CGTGCCCTTA
* *
38875972 GCCCTTGTGCAACACTGACTTTAAAACACGGCCATGACACAC
1 GCCCATGTACAACACTGACTTTAAAACACGGCCATGACACAC
*
38876014 GCCCATGTACAACACTGACTTTAAAACATGGCCATGACACAC
1 GCCCATGTACAACACTGACTTTAAAACACGGCCATGACACAC
38876056 GCCC
1 GCCC
38876060 GTGTGGCCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (42 bp):
GCCCATGTACAACACTGACTTTAAAACACGGCCATGACACAC
Found at i:38877004 original size:44 final size:44
Alignment explanation
Indices: 38876955--38877175 Score: 165
Period size: 47 Copynumber: 4.8 Consensus size: 44
38876945 TATACGTGCT
*
38876955 GATGCATGTCCCAGACATGTCTTACACTTGCACGAC-TCTTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCAC-ACATCTTAGCC
* * ** * **
38876999 GATGCATCTTCCAGACACATCTTACACTGGTTATCATCATCGAAGCC
1 GATGCATGTCCCAGACATGTCTTACACTGG-CA-CA-CATCTTAGCC
* * * *
38877046 GATACTTGTCCCAGACATGTCTTACACTAGCACTCATCTCTACGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACACATCT-TA-GCC
* * * * * *
38877092 AATGCCATGTCCTAGACATGGTCTTACACTGGCACTCATAATGTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCACACAT-CT-TAGCC
* *
38877140 GATGCATGTCCCAAACATGGCTTACACTGGCACACA
1 GATGCATGTCCCAGACATGTCTTACACTGGCACACA
38877176 AGAAATTCAA
Statistics
Matches: 135, Mismatches: 33, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
44 29 0.21
45 4 0.03
46 24 0.18
47 53 0.39
48 23 0.17
49 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACACATCTTAGCC
Found at i:38877083 original size:47 final size:48
Alignment explanation
Indices: 38877032--38877130 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 48
38877022 ACACTGGTTA
* *
38877032 TCATCATCGAAGCCGAT-ACTTGTCCCAGACAT-GTCTTACACTAGCAC
1 TCATC-TCGAAGCCAATGACATGTCCCAGACATGGTCTTACACTAGCAC
* * * * *
38877079 TCATCTCTACGCCAATGCCATGTCCTAGACATGGTCTTACACTGGCAC
1 TCATCTCGAAGCCAATGACATGTCCCAGACATGGTCTTACACTAGCAC
38877127 TCAT
1 TCAT
38877131 AATGTGGCTG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
46 8 0.19
47 17 0.40
48 18 0.42
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.27
Consensus pattern (48 bp):
TCATCTCGAAGCCAATGACATGTCCCAGACATGGTCTTACACTAGCAC
Found at i:38885046 original size:37 final size:36
Alignment explanation
Indices: 38884996--38885082 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
38884986 TACGAAGTCT
38884996 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
38885032 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
38885069 TCACCCGGAACATA
1 T-ACCCGG-ACATA
38885083 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:38885220 original size:49 final size:49
Alignment explanation
Indices: 38885146--38885380 Score: 389
Period size: 49 Copynumber: 4.8 Consensus size: 49
38885136 TCGGCTTTAC
* * * *
38885146 CACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
1 CACATATACATAT--ACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
* *
38885197 CACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCAT
1 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
38885246 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
1 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
*
38885295 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTTAT
1 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
38885344 CACATATACATATACTTTCGCATTCACCACATCGGCC
1 CACATATACATATACTTTCGCATTCACCACATCGGCC
38885381 TAATTATACT
Statistics
Matches: 177, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
49 166 0.94
51 11 0.06
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.29
Consensus pattern (49 bp):
CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
Found at i:38885415 original size:129 final size:129
Alignment explanation
Indices: 38885256--38885509 Score: 463
Period size: 129 Copynumber: 2.0 Consensus size: 129
38885246 CACATATACA
38885256 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCA
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCA
*
38885321 CCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCACCACATCGGCCTAAT
66 CCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCGCATTCACCACATCGGCCTAAT
*
38885385 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCA
* * *
38885450 CCACATCGGCCATTAGGCCTTATCACATATACATACATTTTCGCATTCATCGCATCGGCC
66 CCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCGCATTCACCACATCGGCC
38885510 ATTAGGCCTC
