Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 10 of 136
Found at i:2892105 original size:12 final size:12
Alignment explanation
Indices: 2892088--2892141 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
2892078 TTTTTCAAAA
2892088 TAAAAAATATTT
1 TAAAAAATATTT
2892100 TAAAAAATATTT
1 TAAAAAATATTT
**
2892112 TCTTAAAATA-TT
1 T-AAAAAATATTT
*
2892124 T-ATAAAT-TTT
1 TAAAAAATATTT
2892134 TAAAAAAT
1 TAAAAAAT
2892142 TATTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 7 0.21
11 5 0.15
12 16 0.47
13 6 0.18
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATATTT
Found at i:2892140 original size:21 final size:20
Alignment explanation
Indices: 2892116--2892173 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
2892106 ATATTTTCTT
*
2892116 AAAATATTTATAAATTTTTA
1 AAAATATTTATAAATTTATA
2892136 AAAA-A-TTATTAAAATTTATA
1 AAAATATTTA-T-AAATTTATA
*
2892156 AAAATATTAAATAAATTT
1 AAAATATT-TATAAATTT
2892174 CAAATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 3 0.10
19 2 0.06
20 16 0.52
21 7 0.23
22 2 0.06
23 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATATTTATAAATTTATA
Found at i:2892153 original size:18 final size:18
Alignment explanation
Indices: 2892116--2892166 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 18
2892106 ATATTTTCTT
*
2892116 AAAATATTTATAAATTTTTAA
1 AAAATA-TTA-AAATTTAT-A
2892137 AAAATTATTAAAATTTATA
1 AAAA-TATTAAAATTTATA
2892156 AAAATATTAAA
1 AAAATATTAAA
2892167 TAAATTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.25
19 5 0.18
20 7 0.25
21 7 0.25
22 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATTAAAATTTATA
Found at i:2892844 original size:18 final size:19
Alignment explanation
Indices: 2892821--2892871 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
2892811 TCTTAAATGG
2892821 TTTTTATTAATTTTTAAT-
1 TTTTTATTAATTTTTAATA
2892839 TTTTTAATT--TTATTTAATA
1 TTTTT-ATTAATT-TTTAATA
*
2892858 TTTTTATAAATTTT
1 TTTTTATTAATTTT
2892872 AATGATGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
17 2 0.07
18 13 0.48
19 10 0.37
20 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTATTAATTTTTAATA
Found at i:2895489 original size:12 final size:12
Alignment explanation
Indices: 2895472--2895496 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2895462 TTATGTATAA
2895472 TCACATAACATT
1 TCACATAACATT
2895484 TCACATAACATT
1 TCACATAACATT
2895496 T
1 T
2895497 TAATCCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCACATAACATT
Found at i:2896345 original size:53 final size:52
Alignment explanation
Indices: 2896261--2896366 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 52
2896251 ACATGGCACG
*
2896261 TGTATAGTTTGCTTTTAATCATATCTAATTATTCAGTTAATCATATCAATTT
1 TGTACAGTTTGCTTTTAATCATATCTAATTATTCAGTTAATCATATCAATTT
*
2896313 TGTACAGTTTGCTTTTTAATCATATCTAATTATTCCGTTAATCATATCAATTT
1 TGTACAGTTTGC-TTTTAATCATATCTAATTATTCAGTTAATCATATCAATTT
2896366 T
1 T
2896367 TAATAGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 11 0.22
53 40 0.78
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (52 bp):
TGTACAGTTTGCTTTTAATCATATCTAATTATTCAGTTAATCATATCAATTT
Found at i:2903981 original size:12 final size:12
Alignment explanation
Indices: 2903964--2904002 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
2903954 GAAAATATTT
*
2903964 TATATTAAAAAA
1 TATATTAATAAA
2903976 TATATTTATATAAA
1 TATA-TTA-ATAAA
2903990 TATATTAATAAA
1 TATATTAATAAA
2904002 T
1 T
2904003 GATTGTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 10 0.42
13 6 0.25
14 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATTAATAAA
Found at i:2912185 original size:21 final size:21
Alignment explanation
Indices: 2912144--2912196 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2912134 AGAGGCCTAG
*
2912144 GTTCTGATACC-CATACTTAT
1 GTTCTTATACCTCATACTTAT
2912164 GTTCTTATACCTCATA-TCTAT
1 GTTCTTATACCTCATACT-TAT
*
2912185 GTTCCTATACCT
1 GTTCTTATACCT
2912197 TGGGTTTCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.43
Consensus pattern (21 bp):
GTTCTTATACCTCATACTTAT
Found at i:2912291 original size:21 final size:20
Alignment explanation
Indices: 2912215--2912292 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 20
2912205 CGATACATAG
*
2912215 ATCTATGTTCCAGTACCTCAT
1 ATCTATGTTCTA-TACCTCAT
* * *
2912236 ACCTAGGTTCCGATA-CTCAT
1 ATCTATGTT-CTATACCTCAT
2912256 A-CTCATGTTCTTATACCTCAT
1 ATCT-ATGTTC-TATACCTCAT
2912277 ATCTATGTTTCTATAC
1 ATCTATG-TTCTATAC
2912293 TTTGGGTCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 3 0.07
20 13 0.28
21 23 0.50
22 7 0.15
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (20 bp):
ATCTATGTTCTATACCTCAT
Found at i:2921992 original size:38 final size:39
Alignment explanation
Indices: 2921932--2922009 Score: 124
Period size: 38 Copynumber: 2.0 Consensus size: 39
2921922 ATCCAACCCA
*
2921932 ACCCAATTACCCAACCTAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCTAATAAAAATAAAACTAAAGTCT
2921971 ACCCAATTA-CCAA-CTCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCT-AATAAAAATAAAACTAAAGTCT
2922009 A
1 A
2922010 ACTCTAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
37 2 0.05
38 26 0.70
39 9 0.24
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.21
Consensus pattern (39 bp):
ACCCAATTACCCAACCTAATAAAAATAAAACTAAAGTCT
Found at i:2922108 original size:9 final size:9
Alignment explanation
Indices: 2922094--2922145 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
2922084 GGGTATTTTC
2922094 GGTAATTCG
1 GGTAATTCG
* *
2922103 GTTAATTTG
1 GGTAATTCG
*
2922112 AGTAATTCG
1 GGTAATTCG
2922121 GGTAATTCG
1 GGTAATTCG
2922130 GGTAATTCG
1 GGTAATTCG
2922139 GGTAATT
1 GGTAATT
2922146 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.38
Consensus pattern (9 bp):
GGTAATTCG
Found at i:2924613 original size:61 final size:60
Alignment explanation
Indices: 2924493--2924662 Score: 268
Period size: 61 Copynumber: 2.8 Consensus size: 60
2924483 AAACACCAGT
* *
2924493 TAAAGGACAACCTTTGTGGCACAACTCTGATAGGAAAGCCTTTGTGGTGAGTACTGGATG
1 TAAATGACAACCTTTGTGGCACAACTCTGATAGGAAAGCCTTTGTGGCGAGTACTGGATG
* *
2924553 TAAATGACAACCTTTGTGGCACAACTCTGAATAGGAAAGCCTTTTTGGCGAGTATTGGATG
1 TAAATGACAACCTTTGTGGCACAACTCTG-ATAGGAAAGCCTTTGTGGCGAGTACTGGATG
* *
2924614 TAAATGACAACCTTTGTGGCACAACTTTGGACAGGAAAGCCTTTGTGGC
1 TAAATGACAACCTTTGTGGCACAACTCT-GATAGGAAAGCCTTTGTGGC
2924663 AAAACTCTGG
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
60 28 0.28
61 72 0.71
62 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (60 bp):
TAAATGACAACCTTTGTGGCACAACTCTGATAGGAAAGCCTTTGTGGCGAGTACTGGATG
Found at i:2924657 original size:29 final size:29
Alignment explanation
Indices: 2924624--2924690 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
2924614 TAAATGACAA
* *
2924624 CCTTTGTGGCACAACTTTGGACAGGAAAG
1 CCTTTGTGGCAAAACTCTGGACAGGAAAG
*
2924653 CCTTTGTGGCAAAACTCTGGACATGAAAG
1 CCTTTGTGGCAAAACTCTGGACAGGAAAG
2924682 CCTTTGTGG
1 CCTTTGTGG
2924691 GGAGTATTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (29 bp):
CCTTTGTGGCAAAACTCTGGACAGGAAAG
Found at i:2924716 original size:90 final size:91
Alignment explanation
Indices: 2924563--2924746 Score: 271
Period size: 90 Copynumber: 2.0 Consensus size: 91
2924553 TAAATGACAA
* * *
2924563 CCTTTGTGGCACAACTCTGAATAGGAAAGCCTTTTTGGCGAGTATTGGATGTAAATGACAACC-T
1 CCTTTGTGGCAAAACTCTGAACAGGAAAGCCTTTGTGGCGAGTATTGGATGTAAATGACAACCTT
* *
2924627 TTGTGGCACAACTTTGGACAGGAAAG
66 TTGTGGCACAACTCTGGACAAGAAAG
* * *
2924653 CCTTTGTGGCAAAACTCTGGACATGAAAGCCTTTGTGGGGAGTATTGGATGTAAATGACAACCTT
1 CCTTTGTGGCAAAACTCTGAACAGGAAAGCCTTTGTGGCGAGTATTGGATGTAAATGACAACCTT
* *
2924718 TTTTGGCATAACTCTGGACAAGAAAG
66 TTGTGGCACAACTCTGGACAAGAAAG
2924744 CCT
1 CCT
2924747 ATGTAGCGAC
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 57 0.69
91 26 0.31
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (91 bp):
CCTTTGTGGCAAAACTCTGAACAGGAAAGCCTTTGTGGCGAGTATTGGATGTAAATGACAACCTT
TTGTGGCACAACTCTGGACAAGAAAG
Found at i:2924799 original size:152 final size:150
Alignment explanation
Indices: 2924503--2924816 Score: 423
Period size: 152 Copynumber: 2.1 Consensus size: 150
2924493 TAAAGGACAA
* * *
2924503 CCTTTGTGGCACAACTCTGATAGGAAAGCCTTTGTGGTGAGTACTGGATGTAAATGACAACCTTT
1 CCTTTGTGGCAAAACTCTGACAGGAAAGCCTTTGTGGGGAGTACTGGATGTAAATGACAACCTTT
* * * * * * * *
2924568 GTGGCACAACTCTGAATAGGAAAGCCTTTTTGGCGAGTATTGGATGTAAATGACAACCTTTGTGG
66 GTGGCACAACTCTGAACAAGAAAGCCTATGTAGCGACTATTGGATGTAAAGGACAACCTTTCTGG
*
2924633 CACAACTTTGGACAGGAAAG
131 CAAAACTTTGGACAGGAAAG
* *
2924653 CCTTTGTGGCAAAACTCTGGACATGAAAGCCTTTGTGGGGAGTATTGGATGTAAATGACAACCTT
1 CCTTTGTGGCAAAACTCT-GACAGGAAAGCCTTTGTGGGGAGTACTGGATGTAAATGACAACC-T
* * * * *
2924718 TTTTGGCATAACTCTGGACAAGAAAGCCTATGTAGCGACTATTGGATGTAAAGGACCACTTTTCT
64 TTGTGGCACAACTCTGAACAAGAAAGCCTATGTAGCGACTATTGGATGTAAAGGACAACCTTTCT
2924783 GGCAAAACTCTT-GACAGGAAAG
129 GGCAAAACT-TTGGACAGGAAAG
2924805 CCTTTGTGGCAA
1 CCTTTGTGGCAA
2924817 GTATTGGATG
Statistics
Matches: 142, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
150 17 0.12
151 40 0.28
152 83 0.58
153 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (150 bp):
CCTTTGTGGCAAAACTCTGACAGGAAAGCCTTTGTGGGGAGTACTGGATGTAAATGACAACCTTT
GTGGCACAACTCTGAACAAGAAAGCCTATGTAGCGACTATTGGATGTAAAGGACAACCTTTCTGG
CAAAACTTTGGACAGGAAAG
Found at i:2924804 original size:61 final size:62
Alignment explanation
Indices: 2924659--2924833 Score: 235
Period size: 61 Copynumber: 2.8 Consensus size: 62
2924649 AAAGCCTTTG
* * * *
2924659 TGGCAAAACTCTGGACATGAAAGCCTTTGTGGGGAGTATTGGATGTAAATGACAACCTTTTT
1 TGGCAAAACTCTGGACAAGAAAGCCTTTGTGGCGAGTATTGGATGTAAAGGACAACCTTTTC
* * * * *
2924721 TGGCATAACTCTGGACAAGAAAGCCTATGTAGCGACTATTGGATGTAAAGGACCA-CTTTTC
1 TGGCAAAACTCTGGACAAGAAAGCCTTTGTGGCGAGTATTGGATGTAAAGGACAACCTTTTC
* * *
2924782 TGGCAAAACTCTTGACAGGAAAGCCTTTGTGGCAAGTATTGGATGTAAAGGA
1 TGGCAAAACTCTGGACAAGAAAGCCTTTGTGGCGAGTATTGGATGTAAAGGA
2924834 TGCCTTTGTA
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 50 0.52
62 47 0.48
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (62 bp):
