Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 13 of 770
Found at i:3444846 original size:21 final size:21
Alignment explanation
Indices: 3444818--3444866 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3444808 TTTTATTCGT
3444818 AAAAAAATTCAAAAAAAAAAG
1 AAAAAAATTCAAAAAAAAAAG
* ** *
3444839 AGAAAAATTTGAAAACAAAAG
1 AAAAAAATTCAAAAAAAAAAG
3444860 AAAAAAA
1 AAAAAAA
3444867 AGAACAAGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (21 bp):
AAAAAAATTCAAAAAAAAAAG
Found at i:3446171 original size:12 final size:11
Alignment explanation
Indices: 3446152--3446185 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
3446142 TGTTTTTCTC
3446152 TCTTTTTTTTA
1 TCTTTTTTTTA
3446163 TCTTATTTTTTA
1 TCTT-TTTTTTA
3446175 TCCTTTTTTTT
1 T-CTTTTTTTT
3446186 TAAAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 14 0.67
13 3 0.14
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTTTTTTTA
Found at i:3446171 original size:13 final size:13
Alignment explanation
Indices: 3446154--3446187 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3446144 TTTTTCTCTC
3446154 TTTTTTTTAT-CT
1 TTTTTTTTATCCT
*
3446166 TATTTTTTATCCT
1 TTTTTTTTATCCT
3446179 TTTTTTTTA
1 TTTTTTTTA
3446188 AAAAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTATCCT
Found at i:3446959 original size:24 final size:24
Alignment explanation
Indices: 3446927--3446972 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3446917 TTTATCATTT
3446927 ATTTAAAATTGATTTATGGTATTC
1 ATTTAAAATTGATTTATGGTATTC
* * *
3446951 ATTTCAAATTGTTTTATTGTAT
1 ATTTAAAATTGATTTATGGTAT
3446973 ATTATTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (24 bp):
ATTTAAAATTGATTTATGGTATTC
Found at i:3447075 original size:24 final size:24
Alignment explanation
Indices: 3447030--3447295 Score: 169
Period size: 26 Copynumber: 10.4 Consensus size: 24
3447020 TTATTACATA
3447030 TTATTTTAAATTATTTTATATATTAT
1 TTATTTTAAA-T-TTTTATATATTAT
**
3447056 TTATTTTACGTTTTTATATATATTAT
1 TTATTTTA-AATTTT-TATATATTAT
* *
3447082 TTATTTTAAAATTTTACATATTAT
1 TTATTTTAAATTTTTATATATTAT
*
3447106 ATATTTTAAATTTTTATATATGTTAT
1 TTATTTTAAATTTTTATATA--TTAT
* * * *
3447132 GTAGTTCAAACTATTTTATATGTTAT
1 TTATTTTAAA-T-TTTTATATATTAT
*
3447158 TTATTTTAAAATTCTTTTATATATTGT
1 TTATTTT-AAA-T-TTTTATATATTAT
*
3447185 TTATTTCAAACTGTTTTAT-TATTAT
1 TTATTTTAAA-T-TTTTATATATTAT
* *
3447210 TTACTTTAATTTTTTTATATATATTAT
1 TTATTTTAA--ATTTT-TATATATTAT
* * *
3447237 TTATTTGAGATTTTT-T-TTTTAT
1 TTATTTTAAATTTTTATATATTAT
* * *
3447259 TCATTTTGAATTGTTCTTATACATTAT
1 TTATTTT-AAAT-TT-TTATATATTAT
3447286 TTATTTTAAA
1 TTATTTTAAA
3447296 CCATTATTTA
Statistics
Matches: 184, Mismatches: 40, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
22 10 0.05
23 3 0.02
24 29 0.16
25 27 0.15
26 63 0.34
27 44 0.24
28 8 0.04
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
TTATTTTAAATTTTTATATATTAT
Found at i:3447163 original size:52 final size:52
Alignment explanation
Indices: 3447030--3447242 Score: 236
Period size: 52 Copynumber: 4.1 Consensus size: 52
3447020 TTATTACATA
* * **
3447030 TTATTTTAAATTATTTTATATATTATTTATTTTACGTTTTTATATATATTAT
1 TTATTTCAAACTATTTTATATATTATTTATTTTAAATTTTTATATATATTAT
* * * *
3447082 TTATTTTAAA--ATTTTACATATTATATATTTTAAATTTTTATATATGTTAT
1 TTATTTCAAACTATTTTATATATTATTTATTTTAAATTTTTATATATATTAT
* * * *
3447132 GTAGTTCAAACTATTTTATATGTTATTTATTTTAAAATTCTTT-TATATATTGT
1 TTATTTCAAACTATTTTATATATTATTTATTTT-AAATT-TTTATATATATTAT
* * *
3447185 TTATTTCAAACTGTTTTAT-TATTATTTACTTTAATTTTTTTATATATATTAT
1 TTATTTCAAACTATTTTATATATTATTTATTTTAA-ATTTTTATATATATTAT
3447237 TTATTT
1 TTATTT
3447243 GAGATTTTTT
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
50 42 0.31
51 5 0.04
52 56 0.41
53 29 0.21
54 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (52 bp):
TTATTTCAAACTATTTTATATATTATTTATTTTAAATTTTTATATATATTAT
Found at i:3448523 original size:12 final size:12
Alignment explanation
Indices: 3448506--3448530 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3448496 TTTTTTTTTG
3448506 AAAAAAACAAAA
1 AAAAAAACAAAA
3448518 AAAAAAACAAAA
1 AAAAAAACAAAA
3448530 A
1 A
3448531 GGGGAAATAA
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:3448766 original size:11 final size:11
Alignment explanation
Indices: 3448750--3448774 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3448740 TATAACAAAT
3448750 AATAAAAGAAA
1 AATAAAAGAAA
3448761 AATAAAAGAAA
1 AATAAAAGAAA
3448772 AAT
1 AAT
3448775 TTTGAAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (11 bp):
AATAAAAGAAA
Found at i:3448922 original size:23 final size:22
Alignment explanation
Indices: 3448889--3448932 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3448879 CCGGAGCTCC
3448889 CTCTCCCTCTTCCCTTTCTCTT
1 CTCTCCCTCTTCCCTTTCTCTT
**
3448911 CTCTCCCCTCTTCTTTTTCTCT
1 CTCT-CCCTCTTCCCTTTCTCT
3448933 CTTCCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (22 bp):
CTCTCCCTCTTCCCTTTCTCTT
Found at i:3448942 original size:18 final size:18
Alignment explanation
Indices: 3448895--3448945 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
3448885 CTCCCTCTCC
3448895 CTCTTCCCTTTC-TCTTCT
1 CTCTT-CCTTTCTTCTTCT
* *
3448913 CTC-CCCTCTTCTTTTTCT
1 CTCTTCCT-TTCTTCTTCT
3448931 CTCTTCCTTTCTTCT
1 CTCTTCCTTTCTTCT
3448946 GCTGCCAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 17 0.65
19 3 0.12
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (18 bp):
CTCTTCCTTTCTTCTTCT
Found at i:3449619 original size:2 final size:2
Alignment explanation
Indices: 3449612--3449652 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3449602 ATTTTTGTTC
*
3449612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3449653 TTCCATACGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3462216 original size:74 final size:71
Alignment explanation
Indices: 3462016--3462366 Score: 350
Period size: 69 Copynumber: 4.9 Consensus size: 71
3462006 TTTGGGTACT
* * * **
3462016 CTGAGGTATCTTTAATTCATGTTTTCAAAAATCAATTCATATTGCGAGAAATGAGTTGAGCCTCA
1 CTGAGGTATTTTTAATTTATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
3462081 GGTCACACG
65 GGT--CACG
* ** **
3462090 CTGAGGTATTTTTAGTTTATGTTTCAAAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTC
1 CTGAGGTATTTTTAATTTATGTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
3462155 AGGTCACG
64 AGGTCACG
* * *
3462163 CTGAGGTGTTTTTAATTCCTGTTGTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTT-AGCCT
1 CTGAGGTATTTTTAATT--T-ATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* *
3462227 CAAGACACG
63 CAGGTCACG
* * * *
3462236 TTGAGGTAATTTCAATTTATG-TTCCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G
1 CTGAGGTATTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