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 120 1.00
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (129 bp):
TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCA
CCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCGCATTCACCACATCGGCCTAAT
Found at i:38885438 original size:80 final size:80
Alignment explanation
Indices: 38885305--38885460 Score: 312
Period size: 80 Copynumber: 1.9 Consensus size: 80
38885295 CACATATACA
38885305 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
38885370 CCACATCGGCCTAAT
66 CCACATCGGCCTAAT
38885385 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
38885450 CCACATCGGCC
66 CCACATCGGCC
38885461 ATTAGGCCTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.31
Consensus pattern (80 bp):
TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
CCACATCGGCCTAAT
Found at i:38885447 original size:49 final size:49
Alignment explanation
Indices: 38885390--38885638 Score: 399
Period size: 49 Copynumber: 5.1 Consensus size: 49
38885380 CTAATTATAC
* * *
38885390 TTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATAC
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
*
38885439 TTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
* * *
38885488 TTTCGCATTCATCGCATCGGCCATTAGGCCTCATCACATATATATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
38885537 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
* * * *
38885586 TTTCGCATTCATCGCATCGACCATTAGGCCTCATCACATATATATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
38885635 TTTC
1 TTTC
38885639 ACGAATCTTG
Statistics
Matches: 187, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 187 1.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (49 bp):
TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
Found at i:38885516 original size:178 final size:178
Alignment explanation
Indices: 38885210--38885558 Score: 590
Period size: 178 Copynumber: 2.0 Consensus size: 178
38885200 ATATACATAC
38885210 ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCA
*
38885275 CATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCC
66 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
* *
38885340 TTATCACATATACATATACTTTCGCATTCACCACATCGGCCTAATTAT
131 TCATCACATATACATACACTTTCGCATTCACCACATCGGCCTAATTAT
* *
38885388 ACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCA
* * * *
38885453 CATCGGCCATTAGGCCTTATCACATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCC
66 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
* * *
38885518 TCATCACATATATATACATTTTCGCATTCATCACATCGGCC
131 TCATCACATATACATACACTTTCGCATTCACCACATCGGCC
38885559 ATTAGGCCTT
Statistics
Matches: 159, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
178 159 1.00
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.30
Consensus pattern (178 bp):
ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCA
CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
TCATCACATATACATACACTTTCGCATTCACCACATCGGCCTAATTAT
Found at i:38885570 original size:227 final size:227
Alignment explanation
Indices: 38885161--38885596 Score: 737
Period size: 227 Copynumber: 1.9 Consensus size: 227
38885151 ATATATATAC
*
38885161 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCA
*
38885226 CATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCC
66 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
*
38885291 TCATCACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
131 TCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
*
38885356 TACTTTCGCATTCACCACATCGGCCTAATTAT
196 CACTTTCGCATTCACCACATCGGCCTAATTAT
* * *
38885388 ACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCA
* * * *
38885453 CATCGGCCATTAGGCCTTATCACATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCC
66 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
* * *
38885518 TCATCACATATATATACATTTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATA
131 TCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
*
38885583 CATTTTCGCATTCA
196 CACTTTCGCATTCA
38885597 TCGCATCGAC
Statistics
Matches: 194, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
227 194 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (227 bp):
ACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCA
CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
TCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
CACTTTCGCATTCACCACATCGGCCTAATTAT
Found at i:38889618 original size:79 final size:79
Alignment explanation
Indices: 38889481--38889663 Score: 296
Period size: 79 Copynumber: 2.3 Consensus size: 79
38889471 CCAGCATGAT
* * *
38889481 TGCTCTTCGGGACCTAGCCCGGATGCATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGAACTTAG-CCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
38889546 CATCACTAGCACGAA
65 CATCACTAGCACGAA
*
38889561 TGCTCCTCGGAACTTAGTCCGGATACATCACTAGCA-GAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGAACTTAG-CCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
*
38889625 CATCACTAGCACGGA
65 CATCACTAGCACGAA
38889640 TGCTCTTCGGAACTTAGCCGGATA
1 TGCTCTTCGGAACTTAGCCGGATA
38889664 AAACCACAAG
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
78 7 0.07
79 58 0.60
80 31 0.32
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
TGCTCTTCGGAACTTAGCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATAC
ATCACTAGCACGAA
Found at i:38889687 original size:79 final size:79
Alignment explanation
Indices: 38889513--38889688 Score: 257
Period size: 79 Copynumber: 2.2 Consensus size: 79
38889503 ATGCATCACT
38889513 AGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCCTCGGAACTTAG
1 AGCAC-AATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCCTCGGAACTTAG
* * *
38889578 TCCGGATACATCACT
65 TCCGGATAAACCACA
* * *
38889593 AGCAGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGGATGCTCTTCGGAACTTAG-
1 AGCACAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCCTCGGAACTTAGT
38889657 CCGGATAAAACCACA
66 CCGGAT-AAACCACA
38889672 AGCACAATTGC-CTTCGG
1 AGCACAA-TGCTCTTCGG
38889689 GTCTTAACCC
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
78 6 0.07
79 74 0.85
80 7 0.08
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (79 bp):
AGCACAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGCTCCTCGGAACTTAGT
CCGGATAAACCACA
Found at i:38889688 original size:39 final size:40
Alignment explanation
Indices: 38889481--38889663 Score: 298
Period size: 40 Copynumber: 4.6 Consensus size: 40
38889471 CCAGCATGAT
* * * *
38889481 TGCTCTTCGGGACCTAGCCCGGATGCATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
38889521 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
38889561 TGCTCCTCGGAACTTAGTCCGGATACATCACTAGCA-GAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
38889600 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGGA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
38889640 TGCTCTTCGGAACTTAG-CCGGATA
1 TGCTCTTCGGAACTTAGTCCGGATA
38889664 AAACCACAAG
Statistics
Matches: 135, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 45 0.33
40 90 0.67
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:38889726 original size:40 final size:40
Alignment explanation
Indices: 38889672--38889784 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 40
38889662 TAAAACCACA
* * *
38889672 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATA-ACAACT
1 AGCACAAATACCTTCGGGTCTTAGCCCGGGTATATAC-ACT
* *
38889712 CA-CACAAATACCTTCGGGTCTTAGCCCGGATATATTCACT
1 -AGCACAAATACCTTCGGGTCTTAGCCCGGGTATATACACT
* * *
38889752 AGCATAAATGCCTTCGGGACTTAGCCCGGGTAT
1 AGCACAAATACCTTCGGGTCTTAGCCCGGGTAT
38889785 CATTCAAATG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.02
40 58 0.95
41 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
AGCACAAATACCTTCGGGTCTTAGCCCGGGTATATACACT
Found at i:38889727 original size:119 final size:118
Alignment explanation
Indices: 38889483--38889777 Score: 289
Period size: 119 Copynumber: 2.5 Consensus size: 118
38889473 AGCATGATTG
* * *
38889483 CTCTTCGGGACCTAGCCCGGATGCATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACA
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAG-CCGGATAAA
* * ** *
38889548 TCACTAGCACGAATGCTCCTCGGAACTTAGTCCGGATACATCACTAGCAGAATG
65 CCACAAGCACGAATGCTCCTCGGAACTTAACCCGGATACATCACTAGCAGAATA
* * *
38889602 CTCTTCGGAACTTAGTCCGGATACATCACTAGCACGGATGCTCTTCGGAACTTAGCCGGATAAAA
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCGGAT-AAA
* **
38889667 CCACAAGCAC-AATTGC-CTTCGGGTCTTAACCCGGGTATAACAACTCAC-A-CA-AATA
65 CCACAAGCACGAA-TGCTCCTCGGAACTTAACCC-GG-AT-AC-A-TCACTAGCAGAATA
* * ** *
38889722 C-CTTCGGGTCTTAGCCCGGATATATTCACTAGCATAAATGC-CTTCGGGACTTAGCC