TGGCAAAACTCTGGACAAGAAAGCCTTTGTGGCGAGTATTGGATGTAAAGGACAACCTTTTC
Found at i:2924824 original size:213 final size:210
Alignment explanation
Indices: 2924493--2924873 Score: 478
Period size: 213 Copynumber: 1.8 Consensus size: 210
2924483 AAACACCAGT
* * * * * * *
2924493 TAAAGGACAACCTTTGTGGCACAACTCTGATAGGAAAGCCTTTGTGGTGAGTACTGGATGTAAAT
1 TAAAGGACAACCTTTGTGGCACAACTCTGACAAGAAAGCCTATGTAGCGACTACTGGATGTAAAG
* * * * * *
2924558 GACAACCTTTGTGGCACAACTCTGAATAGGAAAGCCTTTTTGGCGAGTATTGGATGTAAATGACA
66 GACAACCTTTCTGGCAAAACTCTGAACAGGAAAGCCTTTGTGGCAAGTATTGGATGTAAAGGA-A
* * * *
2924623 ACCTTTGTGGCACAA-CTTTGGACAGGAAAGCCTTTGTGGCAAAACTCTGGACATGAAAGCCTTT
130 ACCTTTGTAGCA-AAGCTCTAGACAGGAAAACCTTTGTGGCAAAACTCTGGACATGAAAGCCTTT
2924687 GTGGGGAGTATTGGATG
194 GTGGGGAGTATTGGATG
* * * *
2924704 TAAATGACAACCTTTTTTGGCATAACTCTGGACAAGAAAGCCTATGTAGCGACTATTGGATGTAA
1 TAAAGGACAACC-TTTGTGGCACAACTCT-GACAAGAAAGCCTATGTAGCGACTACTGGATGTAA
* *
2924769 AGGACCACTTTTCTGGCAAAACTCTTG-ACAGGAAAGCCTTTGTGGCAAGTATTGGATGTAAAGG
64 AGGACAACCTTTCTGGCAAAACTC-TGAACAGGAAAGCCTTTGTGGCAAGTATTGGATGTAAAGG
**
2924833 ATGCCTTTGTAGCAAAGCTCTAGACAGGAAAACCTTTGTGG
128 AAACCTTTGTAGCAAAGCTCTAGACAGGAAAACCTTTGTGG
2924874 TGAGTACTAA
Statistics
Matches: 141, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
211 13 0.09
212 45 0.32
213 81 0.57
214 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (210 bp):
TAAAGGACAACCTTTGTGGCACAACTCTGACAAGAAAGCCTATGTAGCGACTACTGGATGTAAAG
GACAACCTTTCTGGCAAAACTCTGAACAGGAAAGCCTTTGTGGCAAGTATTGGATGTAAAGGAAA
CCTTTGTAGCAAAGCTCTAGACAGGAAAACCTTTGTGGCAAAACTCTGGACATGAAAGCCTTTGT
GGGGAGTATTGGATG
Found at i:2924869 original size:60 final size:60
Alignment explanation
Indices: 2924652--2924914 Score: 267
Period size: 60 Copynumber: 4.3 Consensus size: 60
2924642 GGACAGGAAA
* * * * *
2924652 GCCTTTGTGGCAAAACTCTGGACATGAAAGCCTTTGTGGGGAGTATTGGATGTAAATGACA
1 GCCTTTGTGGCAAAACTCTAGACAGGAAAGCCTTTGTGGCGAGTATTGGATGTAAAGGA-T
* * * * * * * *
2924713 ACCTTTTTTGGCATAACTCTGGACAAGAAAGCCTATGTAGCGACTATTGGATGTAAAGGA-
1 GCC-TTTGTGGCAAAACTCTAGACAGGAAAGCCTTTGTGGCGAGTATTGGATGTAAAGGAT
* * * *
2924773 CCACTTTTCTGGCAAAACTCTTGACAGGAAAGCCTTTGTGGCAAGTATTGGATGTAAAGGAT
1 GC-C-TTTGTGGCAAAACTCTAGACAGGAAAGCCTTTGTGGCGAGTATTGGATGTAAAGGAT
* * * * * **
2924835 GCCTTTGTAGCAAAGCTCTAGACAGGAAAACCTTTGTGGTGAGTACTAAATGTAAAGGAT
1 GCCTTTGTGGCAAAACTCTAGACAGGAAAGCCTTTGTGGCGAGTATTGGATGTAAAGGAT
2924895 GCCTTTGTGGCAAAACTCTA
1 GCCTTTGTGGCAAAACTCTA
2924915 TGTAAGGCCC
Statistics
Matches: 168, Mismatches: 31, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
60 66 0.39
61 53 0.32
62 49 0.29
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (60 bp):
GCCTTTGTGGCAAAACTCTAGACAGGAAAGCCTTTGTGGCGAGTATTGGATGTAAAGGAT
Found at i:2925000 original size:11 final size:11
Alignment explanation
Indices: 2924984--2925009 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2924974 TTAACCCAGC
2924984 AACAGACCCAA
1 AACAGACCCAA
2924995 AACAGACCCAA
1 AACAGACCCAA
2925006 AACA
1 AACA
2925010 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.35, G:0.08, T:0.00
Consensus pattern (11 bp):
AACAGACCCAA
Found at i:2926122 original size:3 final size:3
Alignment explanation
Indices: 2926066--2926107 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2926056 AATTCTTTTC
2926066 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2926108 AGGTATTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2926428 original size:4 final size:4
Alignment explanation
Indices: 2926419--2926452 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2926409 TAAATTTCGT
2926419 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
2926453 GTTTTGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2934230 original size:25 final size:27
Alignment explanation
Indices: 2934201--2934252 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
2934191 NNATATTTAA
*
2934201 TAAATTATTATT-TTAAAT-AAAATAT
1 TAAATAATTATTATTAAATGAAAATAT
*
2934226 TAAATAATTATTATTTAATGAAAATAT
1 TAAATAATTATTATTAAATGAAAATAT
2934253 CATTTAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 11 0.48
26 5 0.22
27 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TAAATAATTATTATTAAATGAAAATAT
Found at i:2936758 original size:20 final size:18
Alignment explanation
Indices: 2936720--2936758 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2936710 AAATAGTGAG
*
2936720 AATTTATTTTTAAGTATA
1 AATTTATTTTTAAGAATA
2936738 AATTCTATTTTTCAAGAATA
1 AATT-TATTTTT-AAGAATA
2936758 A
1 A
2936759 CAATTCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTTATTTTTAAGAATA
Found at i:2936880 original size:22 final size:22
Alignment explanation
Indices: 2936845--2936895 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2936835 ATTTAAAATT
* * *
2936845 GTTCGAGCCTATACTGGAAGCA
1 GTTCGTGCCCATACTCGAAGCA
2936867 GTTCGTGCCCATACTCGAAGCA
1 GTTCGTGCCCATACTCGAAGCA
*
2936889 ATTCGTG
1 GTTCGTG
2936896 GTATGAGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTTCGTGCCCATACTCGAAGCA
Found at i:2949035 original size:23 final size:23
Alignment explanation
Indices: 2948987--2949036 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2948977 GGGTTTGTTT
* *
2948987 CAAAATTACTCCTTGAGGGGAAA
1 CAAAATTAATCCTTGAGAGGAAA
*
2949010 CAAAATTAATCCCTT-AGAGGAGA
1 CAAAATTAAT-CCTTGAGAGGAAA
2949033 CAAA
1 CAAA
2949037 TCCTTTGGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (23 bp):
CAAAATTAATCCTTGAGAGGAAA
Found at i:2961678 original size:3 final size:3
Alignment explanation
Indices: 2961670--2961722 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
2961660 TATTTCCACT
* *
2961670 TTC TTC TTC GTT- TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC ATC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2961715 TTC TTC TT
1 TTC TTC TT
2961723 TGGCTTCTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2961729 original size:18 final size:18
Alignment explanation
Indices: 2961690--2961729 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2961680 TTTTCTTCTT
* **
2961690 CTTCTTCTTCTTCTTTTT
1 CTTCATCTTCTTCTTTGG
2961708 CTTCATCTTCTTCTTTGG
1 CTTCATCTTCTTCTTTGG
2961726 CTTC
1 CTTC
2961730 TCAATCTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.30, G:0.05, T:0.62
Consensus pattern (18 bp):
CTTCATCTTCTTCTTTGG
Found at i:2962207 original size:3 final size:3
Alignment explanation
Indices: 2962199--2962226 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2962189 TTCCTGTTAC
2962199 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
2962227 TGAAGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:2962234 original size:3 final size:3
Alignment explanation
Indices: 2962228--2962252 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2962218 ATCATCATCT
2962228 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
2962253 CAGCTCCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2963531 original size:21 final size:20
Alignment explanation
Indices: 2963499--2963539 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2963489 CATTCGTCAG
2963499 CATCTTAACTTATAACATCA
1 CATCTTAACTTATAACATCA
* *
2963519 CATCATTATCTTATAAGATCA
1 CATC-TTAACTTATAACATCA
2963540 TGTTGTCACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (20 bp):
CATCTTAACTTATAACATCA
Found at i:2972269 original size:17 final size:17
Alignment explanation
Indices: 2972235--2972282 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
2972225 CTGTAGATCA
2972235 TTGGAAGGCTCGAT-TTGG
1 TTGGAA-GCTCG-TCTTGG
2972253 TTGGAAGCTCGTCTTGG
1 TTGGAAGCTCGTCTTGG
2972270 TTGGAAGCTCGTC
1 TTGGAAGCTCGTC
2972283 AGAGACCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.03
17 22 0.76
18 6 0.21
ACGTcount: A:0.15, C:0.17, G:0.35, T:0.33
Consensus pattern (17 bp):
TTGGAAGCTCGTCTTGG
Found at i:2978818 original size:19 final size:20
Alignment explanation
Indices: 2978782--2978819 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2978772 TTACTATTAA
* *
2978782 ATGGTGGTTGATTGATCTTG
1 ATGGTGGTTCATTAATCTTG
2978802 ATGG-GGTTCATTAATCTT
1 ATGGTGGTTCATTAATCTT
2978820 TGAATTAGGG
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:0.18, C:0.08, G:0.29, T:0.45
Consensus pattern (20 bp):
ATGGTGGTTCATTAATCTTG
Found at i:2980768 original size:17 final size:17
Alignment explanation
Indices: 2980742--2980774 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2980732 TCACGATGTT
*
2980742 GGTATTGTGATACCAAA
1 GGTATCGTGATACCAAA
2980759 GGTATCGTGATACCAA
1 GGTATCGTGATACCAA
2980775 GGAATAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (17 bp):
GGTATCGTGATACCAAA
Found at i:3000486 original size:38 final size:38
Alignment explanation
Indices: 3000435--3000511 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
3000425 CAGTCATGCC
* *
3000435 AGTTTTTAATAGTAGAAGTGAAT-TGAATTTTTAACAGA
1 AGTTTTTAATAGTAGAAATAAATGT-AATTTTTAACAGA
3000473 AGTTTTTAATAGTAGAAATAAATGTAATTTTTAACAGA
1 AGTTTTTAATAGTAGAAATAAATGTAATTTTTAACAGA
3000511 A
1 A
3000512 AGGGACAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 35 0.97
39 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.39
Consensus pattern (38 bp):
AGTTTTTAATAGTAGAAATAAATGTAATTTTTAACAGA
Found at i:3006251 original size:108 final size:108
Alignment explanation
Indices: 3006062--3006281 Score: 413
Period size: 108 Copynumber: 2.0 Consensus size: 108
3006052 CAAATTAAAG
*
3006062 TACATGGACTAAATCTATAACTTTAGAAAAATTCAAGGACTAATAGAAAATTTTAACCTAGACCT
1 TACATGGACTAAATCTATAACTTTAGAAAAATACAAGGACTAATAGAAAATTTTAACCTAGACCT
* *
3006127 ATCAAGTTGTTTACAACATGAGATCTGTCATGTTGGTCATATC
66 ACCAAGTTGTTTACAACATGAGATCTGTCATGTTGGCCATATC
3006170 TACATGGACTAAATCTATAACTTTAGAAAAATACAAGGACTAATAGAAAATTTTAACCTAGACCT
1 TACATGGACTAAATCTATAACTTTAGAAAAATACAAGGACTAATAGAAAATTTTAACCTAGACCT
3006235 ACCAAGTTGTTTACAACATGAGATCTGTCATGTTGGCCATATC
66 ACCAAGTTGTTTACAACATGAGATCTGTCATGTTGGCCATATC
3006278 TACA
1 TACA
3006282 CGCAATATAT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (108 bp):
TACATGGACTAAATCTATAACTTTAGAAAAATACAAGGACTAATAGAAAATTTTAACCTAGACCT
ACCAAGTTGTTTACAACATGAGATCTGTCATGTTGGCCATATC