* *
3462299 GGCACA
66 GTCACG
* ** * * *
3462305 CTGAGGTATTTTTAGTTTATGTTT-AGAAAATTGACTCATCTTGCGAAAGGTGAGTTAAGCCT
1 CTGAGGTATTTTTAATTTATGTTTCA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
3462367 TTTAATTTCT
Statistics
Matches: 230, Mismatches: 39, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
69 53 0.23
70 41 0.18
71 1 0.00
73 48 0.21
74 45 0.20
75 36 0.16
76 6 0.03
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (71 bp):
CTGAGGTATTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
GTCACG
Found at i:3462595 original size:88 final size:87
Alignment explanation
Indices: 3462385--3462598 Score: 245
Period size: 87 Copynumber: 2.4 Consensus size: 87
3462375 CTGTTTTTCA
* * *
3462385 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTGGCTTACGTGCTGAGCTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTTACATGCTGAGCTATTTTCAAATT
* *
3462450 CTGTTTTCAAATTCCGTTCGTC
66 CTGTTTTCAAATTACGTTCCTC
* * *
3462472 AAAATCAACTCATATTGCAATAGATGAGTTGAGCCTCGG-TTCACATG-TCGAGGTATTTTCAAA
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTT-ACATGCT-GAGCTATTTTCAAA
* * *
3462535 TTCTGTTTTTAATTTTTACTTTCCT-
64 TTCTGTTTTCAA--ATTACGTTCCTC
* **
3462560 AAAATCAACTCATATTGCGAGAGGTGAGTCAAGCCTCGG
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGG
3462599 GGCACGCTGA
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
86 3 0.03
87 63 0.59
88 34 0.32
89 7 0.07
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (87 bp):
AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTTACATGCTGAGCTATTTTCAAATT
CTGTTTTCAAATTACGTTCCTC
Found at i:3463711 original size:12 final size:12
Alignment explanation
Indices: 3463694--3463719 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3463684 TTTTTTTTTG
3463694 AAAAAAAACAAA
1 AAAAAAAACAAA
3463706 AAAAAAAACAAA
1 AAAAAAAACAAA
3463718 AA
1 AA
3463720 GGGGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:3467087 original size:40 final size:40
Alignment explanation
Indices: 3467042--3467209 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
3467032 CGGAATACAA
3467042 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
3467082 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
3467122 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
3467162 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
3467202 CCGGATAT
1 CCGGATAT
3467210 CATTCAATTG
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
39 3 0.03
40 102 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:3475036 original size:40 final size:40
Alignment explanation
Indices: 3474991--3475158 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
3474981 CGGAATACAA
3474991 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
3475031 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
3475071 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
3475111 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
3475151 CCGGATAT
1 CCGGATAT
3475159 CATTCAATTG
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
39 3 0.03
40 102 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:3480038 original size:44 final size:45
Alignment explanation
Indices: 3479924--3480038 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 45
3479914 CTTCGATCTA
* * * * *
3479924 CTCCGCTGGAACTTAAAGGAGATAAGAATTGGTAATTTCAACCTG
1 CTCCACTGCAACTTCAAGAAGATAAGAATTGGTAACTTCAACCTG
** ** *
3479969 CTCCACTGCAACTTCTGGGAA-ATAAG-ATTGGTGGCTTCAATCTG
1 CTCCACTGCAACTTC-AAGAAGATAAGAATTGGTAACTTCAACCTG
*
3480013 CTTCACTGCAACTTCAAGAAGATAAG
1 CTCCACTGCAACTTCAAGAAGATAAG
3480039 TCCGCCATAA
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
43 3 0.05
44 33 0.60
45 17 0.31
46 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (45 bp):
CTCCACTGCAACTTCAAGAAGATAAGAATTGGTAACTTCAACCTG
Found at i:3480168 original size:43 final size:45
Alignment explanation
Indices: 3480121--3480224 Score: 131
Period size: 45 Copynumber: 2.4 Consensus size: 45
3480111 CCGCTACAAC
* *
3480121 TTCAGGGAGATAAGG-CAAGT-ACTTCAACCTGCTCCACTGCTAT
1 TTCAGGGAGATAAGGTCAAGTGACTTCAACCTGCTCAACTGCAAT
** * **
3480164 TTCAGGGAGATAAGGTTTAGTGGCTTCAATTTGCTCAACTGCAAT
1 TTCAGGGAGATAAGGTCAAGTGACTTCAACCTGCTCAACTGCAAT
3480209 TTCAGGGAGATAAGGT
1 TTCAGGGAGATAAGGT
3480225 TTGCCATTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
43 15 0.29
44 3 0.06
45 34 0.65
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (45 bp):
TTCAGGGAGATAAGGTCAAGTGACTTCAACCTGCTCAACTGCAAT
Found at i:3506635 original size:15 final size:16
Alignment explanation
Indices: 3506615--3506644 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3506605 TAACTCACAA
3506615 TTTTATTTT-TTTTTG
1 TTTTATTTTGTTTTTG
3506630 TTTTATTTTGTTTTT
1 TTTTATTTTGTTTTT
3506645 CCTCTCCTCT
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:0.07, C:0.00, G:0.07, T:0.87
Consensus pattern (16 bp):
TTTTATTTTGTTTTTG
Found at i:3512001 original size:30 final size:33
Alignment explanation
Indices: 3511967--3512032 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 33
3511957 TGGCCCTTAA
3511967 TATTTGTATTTT-TATTTA-TTTA-TTTATTT-T
1 TATTTGTATTTTAT-TTTATTTTATTTTATTTAT
*
3511997 TATTTTTATTTTATTTTATTTTATTTTATTTAT
1 TATTTGTATTTTATTTTATTTTATTTTATTTAT
3512030 TAT
1 TAT
3512033 GCTTATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 15 0.48
31 5 0.16
32 7 0.23
33 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (33 bp):
TATTTGTATTTTATTTTATTTTATTTTATTTAT
Found at i:3512008 original size:5 final size:5
Alignment explanation
Indices: 3511967--3512027 Score: 65
Period size: 5 Copynumber: 12.0 Consensus size: 5
3511957 TGGCCCTTAA
3511967 TATTT GTATTT T-TATT TA-TT TA-TT TATTTT TATTTT TATTT TATTT
1 TATTT -TATTT TAT-TT TATTT TATTT TA-TTT TA-TTT TATTT TATTT
3512013 TATTT TATTT TATTT
1 TATTT TATTT TATTT
3512028 ATTATGCTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
4 9 0.18
5 27 0.53
6 15 0.29
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:3514284 original size:30 final size:30
Alignment explanation
Indices: 3514250--3514310 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
3514240 TTCCCGAGCC
3514250 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
3514280 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
3514310 T
1 T
3514311 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:3514925 original size:64 final size:64
Alignment explanation
Indices: 3514845--3515016 Score: 186
Period size: 67 Copynumber: 2.7 Consensus size: 64
3514835 AGACATTATG
* * *
3514845 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAAAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAAAGAGCTACGAGATAA
** * * * *
3514909 ATGTAGCTAGGTCGCATGCATGGTACCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAAAGAGCTACGAGAT
3514974 AA
63 AA
* * *
3514976 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGT
3515017 GTGCAAGAGA
Statistics
Matches: 87, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
63 9 0.10
64 25 0.29
66 21 0.24
67 30 0.34
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAAAGAGCTACGAGATAA
Found at i:3517067 original size:16 final size:16
Alignment explanation
Indices: 3517046--3517077 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3517036 GACTATTAAG
3517046 TTTATTTATTTTTATT
1 TTTATTTATTTTTATT
*
3517062 TTTATTTCTTTTTATT
1 TTTATTTATTTTTATT
3517078 ATTTTCTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTATTTATTTTTATT
Found at i:3520322 original size:28 final size:30
Alignment explanation
Indices: 3520290--3520345 Score: 98
Period size: 28 Copynumber: 1.9 Consensus size: 30
3520280 AGACTGGCAC
3520290 ATGGGCATGTGTCCAG-CC-TGTGGCTCAT
1 ATGGGCATGTGTCCAGCCCGTGTGGCTCAT
3520318 ATGGGCATGTGTCCAGCCCGTGTGGCTC
1 ATGGGCATGTGTCCAGCCCGTGTGGCTC
3520346 TTAAAATCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 16 0.62
29 2 0.08
30 8 0.31
ACGTcount: A:0.12, C:0.27, G:0.34, T:0.27
Consensus pattern (30 bp):
ATGGGCATGTGTCCAGCCCGTGTGGCTCAT
Found at i:3520961 original size:39 final size:39
Alignment explanation
Indices: 3520918--3521046 Score: 129
Period size: 39 Copynumber: 3.4 Consensus size: 39
3520908 ATACACATCT
* * *
3520918 TGTGCCAGATATACGCTTTGTGCACCAGGATACACTTTG
1 TGTGCCAGATATGCGCTTCGTGCACCAGGATGCACTTTG
* * * * *
3520957 TGTGCTAG-TATGCACTTCGTGCGCC-GAGATGCACATCG
1 TGTGCCAGATATGCGCTTCGTGCACCAG-GATGCACTTTG
* * *
3520995 TGTTCCAGATACGCGCTTCGTGCACCAGGATGTACTTTG
1 TGTGCCAGATATGCGCTTCGTGCACCAGGATGCACTTTG
3521034 TGTGCCAG-TATGC
1 TGTGCCAGATATGC
3521047 ATTTTTTGTG
Statistics
Matches: 69, Mismatches: 18, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
37 1 0.01
38 31 0.45
39 36 0.52
40 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.29
Consensus pattern (39 bp):
TGTGCCAGATATGCGCTTCGTGCACCAGGATGCACTTTG
Found at i:3521018 original size:77 final size:77
Alignment explanation
Indices: 3520889--3521047 Score: 210
Period size: 77 Copynumber: 2.1 Consensus size: 77
3520879 ATCCGTCACA
** * * *
3520889 ATGCACTTCGTGTTCCAAGATACACATCTTGTGCCAGATATACGCTTTGTGCACCAGGATACACT
1 ATGCACTTCGTGCGCCAAGATACACATCGTGTGCCAGATACACGCTTCGTGCACCAGGATACACT
*
3520954 TTGTGTGCTAGT
66 TTGTGTGCCAGT
* * * * **
3520966 ATGCACTTCGTGCGCCGAGATGCACATCGTGTTCCAGATACGCGCTTCGTGCACCAGGATGTACT
1 ATGCACTTCGTGCGCCAAGATACACATCGTGTGCCAGATACACGCTTCGTGCACCAGGATACACT
3521031 TTGTGTGCCAGT
66 TTGTGTGCCAGT
3521043 ATGCA
1 ATGCA
3521048 TTTTTTGTGC
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (77 bp):
ATGCACTTCGTGCGCCAAGATACACATCGTGTGCCAGATACACGCTTCGTGCACCAGGATACACT
TTGTGTGCCAGT
Found at i:3521056 original size:19 final size:19
Alignment explanation
Indices: 3521019--3521070 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
3521009 GCTTCGTGCA
* * *
3521019 CCAGGATGTACTTTGTGTG
1 CCAGGATGCATTTTTTGTG
*
3521038 CCAGTATGCATTTTTTGTG
1 CCAGGATGCATTTTTTGTG
*
3521057 CTAGGATGCATTTT
1 CCAGGATGCATTTT
3521071 GCACGCTAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.42
Consensus pattern (19 bp):
CCAGGATGCATTTTTTGTG
Found at i:3522804 original size:9 final size:9
Alignment explanation
Indices: 3522792--3522821 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
3522782 AAATTAACCT
3522792 AAGTAACAC
1 AAGTAACAC
3522801 AAGTAACAC
1 AAGTAACAC
3522810 AAGTAACAC
1 AAGTAACAC
3522819 AAG
1 AAG
3522822 ATGCAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (9 bp):
AAGTAACAC
Found at i:3530144 original size:2 final size:2
Alignment explanation
Indices: 3530137--3530180 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3530127 CTAGAATCAG
3530137 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3530179 AT
1 AT
3530181 GGCTTAGCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3533670 original size:3 final size:3
Alignment explanation
Indices: 3533662--3533708 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3533652 ATAAATGAGT
3533662 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3533709 GCTTCAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3534155 original size:17 final size:18
Alignment explanation
Indices: 3534133--3534170 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3534123 CCACTGTTAG
3534133 CCTTGTTC-T-TTTTGCTT
1 CCTTGTTCGTGTTTTG-TT
3534150 CCTTGTTCGTGTTTTGTT
1 CCTTGTTCGTGTTTTGTT
3534168 CCT
1 CCT
3534171 CTGCGCCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.00, C:0.24, G:0.16, T:0.61
Consensus pattern (18 bp):
CCTTGTTCGTGTTTTGTT
Found at i:3534574 original size:2 final size:2
Alignment explanation
Indices: 3534567--3534609 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3534557 CTCCTTCCAT
* *
3534567 GA GA GA GA GA GA GA TA GA GA GA GA GC GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3534609 G
1 G
3534610 TTGATAATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.49, T:0.02
Consensus pattern (2 bp):
GA
Found at i:3538021 original size:22 final size:21
Alignment explanation
Indices: 3537978--3538030 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
3537968 GTATTAGCGT
* *
3537978 AACAGTTCAGATAAAATGCAA
1 AACAGATCAGATAAAATACAA
*
3537999 AGCAGATCAGATACAAATACAA
1 AACAGATCAGATA-AAATACAA
*
3538021 AACATATCAG
1 AACAGATCAG
3538031 GATCAGATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (21 bp):
AACAGATCAGATAAAATACAA
Found at i:3538812 original size:63 final size:63
Alignment explanation
Indices: 3538727--3538923 Score: 232
Period size: 63 Copynumber: 3.1 Consensus size: 63
3538717 AATATCTCTC
** * *
3538727 ACACGGCCTGGACACATACCCGTGTCTTTGGCCTGTATGACACTAATTCACAAACAGTGTGTT
1 ACACGGCCTGGACACACGCCCGTGTCCTTGGCCTGTATGACACTAATTCACAAACAGTGAGTT
* * * * * *
3538790 ACACAGCCTGGACACACGCCCGTGTCCTTGGCTTGTGTAACCCTAATTCATAAACAGTGAGTT
1 ACACGGCCTGGACACACGCCCGTGTCCTTGGCCTGTATGACACTAATTCACAAACAGTGAGTT
* * * * * * * *
3538853 ACATGGCTTGGACACACGCCCGTGTCCGTAGCCCGTATGACTCTAATTCACAAACAATGGGTT
1 ACACGGCCTGGACACACGCCCGTGTCCTTGGCCTGTATGACACTAATTCACAAACAGTGAGTT
3538916 ACACGGCC
1 ACACGGCC
3538924 AATCACACGG
Statistics
Matches: 109, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 109 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.24
Consensus pattern (63 bp):
ACACGGCCTGGACACACGCCCGTGTCCTTGGCCTGTATGACACTAATTCACAAACAGTGAGTT
Found at i:3539492 original size:19 final size:20
Alignment explanation
Indices: 3539458--3539512 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