1 CTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAATGCTCTTCGGAACTTAGCC
38889778 CGGGTATCAT
Statistics
Matches: 146, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
118 19 0.13
119 98 0.67
120 19 0.13
121 4 0.03
122 2 0.01
123 4 0.03
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (118 bp):
CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCGGATAAAC
CACAAGCACGAATGCTCCTCGGAACTTAACCCGGATACATCACTAGCAGAATA
Found at i:38891693 original size:37 final size:36
Alignment explanation
Indices: 38891643--38891729 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
38891633 TACGAAGTCT
38891643 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
38891679 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
38891716 TCACCCGGAACATA
1 T-ACCCGG-ACATA
38891730 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:38891867 original size:49 final size:49
Alignment explanation
Indices: 38891793--38892027 Score: 389
Period size: 49 Copynumber: 4.8 Consensus size: 49
38891783 TCGGCTTTAC
* * * *
38891793 CACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
1 CACATATACATAT--ACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
* *
38891844 CACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCAT
1 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
38891893 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
1 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
*
38891942 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTTAT
1 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
38891991 CACATATACATATACTTTCGCATTCACCACATCGGCC
1 CACATATACATATACTTTCGCATTCACCACATCGGCC
38892028 TAATTATACT
Statistics
Matches: 177, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
49 166 0.94
51 11 0.06
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.29
Consensus pattern (49 bp):
CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
Found at i:38892106 original size:176 final size:177
Alignment explanation
Indices: 38891857--38892203 Score: 570
Period size: 176 Copynumber: 2.0 Consensus size: 177
38891847 ATATACATAC
38891857 ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATA-ATATACTTTCGCATTCACCA
*
38891922 CATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCC
65 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
* *
38891987 TTATCACATATACATATACTTTCGCATTCACCACATCGGCCTAATTAT
130 TCATCACATATACATACACTTTCGCATTCACCACATCGGCCTAATTAT
* *
38892035 ACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATAT-ATATACTTTCGCATTCACCAC
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATAATATACTTTCGCATTCACCAC
* * * *
38892099 ATCGGCCATTAGGCCTTATCACATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCCT
66 ATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCT
* * *
38892164 CATCACATATATATACATTTTCGCATTCATCACATCGGCC
131 CATCACATATACATACACTTTCGCATTCACCACATCGGCC
38892204 ATTAGGCCTT
Statistics
Matches: 157, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
176 116 0.74
178 41 0.26
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (177 bp):
ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATAATATACTTTCGCATTCACCAC
ATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCT
CATCACATATACATACACTTTCGCATTCACCACATCGGCCTAATTAT
Found at i:38892137 original size:127 final size:128
Alignment explanation
Indices: 38891903--38892154 Score: 443
Period size: 127 Copynumber: 2.0 Consensus size: 128
38891893 CACATATACA
38891903 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCA
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATA-ATATACTTTCGCATTCA
*
38891968 CCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCACCACATCGGCCTAAT
65 CCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCGCATTCACCACATCGGCCTAAT
*
38892032 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATAT-ATATACTTTCGCATTCAC
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATAATATACTTTCGCATTCAC
* * *
38892096 CACATCGGCCATTAGGCCTTATCACATATACATACATTTTCGCATTCATCGCATCGGCC
66 CACATCGGCCATTAGGCCTTATCACATATACATACACTTTCGCATTCACCACATCGGCC
38892155 ATTAGGCCTC
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
127 73 0.62
129 45 0.38
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (128 bp):
TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATAATATACTTTCGCATTCAC
CACATCGGCCATTAGGCCTTATCACATATACATACACTTTCGCATTCACCACATCGGCCTAAT
Found at i:38892156 original size:49 final size:49
Alignment explanation
Indices: 38892037--38892283 Score: 399
Period size: 49 Copynumber: 5.1 Consensus size: 49
38892027 CTAATTATAC
*
38892037 TTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATATATAC--
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
* *
38892084 TTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
* *
38892133 TTTCGCATTCATCGCATCGGCCATTAGGCCTCATCACATATATATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
*
38892182 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
* * *
38892231 TTTCGCATTCATCGCATCGACCATTAGGCCTCATCACATATATATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
38892280 TTTC
1 TTTC
38892284 ACGAATCTTG
Statistics
Matches: 186, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
47 46 0.25
49 140 0.75
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.33
Consensus pattern (49 bp):
TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT
Found at i:38892188 original size:225 final size:226
Alignment explanation
Indices: 38891808--38892241 Score: 717
Period size: 225 Copynumber: 1.9 Consensus size: 226
38891798 ATATATATAC
*
38891808 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATA-ATACACTTTCACATTCACCA
*
38891873 CATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCC
65 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
*
38891938 TCATCACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
130 TCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
*
38892003 TACTTTCGCATTCACCACATCGGCCTAATTAT
195 CACTTTCGCATTCACCACATCGGCCTAATTAT
* * *
38892035 ACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATAT-ATATACTTTCGCATTCACCAC
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATAATACACTTTCACATTCACCAC
* * * *
38892099 ATCGGCCATTAGGCCTTATCACATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCCT
66 ATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCT
* * *
38892164 CATCACATATATATACATTTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATAC
131 CATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATAC
*
38892229 ATTTTCGCATTCA
196 ACTTTCGCATTCA
38892242 TCGCATCGAC
Statistics
Matches: 192, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
225 151 0.79
227 41 0.21
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (226 bp):
ACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATAATACACTTTCACATTCACCAC
ATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCT
CATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATAC
ACTTTCGCATTCACCACATCGGCCTAATTAT
Found at i:38896158 original size:40 final size:39
Alignment explanation
Indices: 38896109--38896264 Score: 262
Period size: 40 Copynumber: 4.0 Consensus size: 39
38896099 CCTAGCCCGG
38896109 CATCACTAGCACGAATGCTCTTCGGAACTTAGTCGGGATA
1 CATCACTAGCACGAATGCTCTTCGGAACTTAGTC-GGATA
*
38896149 CATCACTAGCACGAATGCTCCTCGGAACTTAGTCCGGATA
1 CATCACTAGCACGAATGCTCTTCGGAACTTAGT-CGGATA
38896189 CATCACTAGCA-GAATGCTCTTCGGAACTTAGTCGGATA
1 CATCACTAGCACGAATGCTCTTCGGAACTTAGTCGGATA
*
38896227 CATCACTAGCACGGATGCTCTTCGGAACTTAG-CGGATA
1 CATCACTAGCACGAATGCTCTTCGGAACTTAGTCGGATA
38896265 AAACCAAGCA
Statistics
Matches: 111, Mismatches: 3, Indels: 6
0.93 0.03 0.05
Matches are distributed among these distances:
38 23 0.21
39 39 0.35
40 48 0.43
41 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (39 bp):
CATCACTAGCACGAATGCTCTTCGGAACTTAGTCGGATA
Found at i:38896246 original size:78 final size:80
Alignment explanation
Indices: 38896109--38896258 Score: 268
Period size: 78 Copynumber: 1.9 Consensus size: 80
38896099 CCTAGCCCGG
38896109 CATCACTAGCACGAATGCTCTTCGGAACTTAGTCGGGATACATCACTAGCACGAATGCTCCTCGG
1 CATCACTAGCACGAATGCTCTTCGGAACTTAGTCGGGATACATCACTAGCACGAATGCTCCTCGG
38896174 AACTTAGTCCGGATA
66 AACTTAGTCCGGATA
* *
38896189 CATCACTAGCA-GAATGCTCTTCGGAACTTAGTC-GGATACATCACTAGCACGGATGCTCTTCGG
1 CATCACTAGCACGAATGCTCTTCGGAACTTAGTCGGGATACATCACTAGCACGAATGCTCCTCGG
38896252 AACTTAG
66 AACTTAG
38896259 CGGATAAAAC
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
78 35 0.51
79 22 0.32
80 11 0.16
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CATCACTAGCACGAATGCTCTTCGGAACTTAGTCGGGATACATCACTAGCACGAATGCTCCTCGG
AACTTAGTCCGGATA
Found at i:38898286 original size:37 final size:36