Found at i:3020225 original size:115 final size:111
Alignment explanation
Indices: 3019821--3020390 Score: 421
Period size: 114 Copynumber: 5.0 Consensus size: 111
3019811 GTAAACGGTA
* * * * * *
3019821 TCGTTTTCTTGGTGAGCTTCAAAGACATTAGTGGCACTTTAAACAAAACGCCGCAAAAGTCAAAC
1 TCGTTTTC-TGTTGAGCTTTAGAGACATTAGTGGCGCTTTATA-AAAACGCCGCAAAAGTCAAGC
* * * * * *
3019886 ATTAGCGGCACTTTTACAAAAGCGCCTCAAAACTGTTAAGCAGACGACG
64 ATTAGCGGCGC-TTTACAAAAGCACCTAAAAATTTTTAAGCAAACGACG
* * * * * *
3019935 TCGTTTTCT-TTTAGGTTTAGAGATAGTAGTGGCG-TTTATCAAGAAACGCTGCAAAAGATCATG
1 TCGTTTTCTGTTGAGCTTTAGAGACATTAGTGGCGCTTTAT-AA-AAACGCCGCAAAAG-TCAAG
* * * * * *
3019998 TATTAGCGGCGCTTTCTCCAAAGCGCCATAAAAGTTTTT-ATCAAACGACG
63 CATTAGCGGCGCTTT-ACAAAAGCACC-TAAAAATTTTTAAGCAAACGACG
* * * * ** * * * *
3020048 TCATTTTATTGTTGAGCTTTAGACACATTAGTGGCGTTTTAGGGAAAATGCCGCAGATGTCAATC
1 TCGTTTT-CTGTTGAGCTTTAGAGACATTAGTGGCGCTTTA-TAAAAACGCCGCAAAAGTCAAGC
** *
3020113 ATTAGCGGCGCTTTACGGGAAGCACCGTAAAAATTTTTAAGCAAACGGCG
64 ATTAGCGGCGCTTTAC-AAAAGCACC-TAAAAATTTTTAAGCAAACGACG
*
3020163 TCGTTTTTCTGTTGAGCTTTAGAGACATTAGTGGCGCTTTACTAAAAACGCCACAAAAGTCAAGC
1 TCG-TTTTCTGTTGAGCTTTAGAGACATTAGTGGCGCTTTA-TAAAAACGCCGCAAAAGTCAAGC
* * * *
3020228 ATTAGCGACGCTTTATCAAAAGCATC-ACAATAGTTTTAAGCAAACGACG
64 ATTAGCGGCGCTTTA-CAAAAGCACCTA-AAAATTTTTAAGCAAACGACG
* * * * ** *
3020277 AT-GTTTTCTTTTTCAGCTTTCGAGATATTAGTGGCGCATTCCTAAAAACGCCGCAAAAGGCAAG
1 -TCGTTTTC-TGTTGAGCTTTAGAGACATTAGTGGCGC-TTTATAAAAACGCCGCAAAAGTCAAG
* * * * * *
3020341 AATTAGAGGTGCTTTCACAATAGCACCGCAAAAGTTTTTAAGCAAACGAC
63 CATTAGCGGCGCTTT-ACAAAAGCACC-TAAAAATTTTTAAGCAAACGAC
3020391 AACGTTTTAT
Statistics
Matches: 354, Mismatches: 82, Indels: 39
0.75 0.17 0.08
Matches are distributed among these distances:
111 5 0.01
112 34 0.10
113 45 0.13
114 131 0.37
115 128 0.36
116 11 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (111 bp):
TCGTTTTCTGTTGAGCTTTAGAGACATTAGTGGCGCTTTATAAAAACGCCGCAAAAGTCAAGCAT
TAGCGGCGCTTTACAAAAGCACCTAAAAATTTTTAAGCAAACGACG
Found at i:3020692 original size:39 final size:39
Alignment explanation
Indices: 3020641--3020727 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
3020631 TTAAGGGTTG
*
3020641 AGGTTTAAGGTTTATAGTTTATATATGTTTTATGATTCA
1 AGGTTTAAGGTTTATAGTTTATATATGTTTTATGAGTCA
* *
3020680 GGGTTTAGGGTTTATAGTTTATATATGTTTTATGAGTCA
1 AGGTTTAAGGTTTATAGTTTATATATGTTTTATGAGTCA
3020719 AGGTTTAAG
1 AGGTTTAAG
3020728 AAATATGGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.48
Consensus pattern (39 bp):
AGGTTTAAGGTTTATAGTTTATATATGTTTTATGAGTCA
Found at i:3021135 original size:14 final size:14
Alignment explanation
Indices: 3020996--3021135 Score: 61
Period size: 14 Copynumber: 9.9 Consensus size: 14
3020986 GGGGCTTAAA
*
3020996 GTTTAGGGTTTAAG
1 GTTTAGGGTTTATG
*
3021010 GTTTATGGG-TTATT
1 GTTTA-GGGTTTATG
* *
3021024 ATTTAGGGTTTGTGG
1 GTTTAGGGTTTAT-G
* *
3021039 GTTTAAGGTTTAAG
1 GTTTAGGGTTTATG
* *
3021053 GGTTAGGGTCTATG
1 GTTTAGGGTTTATG
* * * * *
3021067 ATCTAGTGTCTAAG
1 GTTTAGGGTTTATG
**
3021081 GAATAGGGTTTATG
1 GTTTAGGGTTTATG
*
3021095 GTTTATGGTTT-TCAG
1 GTTTAGGGTTTAT--G
* *
3021110 G-ATAGGGGTTATG
1 GTTTAGGGTTTATG
3021123 GTTTAGGGTTTAT
1 GTTTAGGGTTTAT
3021136 ATTAATTAGT
Statistics
Matches: 87, Mismatches: 32, Indels: 14
0.65 0.24 0.11
Matches are distributed among these distances:
13 6 0.07
14 66 0.76
15 15 0.17
ACGTcount: A:0.20, C:0.03, G:0.34, T:0.44
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:3022902 original size:13 final size:13
Alignment explanation
Indices: 3022884--3022921 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3022874 GAAGTTCTGC
3022884 TTAATGTTGCTGG
1 TTAATGTTGCTGG
*
3022897 TTAATGTTAG-GGG
1 TTAATGTT-GCTGG
3022910 TTAATGTTGCTG
1 TTAATGTTGCTG
3022922 CGAGTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.05
13 19 0.90
14 1 0.05
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (13 bp):
TTAATGTTGCTGG
Found at i:3023605 original size:67 final size:67
Alignment explanation
Indices: 3023463--3023598 Score: 159
Period size: 67 Copynumber: 2.0 Consensus size: 67
3023453 TATTAATATG
* * *
3023463 GATATATAACCTATATTTCAATTTTATTAATAATAAATTTTATAATTTTAAAAATAAATGTAAAT
1 GATATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAATTTTAAAAATAAATATAAAT
**
3023528 GG
66 AA
* ***
3023530 GATATATAACCTATATTCCAAATTTATTAGTAA-ACAATTTT-TAATTTTTAAAAATGGTTATAA
1 GATATATAACCTATATTCCAAATTTATTAATAATA-AATTTTATAA-TTTTAAAAATAAATATAA
3023593 ATAA
64 ATAA
3023597 GA
1 GA
3023599 AGTATAAAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
66 4 0.07
67 54 0.93
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (67 bp):
GATATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAATTTTAAAAATAAATATAAAT
AA
Found at i:3023687 original size:7 final size:7
Alignment explanation
Indices: 3023615--3023639 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3023605 AAAGTGATAT
3023615 ATAATAC
1 ATAATAC
3023622 ATAATAC
1 ATAATAC
3023629 ATAATAC
1 ATAATAC
3023636 ATAA
1 ATAA
3023640 ATTTATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:3023717 original size:52 final size:55
Alignment explanation
Indices: 3023619--3023732 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 55
3023609 TGATATATAA
* *
3023619 TACATAATACATAATACATAAATTTATCAATCATATAATACATTATATACAAACT
1 TACATAATACATAATAAATAAATATATCAATCATATAATACATTATATACAAACT
*
3023674 TACATAATACATAACTTAAAT-AATATA-CAAT-ATATAA-AC-TTATATATAAACT
1 TACATAATACATAA--TAAATAAATATATCAATCATATAATACATTATATACAAACT
*
3023726 TGCATAA
1 TACATAA
3023733 CTTATATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
52 18 0.34
53 2 0.04
54 6 0.11
55 18 0.34
56 5 0.09
57 4 0.08
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (55 bp):
TACATAATACATAATAAATAAATATATCAATCATATAATACATTATATACAAACT
Found at i:3023783 original size:9 final size:9
Alignment explanation
Indices: 3023771--3024111 Score: 237
Period size: 9 Copynumber: 38.8 Consensus size: 9
3023761 AAACATAGCC
3023771 TACATAACT
1 TACATAACT
3023780 TACATAACT
1 TACATAACT
*
3023789 TACATAAAT
1 TACATAACT
*
3023798 TAAATAACT
1 TACATAACT
3023807 TACATAACGT
1 TACATAAC-T
3023817 ACGTACATAA--
1 ---TACATAACT
3023827 TACATAACCT
1 TACATAA-CT
3023837 TAC-TAACT
1 TACATAACT
3023845 TACATAACT
1 TACATAACT
3023854 TACATAAAACCT
1 TACAT--AA-CT
*
3023866 T-CCTAACT
1 TACATAACT
*
3023874 TACATTA-T
1 TACATAACT
3023882 ATAC--AACT
1 -TACATAACT
3023890 TACATAA--
1 TACATAACT
** *
3023897 TATGTTACT
1 TACATAACT
*
3023906 TTCATAACT
1 TACATAACT
3023915 TACATAACT
1 TACATAACT
3023924 TACAGT-ACT
1 TACA-TAACT
3023933 TACATAA--
1 TACATAACT
3023940 TACATAA--
1 TACATAACT
*
3023947 TACATAACA
1 TACATAACT
3023956 TACATAA--
1 TACATAACT
3023963 TACATAACT
1 TACATAACT
3023972 TACATAACT
1 TACATAACT
3023981 TACATAACT
1 TACATAACT
*
3023990 TACATAACA
1 TACATAACT
3023999 TACATAA--
1 TACATAACT
3024006 TACATAACT
1 TACATAACT
3024015 TACATAA--
1 TACATAACT
*
3024022 TACACAACT
1 TACATAACT
3024031 TACATAACT
1 TACATAACT
*
3024040 CACATAA-T
1 TACATAACT
3024048 ATAC--AACT
1 -TACATAACT
*
3024056 CACATAACT
1 TACATAACT
3024065 TACATAA--
1 TACATAACT
3024072 TACATAACTT
1 TACATAAC-T
3024082 AATACATAACTT
1 --TACATAAC-T
3024094 AGTACATAACT
1 --TACATAACT
3024105 TACATAA
1 TACATAA
3024112 TACATAAAAA
Statistics
Matches: 271, Mismatches: 24, Indels: 74
0.73 0.07 0.20
Matches are distributed among these distances:
7 60 0.22
8 13 0.05
9 159 0.59
10 5 0.02
11 5 0.02
12 22 0.08
13 7 0.03
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
TACATAACT
Found at i:3023878 original size:47 final size:48
Alignment explanation
Indices: 3023769--3024038 Score: 129
Period size: 47 Copynumber: 6.0 Consensus size: 48
3023759 TAAAACATAG
*
3023769 CCTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACGTA
1 CCTACATAACTTACATAACTTACATAAATTAAATAACTTACATAAC-AA
* * *
3023818 CGTACATAA--TACATAACCTTAC-TAACTTACATAACTTACATAA-AA
1 CCTACATAACTTACATAA-CTTACATAAATTAAATAACTTACATAACAA
* * * * ** * * *
3023863 CCTTCCTAACTTACATTA-TATAC--AACTTACATAATATGTTACTTTCATAA
1 CCTACATAACTTACATAACT-TACATAAATT--A-AATAACTTAC-ATAACAA
* *
3023913 CTTACATAACTTACAGT-ACTTACAT-AA-TACATAA--TACATAAC-A
1 CCTACATAACTTACA-TAACTTACATAAATTAAATAACTTACATAACAA
* *
3023956 --TACATAA--TACATAACTTACATAACTTACATAACTTACATAAC-A
1 CCTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACAA
* *
3023999 --TACATAA--TACATAACTTACAT-AA-TACACAACTTACATAAC
1 CCTACATAACTTACATAACTTACATAAATTAAATAACTTACATAAC
3024039 TCACATAATA
Statistics
Matches: 178, Mismatches: 25, Indels: 44
0.72 0.10 0.18
Matches are distributed among these distances:
38 1 0.01
39 12 0.07
40 1 0.01
41 30 0.17
42 1 0.01
43 31 0.17
44 2 0.01
45 16 0.09
46 3 0.02
47 36 0.20
48 13 0.07
49 10 0.06
50 19 0.11
51 3 0.02
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.31
Consensus pattern (48 bp):
CCTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACAA
Found at i:3023958 original size:16 final size:16
Alignment explanation
Indices: 3023939--3024118 Score: 129
Period size: 16 Copynumber: 11.9 Consensus size: 16
3023929 TACTTACATA
3023939 ATACATAATACATAAC
1 ATACATAATACATAAC
3023955 ATACATAATACATAAC
1 ATACATAATACATAAC
* *
3023971 TTACAT-A-AC-TTAC
1 ATACATAATACATAAC
3023984 ATA-ACT--TACATAAC
1 ATACA-TAATACATAAC
3023998 ATACATAATACATAAC
1 ATACATAATACATAAC
* *
3024014 TTACATAATACACAAC
1 ATACATAATACATAAC
* *
3024030 TTACATAACTCACATAAT
1 ATACATAA-T-ACATAAC
*
3024048 ATACA-ACTCACATAAC
1 ATACATAAT-ACATAAC
*
3024064 TTACATAATACATAAC
1 ATACATAATACATAAC
3024080 -T---TAATACATAAC
1 ATACATAATACATAAC
*
3024092 -T---TAGTACATAAC
1 ATACATAATACATAAC
*
3024104 TTACATAATACATAA
1 ATACATAATACATAA
3024119 AAATATATCA
Statistics
Matches: 136, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
12 23 0.17
13 9 0.07
14 9 0.07
15 3 0.02
16 79 0.58
17 4 0.03
18 9 0.07
ACGTcount: A:0.50, C:0.21, G:0.01, T:0.29
Consensus pattern (16 bp):
ATACATAATACATAAC
Found at i:3024009 original size:25 final size:25
Alignment explanation
Indices: 3023771--3024118 Score: 162
Period size: 25 Copynumber: 13.3 Consensus size: 25
3023761 AAACATAGCC