3539448 AGAAACAGGG
* *
3539458 AAAGAAGGATAGAAAATGCAA
1 AAAGAAAGAAAGAAAATG-AA
3539479 AAAG-AA-AAAGAAAA-GAA
1 AAAGAAAGAAAGAAAATGAA
3539496 AAAGAAAGAAAGAAAAT
1 AAAGAAAGAAAGAAAAT
3539513 TAACTAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 6 0.21
18 3 0.10
19 15 0.52
20 1 0.03
21 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAATGAA
Found at i:3539494 original size:11 final size:11
Alignment explanation
Indices: 3539478--3539506 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3539468 AGAAAATGCA
3539478 AAAAGAAAAAG
1 AAAAGAAAAAG
3539489 AAAAGAAAAAG
1 AAAAGAAAAAG
3539500 -AAAGAAA
1 AAAAGAAA
3539507 GAAAATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:3545308 original size:36 final size:36
Alignment explanation
Indices: 3545237--3545325 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 36
3545227 TTTGATATCA
* *** **
3545237 TCGGTTTATCCGACTAGCACTGGGTGTAACTCATTG
1 TCGGTTTATCTGACTAGCACTGGGCACAAAACATTG
3545273 TCGGTTTATCTGACTAGCACTGGGCACAAAACATTG
1 TCGGTTTATCTGACTAGCACTGGGCACAAAACATTG
*
3545309 TCGATTTAT-TCGACTAG
1 TCGGTTTATCT-GACTAG
3545326 TGTAGGGCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 1 0.02
36 44 0.98
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (36 bp):
TCGGTTTATCTGACTAGCACTGGGCACAAAACATTG
Found at i:3546070 original size:67 final size:67
Alignment explanation
Indices: 3545962--3546097 Score: 236
Period size: 67 Copynumber: 2.0 Consensus size: 67
3545952 TTCTTTTTCT
* *
3545962 AACCTTTGAAACGTGTGTTTATAAAAATGAAAGATGTGCAATTGGCATATAAATGAATGCATGTT
1 AACCTTTGAAACGTGTGTGTATAAAAACGAAAGATGTGCAATTGGCATATAAATGAATGCATGTT
3546027 TG
66 TG
* *
3546029 AACCTTTGAAACGTGTGTGTATAGAAACGAAAGATGTGCAATTGGCATATAAATGAATTCATGTT
1 AACCTTTGAAACGTGTGTGTATAAAAACGAAAGATGTGCAATTGGCATATAAATGAATGCATGTT
3546094 TG
66 TG
3546096 AA
1 AA
3546098 TGGTTCAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (67 bp):
AACCTTTGAAACGTGTGTGTATAAAAACGAAAGATGTGCAATTGGCATATAAATGAATGCATGTT
TG
Found at i:3548491 original size:43 final size:43
Alignment explanation
Indices: 3548430--3548512 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
3548420 AAGACTATAC
3548430 GAGATTTTGTAGTACCTGTCTTGGATGACTTACAACCGGGTAT
1 GAGATTTTGTAGTACCTGTCTTGGATGACTTACAACCGGGTAT
3548473 GAGATTTTGTAGTACCTGTCTTGGATGACTTACAACCGGG
1 GAGATTTTGTAGTACCTGTCTTGGATGACTTACAACCGGG
3548513 AGTTGTTAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (43 bp):
GAGATTTTGTAGTACCTGTCTTGGATGACTTACAACCGGGTAT
Found at i:3552464 original size:2 final size:2
Alignment explanation
Indices: 3552459--3552491 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3552449 TATATACTCT
3552459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3552492 CAAAATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3553308 original size:25 final size:25
Alignment explanation
Indices: 3553279--3553338 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 25
3553269 TTCGAATAAT
*
3553279 CATATATCAGGAAG-TTCAAGTGAGC
1 CATATATCAGGAAGCTTC-AGAGAGC
* *
3553304 C--ATATCGGGAAGCTTCGGAGAGC
1 CATATATCAGGAAGCTTCAGAGAGC
3553327 CATATATCAGGA
1 CATATATCAGGA
3553339 TGCTCATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
23 16 0.57
24 3 0.11
25 9 0.32
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (25 bp):
CATATATCAGGAAGCTTCAGAGAGC
Found at i:3563977 original size:25 final size:26
Alignment explanation
Indices: 3563925--3564020 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
3563915 GAAGAAGTGC
*
3563925 AAAAGGGC-TATGCCCTAG-TTACCG
1 AAAAGGGCTTTTGCCCTAGTTTACCG
3563949 AAAAGGGC-TTTGCCCTAGTTTACCG
1 AAAAGGGCTTTTGCCCTAGTTTACCG
* *
3563974 AAAAGGGCTTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTTGCCCTAGTTTACCG
*
3564000 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGCTTTTGCCCTAGTT
3564021 ATTAAAAGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
24 17 0.26
25 14 0.21
26 35 0.53
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCTAGTTTACCG
Found at i:3565714 original size:6 final size:6
Alignment explanation
Indices: 3565693--3565766 Score: 82
Period size: 6 Copynumber: 12.5 Consensus size: 6
3565683 TCCTCCTATT
* *
3565693 TTTTTA TTATTTA TTCTTA TTCTTA TTTTT- TTATTTA -TTTTA TTTTTA
1 TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA
*
3565741 -TTTTA TTTTTA TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
3565767 CAATTTTATT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
5 11 0.18
6 43 0.72
7 6 0.10
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:3565720 original size:16 final size:14
Alignment explanation
Indices: 3565689--3565786 Score: 62
Period size: 15 Copynumber: 6.8 Consensus size: 14
3565679 TGAATCCTCC
*
3565689 TATTTTTTTATTATT
1 TATTTTATT-TTATT
3565704 TATTCTTATTCTTATT
1 TATT-TTATT-TTATT
3565720 T-TTTTA-TTTATTT
1 TATTTTATTTTA-TT
3565733 TATTTTTATTTTATT
1 TA-TTTTATTTTATT
*
3565748 T-TTAT-TTTTATTT
1 TATTTTATTTTA-TT
*
3565761 TCATTTCAATTTTA-T
1 T-ATTT-TATTTTATT
3565776 TATTTTATTTT
1 TATTTTATTTT
3565787 GAAAAACATA
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
12 8 0.12
13 15 0.22
14 7 0.10
15 18 0.27
16 14 0.21
17 5 0.07
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTTATTTTATT
Found at i:3565722 original size:28 final size:26
Alignment explanation
Indices: 3565689--3565760 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 26
3565679 TGAATCCTCC
3565689 TATTTTTTTATTATTTATTCTTATTCT
1 TATTTTTTTATTATTTATTCTTATT-T
*
3565716 TATTTTTTTATTTATTTTATTTTTATTT
1 TATTTTTTTA-TTA-TTTATTCTTATTT
*
3565744 TATTTTTATTTTTATTT
1 TATTTTT-TTATTATTT
3565761 TCATTTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 13 0.32
28 14 0.35
29 13 0.32
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (26 bp):
TATTTTTTTATTATTTATTCTTATTT
Found at i:3565737 original size:17 final size:17
Alignment explanation
Indices: 3565709--3565760 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
3565699 TTATTTATTC
3565709 TTATTCTTATTTTTTTAT
1 TTATT-TTATTTTTTTAT
*
3565727 TTATTTTATTTTTAT-T
1 TTATTTTATTTTTTTAT
*
3565743 TTATTTT-TATTTTTAT
1 TTATTTTATTTTTTTAT
3565759 TT
1 TT
3565761 TCATTTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 5 0.17
16 11 0.37
17 9 0.30
18 5 0.17
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (17 bp):
TTATTTTATTTTTTTAT
Found at i:3565741 original size:23 final size:23
Alignment explanation
Indices: 3565693--3565786 Score: 93
Period size: 23 Copynumber: 3.9 Consensus size: 23
3565683 TCCTCCTATT
*
3565693 TTTTTATTATTTATTCTTATTCTTA
1 TTTTT-TTATTTATT-TTATTTTTA
3565718 TTTTTTTATTTATTTTATTTTTA
1 TTTTTTTATTTATTTTATTTTTA
* *
3565741 TTTTATT-TTTATTTTTATTTTCA