Alignment explanation
Indices: 38898236--38898322 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
38898226 TACGAAGTCT
38898236 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
38898272 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
38898309 TCACCCGGAACATA
1 T-ACCCGG-ACATA
38898323 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:38898460 original size:49 final size:49
Alignment explanation
Indices: 38898386--38898620 Score: 389
Period size: 49 Copynumber: 4.8 Consensus size: 49
38898376 TCGGCTTTAC
* * * *
38898386 CACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
1 CACATATACATAT--ACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
* *
38898437 CACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCAT
1 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
38898486 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
1 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
*
38898535 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTTAT
1 CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
38898584 CACATATACATATACTTTCGCATTCACCACATCGGCC
1 CACATATACATATACTTTCGCATTCACCACATCGGCC
38898621 TAATTATACT
Statistics
Matches: 177, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
49 166 0.94
51 11 0.06
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.29
Consensus pattern (49 bp):
CACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTCAT
Found at i:38898655 original size:129 final size:129
Alignment explanation
Indices: 38898496--38898749 Score: 463
Period size: 129 Copynumber: 2.0 Consensus size: 129
38898486 CACATATACA
38898496 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCA
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCA
*
38898561 CCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCACCACATCGGCCTAAT
66 CCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCGCATTCACCACATCGGCCTAAT
*
38898625 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCA
* * *
38898690 CCACATCGGCCATTAGGCCTTATCACATATACATACATTTTCGCATTCATCGCATCGGCC
66 CCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCGCATTCACCACATCGGCC
38898750 ATTAGGCCTC
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 120 1.00
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (129 bp):
TATACTTTCGCATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCA
CCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCGCATTCACCACATCGGCCTAAT
Found at i:38898678 original size:80 final size:80
Alignment explanation
Indices: 38898545--38898700 Score: 312
Period size: 80 Copynumber: 1.9 Consensus size: 80
38898535 CACATATACA
38898545 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
38898610 CCACATCGGCCTAAT
66 CCACATCGGCCTAAT
38898625 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
1 TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
38898690 CCACATCGGCC
66 CCACATCGGCC
38898701 ATTAGGCCTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.31
Consensus pattern (80 bp):
TATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCA
CCACATCGGCCTAAT
Found at i:38898687 original size:49 final size:49
Alignment explanation
Indices: 38898630--38898877 Score: 390
Period size: 49 Copynumber: 5.1 Consensus size: 49
38898620 CTAATTATAC
* * *
38898630 TTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATAC
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
*
38898679 TTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
* * *
38898728 TTTCGCATTCATCGCATCGGCCATTAGGCCTCATCACATATATATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
38898777 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
* * * *
38898826 TTTCGCATTCATCGCATCGACCATTAGGCCTCATCACATAT-TATACAT
1 TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
38898874 TTTC
1 TTTC
38898878 ACGAATCTTG
Statistics
Matches: 186, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
48 10 0.05
49 176 0.95
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (49 bp):
TTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATACAT
Found at i:38898756 original size:178 final size:178
Alignment explanation
Indices: 38898450--38898798 Score: 590
Period size: 178 Copynumber: 2.0 Consensus size: 178
38898440 ATATACATAC
38898450 ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCA
*
38898515 CATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCC
66 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
* *
38898580 TTATCACATATACATATACTTTCGCATTCACCACATCGGCCTAATTAT
131 TCATCACATATACATACACTTTCGCATTCACCACATCGGCCTAATTAT
* *
38898628 ACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCA
* * * *
38898693 CATCGGCCATTAGGCCTTATCACATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCC
66 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
* * *
38898758 TCATCACATATATATACATTTTCGCATTCATCACATCGGCC
131 TCATCACATATACATACACTTTCGCATTCACCACATCGGCC
38898799 ATTAGGCCTT
Statistics
Matches: 159, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
178 159 1.00
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.30
Consensus pattern (178 bp):
ACTTTCACATTCACCACATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCA
CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
TCATCACATATACATACACTTTCGCATTCACCACATCGGCCTAATTAT
Found at i:38898810 original size:227 final size:227
Alignment explanation
Indices: 38898401--38898836 Score: 737
Period size: 227 Copynumber: 1.9 Consensus size: 227
38898391 ATATATATAC
*
38898401 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCA
*
38898466 CATCGGCCATTAGGCCTCATCACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCC
66 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
*
38898531 TCATCACATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
131 TCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
*
38898596 TACTTTCGCATTCACCACATCGGCCTAATTAT
196 CACTTTCGCATTCACCACATCGGCCTAATTAT
* * *
38898628 ACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATATACTTTCGCATTCACCA
1 ACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCA
* * * *
38898693 CATCGGCCATTAGGCCTTATCACATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCC
66 CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
* * *
38898758 TCATCACATATATATACATTTTCGCATTCATCACATCGGCCATTAGGCCTTATCACATATACATA
131 TCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
*
38898823 CATTTTCGCATTCA
196 CACTTTCGCATTCA
38898837 TCGCATCGAC
Statistics
Matches: 194, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
227 194 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (227 bp):
ACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCA
CATCGGCCATTAGGCCTCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCC
TCATCACATATACATACACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCACATATACATA
CACTTTCGCATTCACCACATCGGCCTAATTAT
Found at i:38900393 original size:29 final size:29
Alignment explanation
Indices: 38900351--38900434 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
38900341 GCCGTATTTT
**
38900351 TTTCCAGCTTGCACACTTAGTGCCAAATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
*
38900380 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
38900409 TTTCCAGCACGCACACTTAGTGCCAA
1 TTTCCAGCACGCACACTTAGTGCCAA
38900435 TCTCGACACC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCAAATA
Found at i:38908466 original size:29 final size:29
Alignment explanation
Indices: 38908424--38908507 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
38908414 CCGTATTTTT
**
38908424 TTTCCAGCTTGCACACTTAGTGCCAAATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
*
38908453 TTTCCAGCACGCACACTTAGTGCCATATA
1 TTTCCAGCACGCACACTTAGTGCCAAATA
38908482 TTTCCAGCACGCACACTTAGTGCCAA
1 TTTCCAGCACGCACACTTAGTGCCAA
38908508 TCTCGACACC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (29 bp):
TTTCCAGCACGCACACTTAGTGCCAAATA
Found at i:38909857 original size:14 final size:14
Alignment explanation
Indices: 38909833--38909865 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
38909823 AGGATGAGCA
*
38909833 TTCTCTTTTTTT-T
1 TTCTTTTTTTTTCT
38909846 TTCTTTTTTTTTCT
1 TTCTTTTTTTTTCT
38909860 TTCTTT
1 TTCTTT
38909866 ACTAACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTCTTTTTTTTTCT
Found at i:38910619 original size:20 final size:19
Alignment explanation
Indices: 38910594--38910632 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
38910584 TTATAATAGT
38910594 TAATAATAA-AATAAAAGAAA
1 TAATAA-AAGAAT-AAAGAAA
38910614 TAATAAAAGAATAAAGAAA
1 TAATAAAAGAATAAAGAAA
38910633 AAGGAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (19 bp):
TAATAAAAGAATAAAGAAA
Done.