*
3023771 TACATAACTTACATAACTTACATAAA
1 TACATAACTTACATAACATACAT-AA
*
3023797 TTAAATAACTTACATAACGTACGTACATAA
1 -TACATAACTTACATAAC--A--TACATAA
*
3023827 TACATAACCTTAC-TAACTTACATAA
1 TACATAA-CTTACATAACATACATAA
* * *
3023852 CTTACATAAAACCTT-CCTAACTTACATTA
1 --TACAT--AA-CTTACATAACATACATAA
* * * ** *
3023881 TATACAACTTACATAATAT-GTTACT
1 TACATAACTTACATAACATACATA-A
* * *
3023906 TTCATAACTTACATAACTTACAGTACT
1 TACATAACTTACATAACATACA-TA-A
3023933 TACATAA--TACAT-A-ATACATAACA
1 TACATAACTTACATAACATACAT-A-A
*
3023956 TACATAA--TACATAACTTACATAA
1 TACATAACTTACATAACATACATAA
3023979 CTTACATAACTTACATAACATACATAA
1 --TACATAACTTACATAACATACATAA
*
3024006 TACATAACTTACAT-A-ATACACAA
1 TACATAACTTACATAACATACATAA
* * *
3024029 CTTACATAACTCACATAATATACA-AC
1 --TACATAACTTACATAACATACATAA
*
3024055 TCACATAACTTACATAATACATAACTTAA
1 T-ACATAACTTACAT-A-ACAT-ACATAA
*
3024084 TACATAACTTAGTACATAACTTACATAA
1 TACATAAC-T--TACATAACATACATAA
3024112 TACATAA
1 TACATAA
3024119 AAATATATCA
Statistics
Matches: 253, Mismatches: 35, Indels: 65
0.72 0.10 0.18
Matches are distributed among these distances:
22 1 0.00
23 26 0.10
24 9 0.04
25 84 0.33
26 3 0.01
27 57 0.23
28 22 0.09
29 33 0.13
30 8 0.03
31 10 0.04
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (25 bp):
TACATAACTTACATAACATACATAA
Found at i:3024086 original size:12 final size:12
Alignment explanation
Indices: 3024069--3024106 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
3024059 ATAACTTACA
3024069 TAATACATAACT
1 TAATACATAACT
3024081 TAATACATAACT
1 TAATACATAACT
*
3024093 TAGTACATAACT
1 TAATACATAACT
3024105 TA
1 TA
3024107 CATAATACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (12 bp):
TAATACATAACT
Found at i:3030012 original size:43 final size:43
Alignment explanation
Indices: 3029958--3030183 Score: 310
Period size: 43 Copynumber: 5.3 Consensus size: 43
3029948 CACCAAACAA
* *
3029958 TAGCGGCGTTTGTGGGAAAAGCGCTGCT-AAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAG-TCATGACCTT
* * *
3030001 TAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCTT
**
3030044 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGTTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCTT
* ***
3030087 TAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAAGTCATTTTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCTT
* *
3030130 TAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATAACCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCTT
*
3030173 TAGCGGTGTTT
1 TAGCGGCGTTT
3030184 TTGTGGAAGC
Statistics
Matches: 165, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
43 161 0.98
44 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCTT
Found at i:3034315 original size:7 final size:6
Alignment explanation
Indices: 3034299--3034362 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
3034289 GTTTTCCTGC
* *
3034299 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
* *
3034349 AATAAT AATAAT AA
1 AAAAAT AAAAAT AA
3034363 TAGGAATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
5 5 0.10
6 35 0.67
7 7 0.13
8 5 0.10
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:3034345 original size:3 final size:3
Alignment explanation
Indices: 3034314--3034364 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
3034304 TAAAAATGAA
* *
3034314 AAT AA- AAT AA- AAT AGT AAA AAT AAAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
3034358 AAT AAT A
1 AAT AAT A
3034365 GGAATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:3039507 original size:12 final size:12
Alignment explanation
Indices: 3039490--3039534 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
3039480 AAAGTGAGAG
3039490 GATGATGATGGT
1 GATGATGATGGT
3039502 GATGATGATGGT
1 GATGATGATGGT
*
3039514 G--G-TGGTGGT
1 GATGATGATGGT
3039523 GATGATGATGGT
1 GATGATGATGGT
3039535 TGGATTCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 1 0.04
12 19 0.68
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (12 bp):
GATGATGATGGT
Found at i:3041268 original size:25 final size:29
Alignment explanation
Indices: 3041233--3041319 Score: 110
Period size: 30 Copynumber: 3.1 Consensus size: 29
3041223 CATTTTTGTG
3041233 GAAAGTCAAAGATATGGGTATC-AA-A-T
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
3041259 -AAAGTCAAAGATATAGGTATCAAATATT
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
3041287 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
3041318 GA
1 GA
3041320 CATAAGAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
25 20 0.38
26 2 0.04
27 1 0.02
28 1 0.02
30 22 0.42
31 6 0.12
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:3041295 original size:30 final size:30
Alignment explanation
Indices: 3041231--3041318 Score: 114
Period size: 25 Copynumber: 3.1 Consensus size: 30
3041221 TCCATTTTTG
3041231 TGGAAAGTCAAAGATATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
3041258 T--AAAGTCAAAGATATAGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
3041286 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
3041317 TG
1 TG
3041319 ACATAAGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
25 20 0.38
26 2 0.04
27 2 0.04
28 1 0.02
30 20 0.38
31 7 0.13
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:3045721 original size:30 final size:30
Alignment explanation
Indices: 3045678--3045951 Score: 503
Period size: 30 Copynumber: 9.1 Consensus size: 30
3045668 TCCATATTTA
* *
3045678 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
3045708 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
3045738 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
3045768 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
3045798 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
3045828 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
3045858 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
3045888 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
3045918 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
3045949 TGG
1 TGG
3045952 CATAATAAAA
Statistics
Matches: 238, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
30 230 0.97
31 8 0.03
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:3052538 original size:40 final size:40
Alignment explanation
Indices: 3052493--3052579 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 40
3052483 GCTATGTTTA
3052493 GCACTTAATATGAAATTC-GAGATAGCTTCAGCTATTTATG
1 GCACTTAATATGAAATTCGGA-ATAGCTTCAGCTATTTATG
* * ** * *
3052533 GCACTTAGTGTGCGATTTGGAATAGCTTCGGCTATTTATG
1 GCACTTAATATGAAATTCGGAATAGCTTCAGCTATTTATG
*
3052573 ACACTTA
1 GCACTTA
3052580 GTGTGCGAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 37 0.95
41 2 0.05
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (40 bp):
GCACTTAATATGAAATTCGGAATAGCTTCAGCTATTTATG
Found at i:3052619 original size:41 final size:40
Alignment explanation
Indices: 3052511--3052649 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 40
3052501 TATGAAATTC
**
3052511 GAGATAGCTTCAGCTATTTATGGCACTTAGTGTGCGATTT
1 GAGATAGCTTCAGCTATTTATGGCACTTAGTGTGCGAGAT
* *
3052551 G-GAATAGCTTCGGCTATTTATGACACTTAGTGTGCGAGACT
1 GAG-ATAGCTTCAGCTATTTATGGCACTTAGTGTGCGAGA-T
* * *
3052592 GAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGAGAT
1 GAGATAGCTTCAGCTATTTATGGCACTTAGTGTGCGAGAT
*
3052632 TATGATAGCTTCAGCTAT
1 GA-GATAGCTTCAGCTAT
3052650 ACGATGGCAA
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 35 0.41
41 49 0.57
42 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (40 bp):
GAGATAGCTTCAGCTATTTATGGCACTTAGTGTGCGAGAT
Found at i:3056434 original size:49 final size:49
Alignment explanation
Indices: 3056381--3056487 Score: 133
Period size: 49 Copynumber: 2.2 Consensus size: 49
3056371 TGGTTTGACC
* * * *
3056381 ATGGCATCGGTAAGTGATATGTGATTCCGTATAAGACCATAGCTGGGCT
1 ATGGCATCGGTAAGTGATAAGTGATTACGTATAAGACCACAGCTGGACT
* * * *
3056430 ATGGCATCGGTATGTGATAAGTGATTATGTGTAAGACCACAGTTGGACT
1 ATGGCATCGGTAAGTGATAAGTGATTACGTATAAGACCACAGCTGGACT
*
3056479 ACGGCATCG
1 ATGGCATCG
3056488 AGAAAACGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (49 bp):
ATGGCATCGGTAAGTGATAAGTGATTACGTATAAGACCACAGCTGGACT
Found at i:3060000 original size:40 final size:40
Alignment explanation
Indices: 3059943--3060042 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
3059933 TAATGATAAA
*
3059943 TCGGCTATGTT-TAGCACTTAATATGAAATTC-GAGATAGCT
1 TCGGCTAT-TTATGGCACTTAATATGAAATTCGGA-ATAGCT
* * ** *
3059983 TCGGCTATTTATGGCACTTAGTGTGCGATTTGGAATAGCT
1 TCGGCTATTTATGGCACTTAATATGAAATTCGGAATAGCT
*
3060023 TCGGCTATTTATGACACTTA
1 TCGGCTATTTATGGCACTTA
3060043 GTGTGCGAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
39 2 0.04
40 47 0.92
41 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (40 bp):
TCGGCTATTTATGGCACTTAATATGAAATTCGGAATAGCT
Found at i:3060082 original size:41 final size:41
Alignment explanation
Indices: 3059973--3060093 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 41
3059963 ATATGAAATT
***
3059973 CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGATTT
1 CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGAC
* *
3060014 GGA-ATAGCTTCGGCTATTTATGACACTTAGTGTGCGAGAC
1 CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGAC
* * *
3060054 CGAGATAGCTTTGGCTATGTAAGGCACTTAGTGTGCGAGA
1 CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGA
3060094 TTATGATAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
40 35 0.51
41 34 0.49
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (41 bp):
CGAGATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGAC
Found at i:3060102 original size:41 final size:41
Alignment explanation
Indices: 3059976--3060106 Score: 153
Period size: 41 Copynumber: 3.2 Consensus size: 41
3059966 TGAAATTCGA
3059976 GATAGCTTCGGCTATTTATGGCACTTAGTGTGC--GATT-T
1 GATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGATTAT
* **
3060014 GGAATAGCTTCGGCTATTTATGACACTTAGTGTGCGAGACCGA-
1 -G-ATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGA-TTAT
* * *
3060057 GATAGCTTTGGCTATGTAAGGCACTTAGTGTGCGAGATTAT