1 TTTTTTTATTTA-TTTTATTTTTA
3565764 TTTCAATTTTA-TTATTTTATTTT
1 TTT---TTTTATTTATTTTATTTT
3565787 GAAAAACATA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
22 4 0.07
23 27 0.45
24 9 0.15
25 14 0.23
26 6 0.10
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTTATTTATTTTATTTTTA
Found at i:3565766 original size:29 final size:28
Alignment explanation
Indices: 3565689--3565786 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 28
3565679 TGAATCCTCC
* *
3565689 TATTTTT-TTATTA-TTTATTCTTATTCT
1 TATTTTTATTTTTATTTTATTTTTATT-T
3565716 TATTTTT-TTATTTATTTTATTTTTATTT
1 TATTTTTATT-TTTATTTTATTTTTATTT
**
3565744 TATTTTTATTTTTATTTTCATTTCAATTT
1 TATTTTTATTTTTATTTT-ATTTTTATTT
3565773 TATTATTTTATTTT
1 TA-T-TTTTATTTT
3565787 GAAAAACATA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.15
28 19 0.31
29 23 0.38
30 1 0.02
31 9 0.15
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (28 bp):
TATTTTTATTTTTATTTTATTTTTATTT
Found at i:3569501 original size:90 final size:90
Alignment explanation
Indices: 3569348--3569765 Score: 510
Period size: 90 Copynumber: 4.7 Consensus size: 90
3569338 ATAGATCACC
* *
3569348 GATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCA
1 GATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCA
3569413 TTTGTTTACATCGAAGCAGATAGAA
66 TTTGTTTACATCGAAGCAGATAGAA
* *
3569438 GATGATAGATTTGGCGTCTCTGTATTAGACGGGGAGCGGATC-ACAGATAGCAGATCTGACATTC
1 GATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGA-AGATAGCAGATCTGACATTC
* * * * *
3569502 GTATATTTACATCGAAGCAGATCGGA
65 ATTTGTTTACATCGAAGCAGATAGAA
* * * * * *
3569528 GATGAAAAATTTGACGTCTCTGTATTAGACGGGGAGCATATCGTAGATAGCAAATCTG--A-T-A
1 GATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCA
* * *
3569589 TTCGTGT--ATCGAAGTAGATCA-AA
66 TTTGTTTACATCGAAGCAGAT-AGAA
* * * *
3569612 GATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCGAAGATAGTAGATCTAACATTCG
1 GATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCA
* *
3569677 TGTGTTTACATCGAAGCAGATCGAA
66 TTTGTTTACATCGAAGCAGATAGAA
* * * *
3569702 GATGACGGATTTGGCGTCTCTATATTAGATGGGGAGCAGATCGAAGATAGCAGATTTGACATTC
1 GATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTC
3569766 TTGAGTTATA
Statistics
Matches: 272, Mismatches: 46, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
84 61 0.22
86 4 0.01
87 2 0.01
88 5 0.02
89 1 0.00
90 199 0.73
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (90 bp):
GATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCA
TTTGTTTACATCGAAGCAGATAGAA
Found at i:3569676 original size:174 final size:178
Alignment explanation
Indices: 3569364--3569753 Score: 513
Period size: 174 Copynumber: 2.2 Consensus size: 178
3569354 AGATTTGGCA
* * * *
3569364 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCATTTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAAATCTGA-ATTCATTCGTGTA-ATCGAAG
* *
3569429 CAGATAGAAGATGATAGATTTGGCGTCTCTGTATTAGACGGGGAGCGGATCACAGATAGCAGATC
64 CAGATAGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCACAGATAGCAGATC
* *
3569494 TGACATTCGTATATTTACATCGAAGCAGATCGGAGATGAAAAATTTGACG
129 TAACATTCGTATATTTACATCGAAGCAGATCGAAGATGAAAAATTTGACG
* * *
3569544 TCTCTGTATTAGACGGGGAGCATATCGTAGATAGCAAATCTG-A-T-ATTCGTGT-ATCGAAGTA
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAAATCTGAATTCATTCGTGTAATCGAAGCA
* *
3569605 GATCA-AAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCGA-AGATAGTAGATC
66 GAT-AGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATC-ACAGATAGCAGATC
* * *** *
3569668 TAACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACGGATTTGGCG
129 TAACATTCGTATATTTACATCGAAGCAGATCGAAGATGAAAAATTTGACG
* *
3569718 TCTCTATATTAGATGGGGAGCAGATCGAAGATAGCA
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCA
3569754 GATTTGACAT
Statistics
Matches: 185, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
174 137 0.74
175 2 0.01
176 6 0.03
177 1 0.01
178 1 0.01
180 38 0.21
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (178 bp):
TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAAATCTGAATTCATTCGTGTAATCGAAGCA
GATAGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCACAGATAGCAGATCTA
ACATTCGTATATTTACATCGAAGCAGATCGAAGATGAAAAATTTGACG
Found at i:3569758 original size:45 final size:45
Alignment explanation
Indices: 3569604--3569759 Score: 122
Period size: 45 Copynumber: 3.5 Consensus size: 45
3569594 GTATCGAAGT
* * *
3569604 AGATCAAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGT
1 AGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGATGGGGAGC
* * ** * * * * *
3569649 AGATCGAAGAT-AGTAGATCTAACAT-TCGTGTGTTTACAT-CGAAGC
1 AGATCGAAGATGA-CAGATTTGGCGTCTC-TGT-ATTAGATGGGGAGC
* *
3569694 AGATCGAAGATGACGGATTTGGCGTCTCTATATTAGATGGGGAGC
1 AGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGATGGGGAGC
3569739 AGATCGAAGAT-AGCAGATTTG
1 AGATCGAAGATGA-CAGATTTG
3569760 ACATTCTTGA
Statistics
Matches: 80, Mismatches: 24, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
44 9 0.11
45 64 0.80
46 7 0.09
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (45 bp):
AGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGATGGGGAGC
Found at i:3571731 original size:40 final size:35
Alignment explanation
Indices: 3571628--3571794 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
3571618 CATGGCAAAG
*
3571628 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
*
3571663 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
*
3571698 TGTGAAATGTAGGGATGGTATTATCAAACCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTAT-----CCATACTGAGT
** * *
3571738 TAAGAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGT
**
3571773 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
3571795 TCAATGAGGA
Statistics
Matches: 115, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
35 86 0.75
39 1 0.01
40 28 0.24
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.32
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
Found at i:3571748 original size:75 final size:74
Alignment explanation
Indices: 3571652--3571798 Score: 197
Period size: 75 Copynumber: 2.0 Consensus size: 74
3571642 ATGGTATCAT
** * * **
3571652 CCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-CCATACTGAGCTGTGAAATGTAGGGATGG
1 CCATACTGAGTTAAGAAATGTAGGTATGGCATT-TCCCATACCGAGCTGAAAAATGTAGGGATGG
3571716 TATTATCAAAC
65 TATT-TCAAAC
* *
3571727 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTCCCATACCGAGTTGAAAAATGTAGGTATGGT
1 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTCCCATACCGAGCTGAAAAATGTAGGGATGGT
3571792 ATTTCAA
66 ATTTCAA
3571799 TGAGGAAAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
74 5 0.08
75 58 0.92