1 GATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGATTAT
3060098 GATAGCTTC
1 GATAGCTTC
3060107 AGCCATACGA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
39 1 0.01
40 32 0.42
41 40 0.53
42 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (41 bp):
GATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGATTAT
Found at i:3060421 original size:42 final size:42
Alignment explanation
Indices: 3060365--3060461 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
3060355 CTATATGAAC
** *
3060365 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGGTAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
3060407 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
3060449 GGCACTAAGTGTG
1 GGCACTAAGTGTG
3060462 TGATACCGAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
Found at i:3062563 original size:14 final size:16
Alignment explanation
Indices: 3062544--3062576 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3062534 ATAAAATTGG
3062544 AAAGATGA-AAA-AAT
1 AAAGATGATAAATAAT
3062558 AAAGATGATAAATAAT
1 AAAGATGATAAATAAT
3062574 AAA
1 AAA
3062577 ATAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAGATGATAAATAAT
Found at i:3063704 original size:24 final size:24
Alignment explanation
Indices: 3063675--3063733 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
3063665 TATAGCTATC
3063675 CAGAGCTTCCCGTTAATGGCTCTT
1 CAGAGCTTCCCGTTAATGGCTCTT
* *
3063699 CAGAGCTACCCGTTATTGGCTCTT
1 CAGAGCTTCCCGTTAATGGCTCTT
3063723 -ATGAGCTTCCC
1 CA-GAGCTTCCC
3063734 CTTAGACAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.32
Consensus pattern (24 bp):
CAGAGCTTCCCGTTAATGGCTCTT
Found at i:3072211 original size:15 final size:15
Alignment explanation
Indices: 3072191--3072237 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
3072181 ATTTTCAAGC
3072191 TTATTTTGGTCATGT
1 TTATTTTGGTCATGT
*
3072206 TTATTTTGGTCATGC
1 TTATTTTGGTCATGT
3072221 TTATTTTGGTCATGT
1 TTATTTTGGTCATGT
3072236 TT
1 TT
3072238 TAACTTTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.13, C:0.09, G:0.19, T:0.60
Consensus pattern (15 bp):
TTATTTTGGTCATGT
Found at i:3082121 original size:40 final size:36
Alignment explanation
Indices: 3082031--3082206 Score: 118
Period size: 36 Copynumber: 4.7 Consensus size: 36
3082021 TATGTATTTG
* * * *
3082031 TCGGTTTATCCGGCTAGTGCTGGGCGCAAATCATTA
1 TCGGTTTATCCGACTAGTGCTGGGCACAATTGATTA
*
3082067 TCGGTTTATTCGACTAGTGCTGGGCACACATTTGATATCA
1 TCGGTTTATCCGACTAGTGCTGGGCACA-A-TTGAT-T-A
*** * * *
3082107 TCGGTTTATCCGACTAGCATTGGGCGCAACTGATTG
1 TCGGTTTATCCGACTAGTGCTGGGCACAATTGATTA
** ** *
3082143 TTTGTTTATCTAACTAGTGTTGGGCACACATTTGATATCA
1 TCGGTTTATCCGACTAGTGCTGGGCACA-A-TTGAT-T-A
* *
3082183 TCGGTTTATCTGACTAGCGCTGGG
1 TCGGTTTATCCGACTAGTGCTGGG
3082207 TGCAAAACAT
Statistics
Matches: 106, Mismatches: 26, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
36 46 0.43
37 3 0.03
38 11 0.10
39 3 0.03
40 43 0.41
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (36 bp):
TCGGTTTATCCGACTAGTGCTGGGCACAATTGATTA
Found at i:3082219 original size:76 final size:76
Alignment explanation
Indices: 3082031--3082291 Score: 223
Period size: 76 Copynumber: 3.5 Consensus size: 76
3082021 TATGTATTTG
* ** * * ** *
3082031 TCGGTTTATCCGGCTAGTGCTGGGCGCAAATCATTATCGGTTTAT-TCGACTAGTGCTGGGCACA
1 TCGGTTTATCCGACTAGCACTGGGCGCAAAACATTGTTTGTTTATCT-AACTAGTGCTGGGCACA
3082095 CATTTGATATCA
65 CATTTGATATCA
* *** *
3082107 TCGGTTTATCCGACTAGCATTGGGCGCAACTGATTGTTTGTTTATCTAACTAGTGTTGGGCACAC
1 TCGGTTTATCCGACTAGCACTGGGCGCAAAACATTGTTTGTTTATCTAACTAGTGCTGGGCACAC
3082172 ATTTGATATCA
66 ATTTGATATCA
* * * * * *
3082183 TCGGTTTATCTGACTAGCGCTGGGTGCAAAACATTG-TTGATCTAT-TCGACTAGTGCAGGGCAC
1 TCGGTTTATCCGACTAGCACTGGGCGCAAAACATTGTTTG-TTTATCT-AACTAGTGCTGGGCAC
*
3082246 AC-----CTATCA
64 ACATTTGATATCA
* ** *
3082254 TTGGTTTATCCGACTAGGGCTGGGCGCAAAACTTTGTT
1 TCGGTTTATCCGACTAGCACTGGGCGCAAAACATTGTT
3082292 ACGATTTATC
Statistics
Matches: 153, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
71 36 0.24
72 1 0.01
75 4 0.03
76 111 0.73
77 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (76 bp):
TCGGTTTATCCGACTAGCACTGGGCGCAAAACATTGTTTGTTTATCTAACTAGTGCTGGGCACAC
ATTTGATATCA
Found at i:3084943 original size:27 final size:27
Alignment explanation
Indices: 3084913--3084967 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3084903 GCCTACCGCT
* * *
3084913 CATTCAGAGTTCGCCAGACATATTATC
1 CATTCAGAATTCACCAGACATAATATC
* *
3084940 CATTTAGAATTCACCATACATAATATC
1 CATTCAGAATTCACCAGACATAATATC
3084967 C
1 C
3084968 CTTTAGATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (27 bp):
CATTCAGAATTCACCAGACATAATATC
Found at i:3084972 original size:27 final size:27
Alignment explanation
Indices: 3084930--3085001 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
3084920 AGTTCGCCAG
* * *
3084930 ACATATTATCCATTTAGAATTC-ACCAT
1 ACATAATATCCCTTTAGAATTCGA-CAA
3084957 ACATAATATCCCTTTAG-ATTCTGACAA
1 ACATAATATCCCTTTAGAATTC-GACAA
*
3084984 ACATACTATCCCTTTAGA
1 ACATAATATCCCTTTAGA
3085002 TAGATGCCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 4 0.11
27 33 0.87
28 1 0.03
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35
Consensus pattern (27 bp):
ACATAATATCCCTTTAGAATTCGACAA
Found at i:3085122 original size:27 final size:27
Alignment explanation
Indices: 3085092--3085214 Score: 158
Period size: 27 Copynumber: 4.6 Consensus size: 27
3085082 TAAATCGCCG
* * *
3085092 CAAAAGCTTCCATCTCATTA-ATTGCCA
1 CAAAGGCTTCCATTTCA-TAGATTTCCA
* * *
3085119 CAAAGGCTTTCGTTTCATAAATTTCCA
1 CAAAGGCTTCCATTTCATAGATTTCCA
*
3085146 CAAAGGCTTTCATTTCATAGATTTCCA
1 CAAAGGCTTCCATTTCATAGATTTCCA
*
3085173 CAAAGGCTTCTATTTCATAGATTTCCA
1 CAAAGGCTTCCATTTCATAGATTTCCA
3085200 CAAAGGCTTCCATTT
1 CAAAGGCTTCCATTT
3085215 TCTGGCGTGT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 2 0.02
27 83 0.98
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (27 bp):
CAAAGGCTTCCATTTCATAGATTTCCA
Found at i:3085180 original size:54 final size:54
Alignment explanation
Indices: 3085056--3085214 Score: 169
Period size: 54 Copynumber: 2.9 Consensus size: 54
3085046 TCCTTTCATC
* * ** * * *
3085056 ATTTGCCACAAAGGCTTTCCTTTCCTTAAATCGCCGCAAAAGCTTCCATCTCATTA
1 ATTT-CCACAAAGGCTTTCATTT-CATAAATTTCCACAAAGGCTTCCATTTCATTA
* * *
3085112 ATTGCCACAAAGGCTTTCGTTTCATAAATTTCCACAAAGGCTTTCATTTCA-TA
1 ATTTCCACAAAGGCTTTCATTTCATAAATTTCCACAAAGGCTTCCATTTCATTA
*
3085165 GATTTCCACAAAGGC-TTCTATTTCATAGATTTCCACAAAGGCTTCCATTT
1 -ATTTCCACAAAGGCTTTC-ATTTCATAAATTTCCACAAAGGCTTCCATTT
3085215 TCTGGCGTGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
53 5 0.06
54 63 0.72
55 17 0.19
56 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (54 bp):
ATTTCCACAAAGGCTTTCATTTCATAAATTTCCACAAAGGCTTCCATTTCATTA
Found at i:3089118 original size:132 final size:132
Alignment explanation
Indices: 3088932--3089505 Score: 923
Period size: 132 Copynumber: 4.3 Consensus size: 132
3088922 CGGATGTATC
* * *
3088932 CCACTACTGCTTAGGGGGATAGGACTAATGGCTTAAATTTTCTTCTCCACTGTCTTGGGAAGATA
1 CCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTCTTGGGAAGATA
* ** * *
3088997 AGATTCACCATTTTTAATTTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACTTA
66 AGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
3089062 CT
131 CT
* *
3089064 CCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCGCTGTCTTGGGAAGATA
1 CCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTCTTGGGAAGATA
*
3089129 AGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAGCCTA
66 AGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
3089194 CT
131 CT
* * *
3089196 CCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCTTAGGAAGATA
1 CCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTCTTGGGAAGATA
* * *
3089261 AGATTCACCATCTTTGATATGCTCTACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
66 AGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
3089326 CT
131 CT
* *
3089328 CCACTACTGCTTAGGGAGATAGGTCTAATGGCTTAAATCTACTTCTCTACTGTCTTGGGAAGATA
1 CCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTCTTGGGAAGATA
* * *
3089393 AGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGATAGAATCTACAATCTTCAACCTA
66 AGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
3089458 CT
131 CT
* *
3089460 TCACTACTGCTTAGGGAGATAGTGACTAATGGCTTCAATCTACTTC
1 CCACTACTGCTTAGGGAGATAG-GACTAATGGCTTAAATCTACTTC
3089506 GCTGTTAGTA
Statistics
Matches: 410, Mismatches: 31, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
132 389 0.95
133 21 0.05
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (132 bp):
CCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTCTTGGGAAGATA
AGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
CT
Found at i:3089334 original size:44 final size:44
Alignment explanation
Indices: 3089018--3089481 Score: 249
Period size: 44 Copynumber: 10.5 Consensus size: 44
3089008 TTTTAATTTG
* * * *
3089018 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACTTA
1 CTCCACTACTGCTTAGGGAGATAGAATCTACAATCTTCAACCTA
* * * *
3089062 CTCCACTACTGCTTAGGGAGATAGGA-CT--AATGGCTTAAATCTG
1 CTCCACTACTGCTTAGGGAGATAGAATCTACAAT--CTTCAACCTA
* * ** * * * * *
3089105 CTTCTCCGCTGTCTT-GGGAAGATAAGATTC-ACCATCTTCGATCTG
1 CTCCACTACTG-CTTAGGG-AGAT-AGAATCTACAATCTTCAACCTA
* * * *
3089150 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAGCCTA
1 CTCCACTACTGCTTAGGGAGATAGAATCTACAATCTTCAACCTA
* * *
3089194 CTCCACTACTGCTTAGGGAGATAGGA-CT--AATGGCTTAAATCTGCTT
1 CTCCACTACTGCTTAGGGAGATAGAATCTACAAT--CTTCAA-C--CTA
* * * ** ** *
3089240 CTCCACTA-T-CTTAGGAAGATAAGATTC-ACCATCTTTGATATG
1 CTCCACTACTGCTTAGGGAGAT-AGAATCTACAATCTTCAACCTA
* * * *
3089282 CTCTACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAGAATCTACAATCTTCAACCTA
* * *
3089326 CTCCACTACTGCTTAGGGAGATAG-GTCT--AATGGCTTAAATCTA
1 CTCCACTACTGCTTAGGGAGATAGAATCTACAAT--CTTCAACCTA
* * * * * *
3089369 CTTCTCTACTGTCTT-GGGAAGATAAGATTC-ACCATCTTCGATCTA
1 CTCCACTACTG-CTTAGGG-AGAT-AGAATCTACAATCTTCAACCTA
*
3089414 CTCCACTACTGCTTAGGGTGATAGAATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAGAATCTACAATCTTCAACCTA
*
3089458 CTTCACTACTGCTTAGGGAGATAG
1 CTCCACTACTGCTTAGGGAGATAG
3089482 TGACTAATGG
Statistics
Matches: 311, Mismatches: 77, Indels: 64
0.69 0.17 0.14
Matches are distributed among these distances:
41 9 0.03
42 8 0.03
43 63 0.20
44 162 0.52
45 49 0.16
46 14 0.05
47 6 0.02
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAGAATCTACAATCTTCAACCTA
Found at i:3089561 original size:45 final size:45
Alignment explanation
Indices: 3089492--3089717 Score: 194
Period size: 45 Copynumber: 5.1 Consensus size: 45
3089482 TGACTAATGG
* * *
3089492 CTTCAATCTACTTC-GCTGTTAGTACAGCAAGGCAAGATCTGCTAT
1 CTTCAGTCTA-TTCTGCTGTCAGTACAGGAAGGCAAGATCTGCTAT
* * *
3089537 CTTCAGTCTATTCTGCTGTCAGTACAGGAAGGCAAG-GCTGGTGT
1 CTTCAGTCTATTCTGCTGTCAGTACAGGAAGGCAAGATCTGCTAT
* * *
3089581 CTT-AGATCTACTT-TGTTGCCAGTACAGGAAAGCAAGATCTGCTAT
1 CTTCAG-TCTA-TTCTGCTGTCAGTACAGGAAGGCAAGATCTGCTAT
** * * * *
3089626 CTTCAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAG-GCTGGTTT
1 CTTCAGTCTATTCTGCTGTCAGTACAGGAAGGCAAGATCTGCTAT
* * ** *
3089670 CTTCAATCTGCTT-TGCCATCAGTACAGGAAGGCATGATCTGCTAT
1 CTTCAGTCT-ATTCTGCTGTCAGTACAGGAAGGCAAGATCTGCTAT
3089715 CTT
1 CTT
3089718 TATTGATCTG
Statistics
Matches: 142, Mismatches: 31, Indels: 16
0.75 0.16 0.08
Matches are distributed among these distances:
43 2 0.01
44 68 0.48
45 70 0.49
46 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (45 bp):
CTTCAGTCTATTCTGCTGTCAGTACAGGAAGGCAAGATCTGCTAT
Found at i:3089608 original size:44 final size:45
Alignment explanation
Indices: 3089492--3089703 Score: 184
Period size: 44 Copynumber: 4.8 Consensus size: 45
3089482 TGACTAATGG
* * * * * *
3089492 CTTCA-ATCTACTTCGCTGTTAGTACAGCAAGGCAAGATCTGCTAT
1 CTTCAGATCTGCTTTGCTGTCAGTACAGGAAGGCAAG-GCTGGTAT
* *
3089537 CTTCAG-TCT-ATTCTGCTGTCAGTACAGGAAGGCAAGGCTGGTGT
1 CTTCAGATCTGCTT-TGCTGTCAGTACAGGAAGGCAAGGCTGGTAT
* * * * * *
3089581 CTT-AGATCTACTTTGTTGCCAGTACAGGAAAGCAAGATCTGCTAT
1 CTTCAGATCTGCTTTGCTGTCAGTACAGGAAGGCAAG-GCTGGTAT
** *
3089626 CTTCAG-TCTGCTCCGCTGTCAGTACAGGAAGGCAAGGCTGGTTT
1 CTTCAGATCTGCTTTGCTGTCAGTACAGGAAGGCAAGGCTGGTAT
**
3089670 CTTCA-ATCTGCTTTGCCATCAGTACAGGAAGGCA
1 CTTCAGATCTGCTTTGCTGTCAGTACAGGAAGGCA
3089704 TGATCTGCTA
Statistics
Matches: 133, Mismatches: 27, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
43 2 0.02
44 67 0.50
45 62 0.47
46 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (45 bp):
CTTCAGATCTGCTTTGCTGTCAGTACAGGAAGGCAAGGCTGGTAT
Found at i:3089617 original size:89 final size:89
Alignment explanation
Indices: 3089512--3089717 Score: 288
Period size: 89 Copynumber: 2.3 Consensus size: 89
3089502 CTTCGCTGTT
* * *
3089512 AGTACAGCAAGGCAAGATCTGCTATCTTCAGTCTATTCTGCTGTCAGTACAGGAAGGCAAGGCTG
1 AGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTACTCCGCTGTCAGTACAGGAAGGCAAGGCTG
***
3089577 GTGTCTT-AGATCTACTTTGTTGCC
66 GTGTCTTCA-ATCTACTTTGCCACC
* *
3089601 AGTACAGGAAAGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGGCTG
1 AGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTACTCCGCTGTCAGTACAGGAAGGCAAGGCTG
* * *
3089666 GTTTCTTCAATCTGCTTTGCCATC
66 GTGTCTTCAATCTACTTTGCCACC
*
3089690 AGTACAGGAAGGCATGATCTGCTATCTT
1 AGTACAGGAAGGCAAGATCTGCTATCTT
3089718 TATTGATCTG
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
89 102 0.99
90 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (89 bp):
AGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTACTCCGCTGTCAGTACAGGAAGGCAAGGCTG
GTGTCTTCAATCTACTTTGCCACC
Found at i:3090953 original size:10 final size:10
Alignment explanation
Indices: 3090938--3090982 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
3090928 CTTTGTCTTT
3090938 TTCTTTTTTC
1 TTCTTTTTTC
3090948 TTCTTTTTTC
1 TTCTTTTTTC
*
3090958 TT-TTTTATC
1 TTCTTTTTTC
*
3090967 -T-TTTCTTC
1 TTCTTTTTTC
3090975 TTCTTTTT
1 TTCTTTTT
3090983 CAAAATATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 6 0.21
9 7 0.24
10 16 0.55
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:3090957 original size:17 final size:16
Alignment explanation
Indices: 3090935--3090981 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
3090925 CTCCTTTGTC
*
3090935 TTTTTCTTTTTTCTTCT
1 TTTTTCTTTTTT-ATCT
3090952 TTTTTCTTTTTTATCT
1 TTTTTCTTTTTTATCT
3090968 TTTCTTCTTCTTTT
1 TTT-TTCTT-TTTT
3090982 TCAAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.22
17 17 0.63
18 4 0.15
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTTATCT
Found at i:3095655 original size:15 final size:16
Alignment explanation
Indices: 3095622--3095655 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3095612 TTTATGCAAG
*
3095622 TATGTATATACACGTT
1 TATGTATATACAAGTT
3095638 TATGTATATA-AAGTT
1 TATGTATATACAAGTT
3095653 TAT
1 TAT
3095656 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (16 bp):
TATGTATATACAAGTT
Found at i:3096508 original size:22 final size:22
Alignment explanation
Indices: 3096480--3096524 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3096470 GGCTACTCGG
3096480 CCCTCCCATCGCAACGCACCAA
1 CCCTCCCATCGCAACGCACCAA
3096502 CCCTCCCATCGCAACGCACCAA
1 CCCTCCCATCGCAACGCACCAA
3096524 C
1 C
3096525 GCTTGGCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.56, G:0.09, T:0.09
Consensus pattern (22 bp):
CCCTCCCATCGCAACGCACCAA
Found at i:3112229 original size:58 final size:58
Alignment explanation
Indices: 3112159--3112275 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
3112149 CATCGGGCAG
3112159 AACCCAAGTAGAATAGATCCTGAATTCGTGCATGGATTTATTCACTTGTGACGTTCAT
1 AACCCAAGTAGAATAGATCCTGAATTCGTGCATGGATTTATTCACTTGTGACGTTCAT
3112217 AACCCAAGTAGAATAGATCCTGAATTCGTGCATGGATTTATTCACTTGTGACGTTCAT
1 AACCCAAGTAGAATAGATCCTGAATTCGTGCATGGATTTATTCACTTGTGACGTTCAT
3112275 A
1 A
3112276 GTGTAACATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (58 bp):
AACCCAAGTAGAATAGATCCTGAATTCGTGCATGGATTTATTCACTTGTGACGTTCAT
Found at i:3117743 original size:29 final size:30
Alignment explanation
Indices: 3117682--3117743 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
3117672 TGGTTATAAC
*
3117682 AAGTATCAAAAGCTTATTCATCAAAAACGA
1 AAGTATCAAAAGCTTATTCATCAAAAAAGA
* *
3117712 AAGTATCAAAAG-TTTTTTATCAAAAAAGA
1 AAGTATCAAAAGCTTATTCATCAAAAAAGA
3117741 AAG
1 AAG
3117744 CATAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (30 bp):
AAGTATCAAAAGCTTATTCATCAAAAAAGA
Found at i:3122046 original size:4 final size:4
Alignment explanation
Indices: 3122037--3122063 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3122027 AAGATGAATT
3122037 GATA GATA GATA GATA GATA GATA GAT
1 GATA GATA GATA GATA GATA GATA GAT
3122064 TGAGAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
GATA
Found at i:3124642 original size:20 final size:21
Alignment explanation
Indices: 3124617--3124656 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3124607 GGGTCAGAAG
3124617 AAAAAGTTTAGGAG-GAAAAT
1 AAAAAGTTTAGGAGAGAAAAT
*
3124637 AAAAAGTTTTGGAGAGAAAA
1 AAAAAGTTTAGGAGAGAAAA
3124657 AGTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (21 bp):
AAAAAGTTTAGGAGAGAAAAT
Found at i:3124670 original size:23 final size:23
Alignment explanation
Indices: 3124643--3124686 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3124633 AAATAAAAAG
3124643 TTTTGGAGAGAAAAAGTTTAATA
1 TTTTGGAGAGAAAAAGTTTAATA
*
3124666 TTTTGGAGAGAAAATGTTTAA
1 TTTTGGAGAGAAAAAGTTTAA
3124687 AAAAATTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (23 bp):
TTTTGGAGAGAAAAAGTTTAATA
Found at i:3131214 original size:21 final size:21
Alignment explanation
Indices: 3131189--3131228 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3131179 AATAAATGCT
3131189 AAAACTCTAA-ATTCTAAACCC
1 AAAAC-CTAAGATTCTAAACCC
3131210 AAAACCTAAGATTCTAAAC
1 AAAACCTAAGATTCTAAAC
3131229 TCTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.50, C:0.25, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAACCTAAGATTCTAAACCC
Found at i:3143631 original size:40 final size:40
Alignment explanation
Indices: 3143585--3143762 Score: 214
Period size: 40 Copynumber: 4.5 Consensus size: 40
3143575 GATAATTTTT
* *
3143585 TGTGCCCAGCGCTAGCCGGATAAACTGACAATATCAAATG
1 TGTGCCCAGCACTAGTCGGATAAACTGACAATATCAAATG
** *
3143625 TGTGCCCAGCACTAGTTAGATAAACTAACAATATCAAATG
1 TGTGCCCAGCACTAGTCGGATAAACTGACAATATCAAATG
** * *
3143665 TGTGCCCAGTGCTAGTCGGATAAACCGACGATATCAAATG
1 TGTGCCCAGCACTAGTCGGATAAACTGACAATATCAAATG
* * *
3143705 TGTGCCCAGCACTATTTGGATAAACCT-ACAATATCAAATA
1 TGTGCCCAGCACTAGTCGGATAAA-CTGACAATATCAAATG
* *
3143745 TGTGTCCATCACTAGTCG
1 TGTGCCCAGCACTAGTCG
3143763 AATTAATAAC
Statistics
Matches: 114, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
40 113 0.99
41 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (40 bp):
TGTGCCCAGCACTAGTCGGATAAACTGACAATATCAAATG
Found at i:3143699 original size:80 final size:80
Alignment explanation
Indices: 3143585--3143748 Score: 249
Period size: 80 Copynumber: 2.0 Consensus size: 80
3143575 GATAATTTTT
*
3143585 TGTGCCCAGCGCTAGCCGGATAAACTGACAATATCAAATGTGTGCCCAGCACTAGTTAGATAAA-
1 TGTGCCCAGCGCTAGCCGGATAAACCGACAATATCAAATGTGTGCCCAGCACTAGTTAGATAAAC
*
3143649 CTAACAATATCAAATG
66 CT-ACAATATCAAATA
* * * * *
3143665 TGTGCCCAGTGCTAGTCGGATAAACCGACGATATCAAATGTGTGCCCAGCACTATTTGGATAAAC
1 TGTGCCCAGCGCTAGCCGGATAAACCGACAATATCAAATGTGTGCCCAGCACTAGTTAGATAAAC
3143730 CTACAATATCAAATA
66 CTACAATATCAAATA
3143745 TGTG
1 TGTG
3143749 TCCATCACTA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
80 74 0.97
81 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (80 bp):
TGTGCCCAGCGCTAGCCGGATAAACCGACAATATCAAATGTGTGCCCAGCACTAGTTAGATAAAC
CTACAATATCAAATA
Found at i:3153486 original size:36 final size:35
Alignment explanation
Indices: 3153422--3153496 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
3153412 CGTGTCGAGG
* * * *
3153422 AGTGTTGGGCACTCCATTTGTTGGTTATACCGGCC
1 AGTGCTGGGCACTCCATCTGTCGGTTATACCGACC
*
3153457 AGTGCTGGGCACATCTATCTGTCGGTTATACCGACC
1 AGTGCTGGGCAC-TCCATCTGTCGGTTATACCGACC
3153493 AGTG
1 AGTG
3153497 TAAGGCGCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 11 0.32
36 23 0.68
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (35 bp):