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (74 bp):
CCATACTGAGTTAAGAAATGTAGGTATGGCATTTCCCATACCGAGCTGAAAAATGTAGGGATGGT
ATTTCAAAC
Found at i:3573858 original size:9 final size:9
Alignment explanation
Indices: 3573834--3573887 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
3573824 TCCTTTTATA
*
3573834 TATATATATA
1 TATATAT-TT
3573844 TATATATTT
1 TATATATTT
*
3573853 TATATAATT
1 TATATATTT
*
3573862 TATTTATTT
1 TATATATTT
*
3573871 TAAATATTT
1 TATATATTT
*
3573880 TGTATATT
1 TATATATT
3573888 ATTTATTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
9 29 0.81
10 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
TATATATTT
Found at i:3573862 original size:10 final size:11
Alignment explanation
Indices: 3573827--3573891 Score: 52
Period size: 9 Copynumber: 6.3 Consensus size: 11
3573817 ATTTTAATCC
3573827 TTTTATATATA
1 TTTTATATATA
*
3573838 TATATATATATA
1 T-TTTATATATA
3573850 TTTTATATA-A
1 TTTTATATATA
3573860 -TTTAT-T-TA
1 TTTTATATATA
3573868 TTTTA-A-ATA
1 TTTTATATATA
*
3573877 TTTTGTATATTA
1 TTTTATATA-TA
3573889 TTT
1 TTT
3573892 ATTTTACTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
8 2 0.05
9 15 0.35
10 2 0.05
11 9 0.21
12 15 0.35
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTTTATATATA
Found at i:3573891 original size:29 final size:30
Alignment explanation
Indices: 3573845--3573904 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
3573835 ATATATATAT
*
3573845 ATATATTTTATATAATTTA-TTTATTTTAA
1 ATATATTTTATATAATTTATTTTACTTTAA
*
3573874 ATAT-TTTGTATATTATTTATTTTACTTTAA
1 ATATATTT-TATATAATTTATTTTACTTTAA
3573904 A
1 A
3573905 CCTTATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 14 0.52
30 10 0.37
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (30 bp):
ATATATTTTATATAATTTATTTTACTTTAA
Found at i:3573895 original size:25 final size:27
Alignment explanation
Indices: 3573847--3573897 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
3573837 ATATATATAT
3573847 ATATTTTATATAATTTATTTATTTTAA
1 ATATTTTATATAATTTATTTATTTTAA
*
3573874 ATATTTTGTAT-A-TTATTTATTTTA
1 ATATTTTATATAATTTATTTATTTTA
3573898 CTTTAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 1 0.04
27 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
ATATTTTATATAATTTATTTATTTTAA
Found at i:3573916 original size:30 final size:28
Alignment explanation
Indices: 3573850--3573916 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
3573840 TATATATATA
* *
3573850 TTTTATATAATTTATTTATTTTAAATAT
1 TTTTATATAATTTATTTACTTTAAACAT
* *
3573878 TTTGTATATTATTTATTTTACTTTAAACCT
1 TTT-TATATAATTTA-TTTACTTTAAACAT
3573908 TATTTATAT
1 T-TTTATAT
3573917 GTAAAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 10 0.31
30 17 0.53
31 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (28 bp):
TTTTATATAATTTATTTACTTTAAACAT
Found at i:3573957 original size:12 final size:12
Alignment explanation
Indices: 3573940--3573990 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
3573930 ATTTTATTTG
3573940 TATTATTTATTA
1 TATTATTTATTA
3573952 TATTATTTA-TA
1 TATTATTTATTA
* *
3573963 TTTTA-TT-GTA
1 TATTATTTATTA
3573973 TATTATTTATTA
1 TATTATTTATTA
3573985 TATTAT
1 TATTAT
3573991 GTATAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.24
11 8 0.24
12 17 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTATTTATTA
Found at i:3573974 original size:21 final size:20
Alignment explanation
Indices: 3573946--3573995 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
3573936 TTTGTATTAT
*
3573946 TTAT-TATATTATTTATATT
1 TTATGTATATTATTTATATA
3573965 TTATTGTATATTATTTATTATA
1 TTA-TGTATATTATTTA-TATA
3573987 TTATGTATA
1 TTATGTATA
3573996 ATTTTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 1 0.04
21 17 0.63
22 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TTATGTATATTATTTATATA
Found at i:3573981 original size:14 final size:13
Alignment explanation
Indices: 3573925--3573990 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 13
3573915 ATGTAAAAAA
3573925 TATTTATTT-TAT
1 TATTTATTTATAT
* *
3573937 T-TGTATTATTTAT
1 TATTTATT-TATAT
3573950 TATATTATTTATA-
1 TAT-TTATTTATAT
3573963 T-TTTATTGTATAT
1 TATTTATT-TATAT
3573976 TATTTA-TTATAT
1 TATTTATTTATAT
3573988 TAT
1 TAT
3573991 GTATAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
11 10 0.23
12 15 0.34
13 7 0.16
14 8 0.18
15 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
TATTTATTTATAT
Found at i:3573981 original size:33 final size:32
Alignment explanation
Indices: 3573929--3574002 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 32
3573919 AAAAAATATT
* *
3573929 TATTTTATTTGTATTATTTATTATATTATTTA
1 TATTTTATTTATATTATTTATTATATTATGTA
3573961 TATTTTATTGTATATTATTTATTATATTATGTA
1 TATTTTATT-TATATTATTTATTATATTATGTA
3573994 TAATTTTAT
1 T-ATTTTAT
3574003 AAAATTTGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 9 0.24
33 22 0.58
34 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (32 bp):
TATTTTATTTATATTATTTATTATATTATGTA
Found at i:3574056 original size:15 final size:15
Alignment explanation
Indices: 3574017--3574057 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
3574007 TTTGTAAATT
3574017 ATTATTAAATATTAC
1 ATTATTAAATATTAC
* *
3574032 ATTTTTATATA-T-C
1 ATTATTAAATATTAC
3574045 ATTATTAAATATT
1 ATTATTAAATATT
3574058 TAGTATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATTAAATATTAC
Found at i:3574071 original size:21 final size:21
Alignment explanation
Indices: 3574024--3574071 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3574014 ATTATTATTA
* *
3574024 AATATTACATTTTTATATATC
1 AATATTAAATATTTATATATC
*
3574045 ATTATTAAATATTTAGTATAT-
1 AATATTAAATATTTA-TATATC
3574066 AATATT
1 AATATT
3574072 CTAAAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
AATATTAAATATTTATATATC
Found at i:3586144 original size:45 final size:44
Alignment explanation
Indices: 3586095--3586502 Score: 218
Period size: 45 Copynumber: 9.2 Consensus size: 44
3586085 CACCGATGAC
* *
3586095 AGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCGAAGATAGT
1 AGATTTGACGTCTCTGTATTAGAC-GGGAGCAGATCGAAGATAGT
* * * * *
3586140 AGATTTGACAT-TCGTGTGTTTACATC-GAAACAGATCGAAGAT-GAT
1 AGATTTGACGTCTC-TGT-ATTAGA-CGGGAGCAGATCGAAGATAG-T
* * *
3586185 AGATTTGACGTCTTTGTATTAGACGGGGAGCTGATCGAAGATAGC
1 AGATTTGACGTCTCTGTATTAGAC-GGGAGCAGATCGAAGATAGT
* * * * *
3586230 AGATCTGACAT-TCGTGTATTTACATC-GAAGCAGATCGGAGAT-GAT
1 AGATTTGACGTCTC-TGTA-TTAGA-CGGGAGCAGATCGAAGATAG-T
* * *
3586275 AAATTTGACGTCTCTGTATTAGACGGAGAGCAGATCGTAGATAGC
1 AGATTTGACGTCTCTGTATTAGACGG-GAGCAGATCGAAGATAGT
* * * * *
3586320 AGATCTGACAT-TCGTGTA-T---C-GAAGCAGATCAAAGAT-GAC
1 AGATTTGACGTCTC-TGTATTAGACGGGAGCAGATCGAAGATAG-T