AGTGCTGGGCACTCCATCTGTCGGTTATACCGACC
Found at i:3156601 original size:25 final size:27
Alignment explanation
Indices: 3156571--3156638 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
3156561 AAAATTGGTA
3156571 AGACATTTTCCATTCT-TCTCTAAGCA-
1 AGACATTTTCCATTCTCT-TCTAAGCAC
3156597 A-ACATTTTCCATTCTCTTCTAAGCAGC
1 AGACATTTTCCATTCTCTTCTAAGCA-C
3156624 AGACATTTTCCATTC
1 AGACATTTTCCATTC
3156639 CTCAAAGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 22 0.58
26 2 0.05
27 1 0.03
28 13 0.34
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.38
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAAGCAC
Found at i:3161856 original size:14 final size:14
Alignment explanation
Indices: 3161837--3161864 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3161827 ATAATTTATT
3161837 AATATATATTAATA
1 AATATATATTAATA
3161851 AATATATATTAATA
1 AATATATATTAATA
3161865 TATGTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:3161865 original size:24 final size:25
Alignment explanation
Indices: 3161815--3161867 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
3161805 AATCATTGCA
*
3161815 ATATATGTAAAAATAATTTATTAAT
1 ATATATGTAAAAATAATATATTAAT
3161840 ATATAT-TAATAAAT-ATATATTAAT
1 ATATATGTAA-AAATAATATATTAAT
3161864 ATAT
1 ATAT
3161868 GTAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
ATATATGTAAAAATAATATATTAAT
Found at i:3162375 original size:26 final size:26
Alignment explanation
Indices: 3162339--3162393 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
3162329 ATGTTCATCT
3162339 TTGTTCTTTAACAATCCCTAAAGCAG
1 TTGTTCTTTAACAATCCCTAAAGCAG
3162365 TTGTTCTTTAACAATCCCTAAAGCAG
1 TTGTTCTTTAACAATCCCTAAAGCAG
3162391 TTG
1 TTG
3162394 GCACTACTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (26 bp):
TTGTTCTTTAACAATCCCTAAAGCAG
Found at i:3174679 original size:43 final size:43
Alignment explanation
Indices: 3174610--3174738 Score: 129
Period size: 43 Copynumber: 3.0 Consensus size: 43
3174600 GGCTTGTACA
* * * * * *
3174610 ATGCCAACGTCCCGGACGTTGTCTTACATGTAATCACATATCG
1 ATGCCAACATCCCAGATGTGGTCTTACACGTAAACACATATCG
* *
3174653 ATGTC-ACTGTCCCAGATAG-GGTCTTACACGTAAACACA-AGTCG
1 ATGCCAAC-ATCCCAGAT-GTGGTCTTACACGTAAACACATA-TCG
*
3174696 ATGCCAACATCCCAGATGTGGTCTTACACGAAAACACATATCG
1 ATGCCAACATCCCAGATGTGGTCTTACACGTAAACACATATCG
3174739 GAATCCTATG
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
42 4 0.06
43 63 0.89
44 4 0.06
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCCAACATCCCAGATGTGGTCTTACACGTAAACACATATCG
Found at i:3175523 original size:25 final size:25
Alignment explanation
Indices: 3175495--3175544 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
3175485 TTATTTGTTT
3175495 TATTATAACA-TTATAATATAATATA
1 TATTATAACATTTATAA-ATAATATA
3175520 TATTATAACATTTATAAATAATATA
1 TATTATAACATTTATAAATAATATA
3175545 AAAACTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
TATTATAACATTTATAAATAATATA
Found at i:3175862 original size:149 final size:150
Alignment explanation
Indices: 3175686--3175967 Score: 431
Period size: 149 Copynumber: 1.9 Consensus size: 150
3175676 GCGATTAAGC
* *
3175686 CCTTTTATTTTATCGGACACTTAAACGACGAAATTAAAACACAAAAATTTCACACAAACAAATTC
1 CCTTTTATTTAATCGGACACTCAAACGACGAAATTAAAACACAAAAATTTCACACAAACAAATTC
* * * * *
3175751 ACACATAATAAATACATAAAATAATATTAAAATATTTTTCAAACTCGGATTTGTGGTCCCAAAAC
66 ACACATAATAAACACAGAAAATAATATTAAAATATTTTTCAAACTCAGATTCGCGGTCCCAAAAC
3175816 CACTCTTCTGATTAGGGTCA
131 CACTCTTCTGATTAGGGTCA
* * * **
3175836 CCTTTT-TTTAATCGGACACTCAAACGACGAAATTAAAGCACGAAATTTTCACACAAGTAAATTC
1 CCTTTTATTTAATCGGACACTCAAACGACGAAATTAAAACACAAAAATTTCACACAAACAAATTC
* *
3175900 ACACATAATAAACACAGAAAATAATTTTAAAATATTTTTCTAACTCAGATTCGCGGTCCCAAAAC
66 ACACATAATAAACACAGAAAATAATATTAAAATATTTTTCAAACTCAGATTCGCGGTCCCAAAAC
3175965 CAC
131 CAC
3175968 CATTTCCATT
Statistics
Matches: 118, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
149 112 0.95
150 6 0.05
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.29
Consensus pattern (150 bp):
CCTTTTATTTAATCGGACACTCAAACGACGAAATTAAAACACAAAAATTTCACACAAACAAATTC
ACACATAATAAACACAGAAAATAATATTAAAATATTTTTCAAACTCAGATTCGCGGTCCCAAAAC
CACTCTTCTGATTAGGGTCA
Found at i:3176593 original size:136 final size:136
Alignment explanation
Indices: 3176348--3176611 Score: 438
Period size: 136 Copynumber: 1.9 Consensus size: 136
3176338 TATTTACTCT
3176348 CCCTCATGAAAACATCACATACTTCCTCATATTCTACGTATTCAATCTTGAATACTAATCTTTCA
1 CCCTCATGAAAACATCACATACTTCCTCATATTCTACGTATTCAATCTTGAATACTAATCTTTCA
* * *
3176413 AATGATTATTTAAATGTATTTGCTAAGCATTTATATCACCATTCTTTTGAAAGTCATGAGTAAAG
66 AATGACTATTTAAATGTATTTGCTAAGCATTTATATCACCATTCTTTTAAAAGTCATAAGTAAAG
3176478 GGTTCC
131 GGTTCC
* * * *
3176484 CCCTCATGAAAACATTACATACTTTCTCATATTCTATGTATTCAATCTTGAATACTAGTCTTTCA
1 CCCTCATGAAAACATCACATACTTCCTCATATTCTACGTATTCAATCTTGAATACTAATCTTTCA
* * *
3176549 AATGACTATTTGAATGTATTTGCTAAGCATTTATATCACTATTCTTTTAAAAGTTATAAGTAA
66 AATGACTATTTAAATGTATTTGCTAAGCATTTATATCACCATTCTTTTAAAAGTCATAAGTAA
3176612 GGGGAATTTT
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
136 118 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (136 bp):
CCCTCATGAAAACATCACATACTTCCTCATATTCTACGTATTCAATCTTGAATACTAATCTTTCA
AATGACTATTTAAATGTATTTGCTAAGCATTTATATCACCATTCTTTTAAAAGTCATAAGTAAAG
GGTTCC
Found at i:3178821 original size:25 final size:25
Alignment explanation
Indices: 3178759--3178898 Score: 113
Period size: 25 Copynumber: 5.6 Consensus size: 25
3178749 ATATTTATGT
* * * *
3178759 AAGCTCGTACGAGCTGTA-AACAGG
1 AAGCTCATGCGAGCTGAATAACGGG
* *
3178783 AAGCTCCT-CTGAGCTGAATAGCGGG
1 AAGCTCATGC-GAGCTGAATAACGGG
* *
3178808 AAGCTCATGCGAGCTAAATAATGGG
1 AAGCTCATGCGAGCTGAATAACGGG
* * * *
3178833 AAGCTCATACGAGCTGTATAACAGA
1 AAGCTCATGCGAGCTGAATAACGGG
* * * *
3178858 AAACTCATGCGAGTTGTATAACGAG
1 AAGCTCATGCGAGCTGAATAACGGG
3178883 AAGCTCATGCGAGCTG
1 AAGCTCATGCGAGCTG
3178899 TGATGTGTCC
Statistics
Matches: 91, Mismatches: 22, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
23 1 0.01
24 14 0.15
25 75 0.82
26 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (25 bp):
AAGCTCATGCGAGCTGAATAACGGG
Found at i:3178893 original size:75 final size:74
Alignment explanation
Indices: 3178759--3178897 Score: 181
Period size: 75 Copynumber: 1.9 Consensus size: 74
3178749 ATATTTATGT
* * * * * *
3178759 AAGCTCGTACGAGCTGTAAACAGGAAGCTCCTCTGAGCTGAATAGCGGGAAGCTCATGCGAGCTA
1 AAGCTCATACGAGCTGTAAACAGAAAACTCATCTGAGCTGAATAACGAGAAGCTCATGCGAGCTA
3178824 AATAATGGG
66 AATAATGGG
* *
3178833 AAGCTCATACGAGCTGTATAACAGAAAACTCATGC-GAGTTGTATAACGAGAAGCTCATGCGAGC
1 AAGCTCATACGAGCTGTA-AACAGAAAACTCAT-CTGAGCTGAATAACGAGAAGCTCATGCGAGC
3178897 T
64 T
3178898 GTGATGTGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
74 17 0.31
75 37 0.67
76 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (74 bp):
AAGCTCATACGAGCTGTAAACAGAAAACTCATCTGAGCTGAATAACGAGAAGCTCATGCGAGCTA
AATAATGGG
Found at i:3179637 original size:98 final size:98
Alignment explanation
Indices: 3179465--3179660 Score: 365
Period size: 98 Copynumber: 2.0 Consensus size: 98
3179455 ACAATAAAAC
3179465 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCC
*
3179530 TTTAGAATCCCAAACTCAGAATATTTCCTTTAT
66 TTTAAAATCCCAAACTCAGAATATTTCCTTTAT
*
3179563 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCC
*
3179628 TTTAAAATCCCAAACTCGGAATATTTCCTTTAT
66 TTTAAAATCCCAAACTCAGAATATTTCCTTTAT
3179661 GATTTTTTTA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATCCC
TTTAAAATCCCAAACTCAGAATATTTCCTTTAT
Found at i:3180118 original size:12 final size:12
Alignment explanation
Indices: 3180098--3180137 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3180088 NNNNNNNNNG
*
3180098 TATACATACATA
1 TATATATACATA
3180110 TATATATACA-A
1 TATATATACATA
3180121 -ATATATACATA
1 TATATATACATA
3180132 TATATA
1 TATATA
3180138 GTTTATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 9 0.36
11 2 0.08
12 14 0.56
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (12 bp):
TATATATACATA
Found at i:3180175 original size:19 final size:17
Alignment explanation
Indices: 3180144--3180183 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
3180134 TATAGTTTAT
3180144 AAAAAAAACTACATATAA
1 AAAAAAAACTACAT-TAA
*
3180162 AAAAAATAATTACATTAA
1 AAAAAA-AACTACATTAA
3180180 AAAA
1 AAAA
3180184 TATGCGTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAAAAAACTACATTAA
Found at i:3180219 original size:17 final size:15
Alignment explanation
Indices: 3180197--3180231 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
3180187 GCGTATGTAT
3180197 ATATATATGTATAAAAA
1 ATATATAT-TA-AAAAA
3180214 ATATATATTAAAAAA
1 ATATATATTAAAAAA
3180229 ATA
1 ATA
3180232 ATTAAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 2 0.11
17 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATATATATTAAAAAA
Found at i:3180263 original size:17 final size:17
Alignment explanation
Indices: 3180222--3180266 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3180212 AAATATATAT
3180222 TAAA-AAAATAATTAAA
1 TAAAGAAAATAATTAAA
*
3180238 T-ATGAAAAATAATTAAA
1 TAAAG-AAAATAATTAAA
3180255 TAAAGAAAATAA
1 TAAAGAAAATAA
3180267 AAAAATGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 20 0.83
18 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (17 bp):
TAAAGAAAATAATTAAA
Found at i:3184149 original size:49 final size:50
Alignment explanation
Indices: 3184077--3184203 Score: 168
Period size: 49 Copynumber: 2.6 Consensus size: 50
3184067 AACTCCTCCG
* *
3184077 AGCTGAATAACGGGAAGCTCATGCGAGCCAAATAAC-GAGAAGCTCATG-C
1 AGCTGTATAACGGGAAGCTCATGCGAGCCAAATAACGGA-AAGATCATGTC
* * *
3184126 AGCTGTATAACGGGAAGCTCATGCGAGCTATATAACGGAAAGATCATGTG
1 AGCTGTATAACGGGAAGCTCATGCGAGCCAAATAACGGAAAGATCATGTC
* *
3184176 AGCTGTATAACGAGAAGCTCATACGAGC
1 AGCTGTATAACGGGAAGCTCATGCGAGC
3184204 TGTGGTGTGT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
49 41 0.59
50 28 0.41
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (50 bp):
AGCTGTATAACGGGAAGCTCATGCGAGCCAAATAACGGAAAGATCATGTC
Found at i:3184206 original size:25 final size:25
Alignment explanation
Indices: 3184075--3184206 Score: 151
Period size: 25 Copynumber: 5.3 Consensus size: 25
3184065 GAAACTCCTC
* *
3184075 CGAGCTGAATAACGGGAAGCTCATG
1 CGAGCTGTATAACGAGAAGCTCATG
***
3184100 CGAGCCAAATAACGAGAAGCTCATG
1 CGAGCTGTATAACGAGAAGCTCATG
*
3184125 C-AGCTGTATAACGGGAAGCTCATG
1 CGAGCTGTATAACGAGAAGCTCATG
* *
3184149 CGAGCTATATAACG-GAAAGATCATG
1 CGAGCTGTATAACGAG-AAGCTCATG
* *
3184174 TGAGCTGTATAACGAGAAGCTCATA
1 CGAGCTGTATAACGAGAAGCTCATG
3184199 CGAGCTGT
1 CGAGCTGT
3184207 GGTGTGTCCA
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
24 21 0.23
25 68 0.76
26 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (25 bp):
CGAGCTGTATAACGAGAAGCTCATG
Found at i:3189721 original size:12 final size:12
Alignment explanation
Indices: 3189706--3189732 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3189696 TTACAAACTG
3189706 TTTTATTTATTA
1 TTTTATTTATTA
3189718 TTTTATTTATTA
1 TTTTATTTATTA
3189730 TTT
1 TTT
3189733 CTTTAACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:3189818 original size:18 final size:17
Alignment explanation
Indices: 3189791--3189830 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
3189781 TATACATTTA
3189791 TATTTTATTATCATTGT
1 TATTTTATTATCATTGT
*
3189808 TATTATTATTATCATTTT
1 TATT-TTATTATCATTGT
3189826 TATTT
1 TATTT
3189831 ATTTATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (17 bp):
TATTTTATTATCATTGT
Found at i:3193358 original size:42 final size:43
Alignment explanation
Indices: 3193294--3193385 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 43
3193284 TGTAAGACCT
* * *
3193294 CGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTA
1 CGTGTAAAACCATGTCTCGGACAGTGGCATCGATATATGATTA
* *
3193336 CGTGTAAAACCCTGTCTCGGACAGTGGCATCGATATTTGATTA
1 CGTGTAAAACCATGTCTCGGACAGTGGCATCGATATATGATTA
*
3193379 CATGTAA
1 CGTGTAA
3193386 GAGCTCGTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 28 0.65
43 15 0.35
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (43 bp):
CGTGTAAAACCATGTCTCGGACAGTGGCATCGATATATGATTA
Found at i:3193407 original size:43 final size:41
Alignment explanation
Indices: 3193296--3193408 Score: 111
Period size: 43 Copynumber: 2.7 Consensus size: 41
3193286 TAAGACCTCG
* * *
3193296 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTACG
1 TGTAAAACCCTGTCT-GGACATTGGCATCGTATATGATTACA
* *
3193338 TGTAAAACCCTGTCTCGGACAGTGGCATCGATATTTGATTACA
1 TGTAAAACCCTGTCT-GGACATTGGCATCG-TATATGATTACA
* *
3193381 TGTAAGA-GCTCGTCTGAGACATTGGCAT
1 TGTAAAACCCT-GTCTG-GACATTGGCAT
3193409 TGTACGAGCT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 29 0.49
43 30 0.51
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (41 bp):
TGTAAAACCCTGTCTGGACATTGGCATCGTATATGATTACA
Found at i:3203386 original size:44 final size:44
Alignment explanation
Indices: 3203323--3203588 Score: 255
Period size: 44 Copynumber: 6.0 Consensus size: 44
3203313 TCGTGATGAG
* * *
3203323 TCTTATCTCCCTGAAGTTGCAATAGAGTAGATTAAAGCCACAAA
1 TCTTATCTCCCTAAAGTTGCAATGGAGTAGATTAAAGCTACAAA
* * *
3203367 TCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGTTACAAA
1 TCTTATCTCCCTAAAGTTGCAATGGAGTAGATTAAAGCTACAAA
* * * * * ** *
3203411 TCTTATTTCCCTGAAGTTGCAGTAGAGTATATTGGAGATACAAA
1 TCTTATCTCCCTAAAGTTGCAATGGAGTAGATTAAAGCTACAAA
* * * * * * * *
3203455 TATTGTCTCCTTGAAGTTGCAGTGGAGCATATTAAAGCCACAAA
1 TCTTATCTCCCTAAAGTTGCAATGGAGTAGATTAAAGCTACAAA
* *
3203499 TCTTATCTCCTTGAAA-TTGCAATGGAGTAGATTAAAACTACAAA
1 TCTTATCTCCCT-AAAGTTGCAATGGAGTAGATTAAAGCTACAAA
* ** *
3203543 TCTTATTTCCCTGAAAGTTGCAATGGAACAGATTAAAGTTACAAA
1 TCTTATCTCCCT-AAAGTTGCAATGGAGTAGATTAAAGCTACAAA
3203588 T
1 T
3203589 TACAAATCTT
Statistics
Matches: 184, Mismatches: 36, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
44 157 0.85
45 27 0.15
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (44 bp):
TCTTATCTCCCTAAAGTTGCAATGGAGTAGATTAAAGCTACAAA
Found at i:3203454 original size:88 final size:87
Alignment explanation
Indices: 3203323--3203588 Score: 298
Period size: 88 Copynumber: 3.0 Consensus size: 87
3203313 TCGTGATGAG
**
3203323 TCTTATCTCCCTGAAGTTGCAATAGAGTAGATTAAAGCCACAAATCTTATCTCCCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAATAGAGTAGATT-AAGATACAAATCTTATCTCCCTAAAGTTGCA
* *
3203388 GTGGAGTAGATTGAAGTTACAAA
65 GTGGAGCAGATTAAAGTTACAAA
* * * * * * * *
3203411 TCTTATTTCCCTGAAGTTGCAGTAGAGTATATTGGAGATACAAATATTGTCTCCTTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAATAGAGTAGATT-AAGATACAAATCTTATCTCCCTAAAGTTGCA
* **
3203476 GTGGAGCATATTAAAGCCACAAA
65 GTGGAGCAGATTAAAGTTACAAA
* * * * *
3203499 TCTTATCTCCTTGAAATTGCAATGGAGTAGATTAAAACTACAAATCTTATTTCCCTGAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAATAGAGTAGATTAAGA-TACAAATCTTATCTCCCT-AAAGTTGC
* *
3203564 AATGGAACAGATTAAAGTTACAAA
64 AGTGGAGCAGATTAAAGTTACAAA
3203588 T
1 T
3203589 TACAAATCTT
Statistics
Matches: 142, Mismatches: 34, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
87 2 0.01
88 113 0.80
89 27 0.19
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (87 bp):
TCTTATCTCCCTGAAGTTGCAATAGAGTAGATTAAGATACAAATCTTATCTCCCTAAAGTTGCAG
TGGAGCAGATTAAAGTTACAAA
Found at i:3203816 original size:44 final size:44
Alignment explanation
Indices: 3203744--3203860 Score: 135
Period size: 44 Copynumber: 2.7 Consensus size: 44
3203734 TACAAATCTT
* * * * *
3203744 ATCTCCTTGAAGTTGCAATGAAGTAGATTAAAGATACGAGTCTC
1 ATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGATACGAGTCTA
* *
3203788 ATCTTCCTAAAGTTGCAGTGGAGTAGATTAAAGCTACGAGTCTA
1 ATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGATACGAGTCTA
* ** *
3203832 ATCTCCCTGAAGTTAAAGTAGAGTAGATT
1 ATCTCCCTAAAGTTGCAGTGGAGTAGATT
3203861 GAAGCAACCC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (44 bp):
ATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGATACGAGTCTA
Found at i:3203874 original size:33 final size:33
Alignment explanation
Indices: 3203836--3203901 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3203826 AGTCTAATCT
3203836 CCCTGAAGTTAAAGTAGAGTAGATTGAAGCAAC
1 CCCTGAAGTTAAAGTAGAGTAGATTGAAGCAAC
**
3203869 CCCTGAAGTTGCAGTAGAGTAGATTGAAGCAAC
1 CCCTGAAGTTAAAGTAGAGTAGATTGAAGCAAC
3203902 AAATCATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (33 bp):
CCCTGAAGTTAAAGTAGAGTAGATTGAAGCAAC
Found at i:3205136 original size:6 final size:6
Alignment explanation
Indices: 3205125--3205163 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
3205115 CATTGTTATC
* *
3205125 ATTGTT ATTGTT ATTGTT ATTGTT ATTATC ATTGTT ATT
1 ATTGTT ATTGTT ATTGTT ATTGTT ATTGTT ATTGTT ATT
3205164 TATTTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.21, C:0.03, G:0.13, T:0.64
Consensus pattern (6 bp):
ATTGTT
Found at i:3205146 original size:18 final size:18
Alignment explanation
Indices: 3205104--3205163 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
3205094 TATACTTTCA
3205104 TATT-TTATTATCATTGTT
1 TATTGTTATTATCATTG-T
* *
3205122 ATCATTGTTATTGTTATTGT
1 -T-ATTGTTATTATCATTGT
3205142 TATTGTTATTATCATTGT
1 TATTGTTATTATCATTGT
3205160 TATT
1 TATT
3205164 TATTTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 19 0.54
19 2 0.06
20 4 0.11
21 10 0.29
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (18 bp):
TATTGTTATTATCATTGT
Found at i:3207000 original size:19 final size:19
Alignment explanation
Indices: 3206978--3207043 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
3206968 TTCTTTTCTA
3206978 AATTTTTTAATAATTTTTG
1 AATTTTTTAATAATTTTTG
* **
3206997 AATTTTTAAATAA-TTTAA
1 AATTTTTTAATAATTTTTG
*
3207015 ATATTTTTTTATAATTTTTG
1 A-ATTTTTTAATAATTTTTG
*
3207035 AAATTTTTA
1 AATTTTTTA
3207044 CAAAATTTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
18 4 0.11
19 28 0.78
20 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
AATTTTTTAATAATTTTTG
Found at i:3211102 original size:94 final size:94
Alignment explanation
Indices: 3211025--3211210 Score: 354
Period size: 94 Copynumber: 2.0 Consensus size: 94
3211015 TAGATATATT
*
3211025 ATACAATAGCTTAAAAGGTTTTATTAAAAAATGAAAAATATTGATAAAAATTGAAAGAGAAAAAA
1 ATACAAT-GCTTAAAAGGTTTAATTAAAAAATGAAAAATATTGATAAAAATTGAAAGAGAAAAAA
3211090 AATGAAATTAAAATGGATAGAAACAAAATA
65 AATGAAATTAAAATGGATAGAAACAAAATA
3211120 ATACAATGCTTAAAAGGTTTAATTAAAAAATGAAAAATATTGATAAAAATTGAAAGAGAAAAAAA
1 ATACAATGCTTAAAAGGTTTAATTAAAAAATGAAAAATATTGATAAAAATTGAAAGAGAAAAAAA
3211185 ATGAAATTAAAATGGATAGAAACAAA
66 ATGAAATTAAAATGGATAGAAACAAA
3211211 CAAAAAAGAG
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 83 0.92
95 7 0.08
ACGTcount: A:0.60, C:0.03, G:0.13, T:0.24
Consensus pattern (94 bp):
ATACAATGCTTAAAAGGTTTAATTAAAAAATGAAAAATATTGATAAAAATTGAAAGAGAAAAAAA
ATGAAATTAAAATGGATAGAAACAAAATA
Found at i:3212170 original size:21 final size:22
Alignment explanation
Indices: 3212130--3212170 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3212120 TTTACTAAAT
*
3212130 TAAATATATATATTTCAAATAG
1 TAAATATATATATTTAAAATAG
*
3212152 TAAAT-TATATGTTTAAAAT
1 TAAATATATATATTTAAAAT
3212171 GCATTATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
TAAATATATATATTTAAAATAG
Found at i:3215333 original size:38 final size:38
Alignment explanation
Indices: 3215282--3215354 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
3215272 AACTCTCATA
* *
3215282 CTTTAAGAAAATATCTACCTACTTTTTTAAGGTTTATG
1 CTTTAAGAAAATATCTACCTACCTTTTCAAGGTTTATG
**
3215320 CTTTAA-ATAAATATCTATTTACCTTTTCAAGGTTT
1 CTTTAAGA-AAATATCTACCTACCTTTTCAAGGTTT
3215355 GATTTTAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 1 0.03
38 29 0.97
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.47
Consensus pattern (38 bp):
CTTTAAGAAAATATCTACCTACCTTTTCAAGGTTTATG
Found at i:3217445 original size:10 final size:10
Alignment explanation
Indices: 3217430--3217477 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
3217420 GAAAGTTGTA
*
3217430 TATAAAAATT
1 TATAAAAAGT
3217440 TATAAAAAGT
1 TATAAAAAGT
*
3217450 TATTAAAAG-
1 TATAAAAAGT
3217459 TATTAAAAAGT
1 TA-TAAAAAGT
3217470 TATAAAAA
1 TATAAAAA
3217478 TAATAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (10 bp):
TATAAAAAGT
Done.