**
3586359 AGATTTGGTGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGT
1 AGATTTGACGTCTCTGTATTAGAC-GGGAGCAGATCGAAGATAGT
* * * * * *
3586404 AGATCTAACAT-TCGTGTGTTTACATC-GAAGCAGATCGAAGAT-GAT
1 AGATTTGACGTCTC-TGT-ATTAGA-CGGGAGCAGATCGAAGATAG-T
* * * *
3586449 AGATTTGGCGTCTCTATATTAGATGGGGAGCAGATCGAAGATAGC
1 AGATTTGACGTCTCTGTATTAGA-CGGGAGCAGATCGAAGATAGT
3586494 AGATTTGAC
1 AGATTTGAC
3586503 ATTCTAAAGT
Statistics
Matches: 268, Mismatches: 62, Indels: 66
0.68 0.16 0.17
Matches are distributed among these distances:
38 1 0.00
39 24 0.09
40 4 0.01
41 1 0.00
43 3 0.01
44 25 0.09
45 186 0.69
46 21 0.08
47 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (44 bp):
AGATTTGACGTCTCTGTATTAGACGGGAGCAGATCGAAGATAGT
Found at i:3586239 original size:90 final size:90
Alignment explanation
Indices: 3586089--3586506 Score: 587
Period size: 90 Copynumber: 4.7 Consensus size: 90
3586079 GTAGATCACC
* * * *
3586089 GATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCGAAGATAGTAGATTTGACATTCG
1 GATGATAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCG
*
3586154 TGTGTTTACATCGAAACAGATCGAA
66 TGTGTTTACATCGAAGCAGATCGAA
* * *
3586179 GATGATAGATTTGACGTCTTTGTATTAGACGGGGAGCTGATCGAAGATAGCAGATCTGACATTCG
1 GATGATAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCG
* *
3586244 TGTATTTACATCGAAGCAGATCGGA
66 TGTGTTTACATCGAAGCAGATCGAA
* * * *
3586269 GATGATAAATTTGACGTCTCTGTATTAGACGGAGAGCAGATCGTAGATAGCAGATCTGACATTC-
1 GATGATAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCG
*
3586333 -GTG--T--ATCGAAGCAGATCAAA
66 TGTGTTTACATCGAAGCAGATCGAA
* * * * *
3586353 GATGACAGATTTGGTGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGTAGATCTAACATTCG
1 GATGATAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCG
3586418 TGTGTTTACATCGAAGCAGATCGAA
66 TGTGTTTACATCGAAGCAGATCGAA
* * *
3586443 GATGATAGATTTGGCGTCTCTATATTAGATGGGGAGCAGATCGAAGATAGCAGATTTGACATTC
1 GATGATAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTC
3586507 TAAAGTTATA
Statistics
Matches: 286, Mismatches: 36, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
84 69 0.24
86 4 0.01
88 3 0.01
90 210 0.73
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (90 bp):
GATGATAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCG
TGTGTTTACATCGAAGCAGATCGAA
Found at i:3586399 original size:174 final size:177
Alignment explanation
Indices: 3586097--3586506 Score: 583
Period size: 174 Copynumber: 2.3 Consensus size: 177
3586087 CCGATGACAG
* *
3586097 ATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCGAAGATAGTAGATTTGACATTCGTGTGTTTA
1 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATTTGACATTCG-GTG-TTA
* * * * *
3586162 CATCGAAACAGATCGAAGATGATAGATTTGACGTCTTTGTATTAGACGGGGAGCTGATCGAAGAT
64 -ATCGAAACAGATCAAAGATGACAGATTTGACGTCTCTGTATTAGACAGGGAGCAGATCGAAGAT
* *
3586227 AGCAGATCTGACATTCGTGTATTTACATCGAAGCAGATCGGAGATGATAA
128 AGCAGATCTAACATTCGTGTATTTACATCGAAGCAGATCGAAGATGATAA
* * * *
3586277 ATTTGACGTCTCTGTATTAGACGGAGAGCAGATCGTAGATAGCAGATCTGACATTC-GTG-T-AT
1 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATTTGACATTCGGTGTTAAT
* ** *
3586339 CGAAGCAGATCAAAGATGACAGATTTGGTGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGT
66 CGAAACAGATCAAAGATGACAGATTTGACGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGC
* *
3586404 AGATCTAACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGATAG
131 AGATCTAACATTCGTGTATTTACATCGAAGCAGATCGAAGATGATAA
* *
3586451 ATTTGGCGTCTCTATATTAGATGGGGAGCAGATCGAAGATAGCAGATTTGACATTC
1 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATTTGACATTC
3586507 TAAAGTTATA
Statistics
Matches: 205, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
174 151 0.74
176 1 0.00
178 3 0.01
180 50 0.24
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (177 bp):
ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATTTGACATTCGGTGTTAAT
CGAAACAGATCAAAGATGACAGATTTGACGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGC
AGATCTAACATTCGTGTATTTACATCGAAGCAGATCGAAGATGATAA
Found at i:3587930 original size:2 final size:2
Alignment explanation
Indices: 3587923--3587955 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3587913 TTTTAATCCT
3587923 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3587956 ATTTATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3588013 original size:30 final size:28
Alignment explanation
Indices: 3587949--3588013 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 28
3587939 TATATATATA
* *
3587949 TTATATAATTTATTTATTTTAAATATTT
1 TTATATAATTTATTTACTTTAAACATTT
* *
3587977 TGTATATTATTTATTTTACTTTAAACCTTAT
1 T-TATATAATTTA-TTTACTTTAAACATT-T
3588008 TTATAT
1 TTATAT
3588014 GTAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 10 0.33
30 17 0.57
31 2 0.07
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (28 bp):
TTATATAATTTATTTACTTTAAACATTT
Found at i:3588056 original size:12 final size:12
Alignment explanation
Indices: 3588039--3588089 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
3588029 ATTTTATTTG
3588039 TATTATTTATTA
1 TATTATTTATTA
3588051 TATTATTTA-TA
1 TATTATTTATTA
* *
3588062 TTTTA-TT-GTA
1 TATTATTTATTA
3588072 TATTATTTATTA
1 TATTATTTATTA
3588084 TATTAT
1 TATTAT
3588090 GTATAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.24
11 8 0.24
12 17 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTATTTATTA
Found at i:3588058 original size:21 final size:21
Alignment explanation
Indices: 3588049--3588094 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3588039 TATTATTTAT
3588049 TATATTATTTATATTTTATTG
1 TATATTATTTATATTTTATTG
*
3588070 TATATTATTTATTATATTA-TG
1 TATATTATTTA-TATTTTATTG
3588091 TATA
1 TATA
3588095 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
TATATTATTTATATTTTATTG
Found at i:3588079 original size:33 final size:33
Alignment explanation
Indices: 3588029--3588100 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
3588019 AAAAATATTC
* *
3588029 ATTTTATTTGTATTATTTATTATATTATTTAT-
1 ATTTTATTTATATTATTTATTATATTATGTATA
3588061 ATTTTATTGTATATTATTTATTATATTATGTATA
1 ATTTTATT-TATATTATTTATTATATTATGTATA
3588095 ATTTTA
1 ATTTTA
3588101 AAAAATTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 8 0.22
33 22 0.61
34 6 0.17
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (33 bp):
ATTTTATTTATATTATTTATTATATTATGTATA
Found at i:3588155 original size:15 final size:15
Alignment explanation
Indices: 3588116--3588156 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
3588106 TTTGTAAATT
3588116 ATTATTAAATATTAC
1 ATTATTAAATATTAC
* *
3588131 ATTTTTATATA-T-C
1 ATTATTAAATATTAC
3588144 ATTATTAAATATT
1 ATTATTAAATATT
3588157 TAGTATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATTAAATATTAC
Found at i:3588170 original size:21 final size:21
Alignment explanation
Indices: 3588123--3588170 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3588113 ATTATTATTA
* *
3588123 AATATTACATTTTTATATATC
1 AATATTAAATATTTATATATC
*
3588144 ATTATTAAATATTTAGTATAT-
1 AATATTAAATATTTA-TATATC
3588165 AATATT
1 AATATT
3588171 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
AATATTAAATATTTATATATC
Found at i:3592029 original size:40 final size:40
Alignment explanation
Indices: 3591976--3592186 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
3591966 TCTATCTGGC
* * *
3591976 GTGTTTTAGTTGGATTAGCTCTTATGAGTTTCTATCTAGT
1 GTGTTTGAGTTGGATTAGCTCTTATGAGCTTCTGTCTAGT
* *
3592016 GTGCTTTGA-TTGGATTAGCTCTTATGAGATTCTGTCTAGC
1 GTG-TTTGAGTTGGATTAGCTCTTATGAGCTTCTGTCTAGT
* * * *
3592056 ATGTTTCAGTTGGATTAGCTCTTATGAGCTTCTGTATGGT
1 GTGTTTGAGTTGGATTAGCTCTTATGAGCTTCTGTCTAGT
* * *
3592096 GTGTTTTG-GTTGGATTAGCTCTTTTGAGCTTCTGTTTGGT
1 GTG-TTTGAGTTGGATTAGCTCTTATGAGCTTCTGTCTAGT
* * *
3592136 GTGTTTTAGTTGGATTAGCTCTTATGAGCTTTTGTCTGGT
1 GTGTTTGAGTTGGATTAGCTCTTATGAGCTTCTGTCTAGT
*
3592176 TTGTTT-AGTTG
1 GTGTTTGAGTTG
3592187 ATCTAATGAT
Statistics
Matches: 148, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 12 0.08
40 129 0.87
41 7 0.05
ACGTcount: A:0.14, C:0.11, G:0.26, T:0.49
Consensus pattern (40 bp):
GTGTTTGAGTTGGATTAGCTCTTATGAGCTTCTGTCTAGT
Found at i:3592110 original size:80 final size:80
Alignment explanation
Indices: 3591977--3592181 Score: 275
Period size: 80 Copynumber: 2.6 Consensus size: 80
3591967 CTATCTGGCG
* * * *
3591977 TGTTTTAGTTGGATTAGCTCTTATGAGTTTCTATCTAGTGTGCTTTGATTGGATTAGCTCTTATG
1 TGTTTTAGTTGGATTAGCTCTTATGAGCTTCTGTCTGGTGTGTTTTGATTGGATTAGCTCTTATG
3592042 AGATTCTGTCTAGCA
66 AGATTCTGTCTAGCA
* * * *
3592057 TGTTTCAGTTGGATTAGCTCTTATGAGCTTCTGTATGGTGTGTTTTGGTTGGATTAGCTCTTTTG
1 TGTTTTAGTTGGATTAGCTCTTATGAGCTTCTGTCTGGTGTGTTTTGATTGGATTAGCTCTTATG
* * * **
3592122 AGCTTCTGTTTGGTG
66 AGATTCTGTCTAGCA
* *
3592137 TGTTTTAGTTGGATTAGCTCTTATGAGCTTTTGTCTGGTTTGTTT
1 TGTTTTAGTTGGATTAGCTCTTATGAGCTTCTGTCTGGTGTGTTT
3592182 AGTTGATCTA
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 108 1.00
ACGTcount: A:0.14, C:0.11, G:0.25, T:0.49
Consensus pattern (80 bp):
TGTTTTAGTTGGATTAGCTCTTATGAGCTTCTGTCTGGTGTGTTTTGATTGGATTAGCTCTTATG
AGATTCTGTCTAGCA
Found at i:3592863 original size:20 final size:20
Alignment explanation
Indices: 3592838--3592886 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
3592828 AAGTTTATGA
3592838 TAAGTAAATGAAATAGAAAG
1 TAAGTAAATGAAATAGAAAG
* * *
3592858 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGAAATAGAAAG
*
3592878 AAAGTAAAT
1 TAAGTAAAT
3592887 AGAGTGGTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.22, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGAAATAGAAAG
Found at i:3597187 original size:21 final size:21
Alignment explanation
Indices: 3597163--3597208 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3597153 ACTAACTAAA
*
3597163 ATAAGATAAATAA-ATAAATAC
1 ATAAGATAAA-AACAAAAATAC
3597184 ATAAGATAAAAACAAAAATAC
1 ATAAGATAAAAACAAAAATAC
3597205 ATAA
1 ATAA
3597209 ATATCTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (21 bp):
ATAAGATAAAAACAAAAATAC
Found at i:3598744 original size:39 final size:37
Alignment explanation
Indices: 3598653--3598761 Score: 104
Period size: 37 Copynumber: 3.0 Consensus size: 37
3598643 ATTTAAAAAA
*
3598653 TAAT-ATTATTTTAATAGATTTCATATTTAATTTAATT
1 TAATGATTATCTTAATAGATTT-ATATTTAATTTAATT
*
3598690 TAATGTTTATCTTAATAGTATTT-TA-TTAATTTAATAT
1 TAATGATTATCTTAATAG-ATTTATATTTAATTTAAT-T
*
3598727 TAAAGTGATTATCTTAAT--A-TTAAATTTAATTTAAT
1 T-AA-TGATTATCTTAATAGATTTATATTTAATTTAAT
3598762 GTTTATCTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
35 2 0.03
36 12 0.20
37 18 0.30
38 13 0.21
39 16 0.26
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.54
Consensus pattern (37 bp):
TAATGATTATCTTAATAGATTTATATTTAATTTAATT
Found at i:3598816 original size:12 final size:12
Alignment explanation
Indices: 3598799--3598845 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
3598789 ATTAAATAAG
3598799 ATTTAATATTAA
1 ATTTAATATTAA
*
3598811 ATTTAAT-CTAA
1 ATTTAATATTAA
3598822 TATTT-ATATT-A
1 -ATTTAATATTAA
3598833 ATTTAATATTAA
1 ATTTAATATTAA
3598845 A
1 A
3598846 GTTATTGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 4 0.14
11 11 0.38
12 14 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:3598822 original size:17 final size:18
Alignment explanation
Indices: 3598802--3598845 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
3598792 AAATAAGATT
3598802 TAATATTAAAT-TTAATC
1 TAATATTAAATATTAATC
* *
3598819 TAATATT-TATATTAATT
1 TAATATTAAATATTAATC
3598836 TAATATTAAA
1 TAATATTAAA
3598846 GTTATTGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATTAAATATTAATC
Found at i:3602797 original size:39 final size:39
Alignment explanation
Indices: 3602754--3602835 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
3602744 ATGAATTCAT
3602754 CTTTCTAACTTTTATTTATTTTATTACAATTATTTTATA
1 CTTTCTAACTTTTATTTATTTTATTACAATTATTTTATA
* *
3602793 CTTTCTAACTTTTATTTGTTTTATTATAATTATTTTATA
1 CTTTCTAACTTTTATTTATTTTATTACAATTATTTTATA
3602832 CTTT
1 CTTT
3602836 ATATTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.63
Consensus pattern (39 bp):
CTTTCTAACTTTTATTTATTTTATTACAATTATTTTATA
Found at i:3604854 original size:19 final size:19
Alignment explanation
Indices: 3604822--3604873 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3604812 TTAAATTTTA
*
3604822 AAAAATTCAAAAAATTTATT
1 AAAAATT-ATAAAATTTATT
3604842 ATAAAATT-TAAAATTTATT
1 A-AAAATTATAAAATTTATT
3604861 AAAAATTATAAAA
1 AAAAATTATAAAA
3604874 AAATATATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 16 0.55
20 1 0.03
21 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTATAAAATTTATT
Found at i:3618040 original size:94 final size:94
Alignment explanation
Indices: 3617869--3618053 Score: 280
Period size: 94 Copynumber: 2.0 Consensus size: 94
3617859 GCCTAGACAT
*
3617869 TATGGCCGAATCTGGAAGAGTTACATTAATTTATTTAAAAACTCTTGTTTTAACCAACTTAATTG
1 TATGGCCAAATCTGGAAGAGTTACATTAATTTATTTAAAAACTCTTGTTTTAACCAACTTAATTG
* ** *
3617934 TGTGTTAGAAAAACATAAAACTTGCATAA
66 AGCATTACAAAAACATAAAACTTGCATAA
* * * * *
3617963 TATGGCCAAATTTGGAAGAGTTACATTAGTTTGTTTAAAAACTCTTGTTTTAAGCAACTTAGTTG
1 TATGGCCAAATCTGGAAGAGTTACATTAATTTATTTAAAAACTCTTGTTTTAACCAACTTAATTG
3618028 AGCATTACAAAAACATAAAACTTGCA
66 AGCATTACAAAAACATAAAACTTGCA
3618054 GAACTCTTAC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 81 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (94 bp):
TATGGCCAAATCTGGAAGAGTTACATTAATTTATTTAAAAACTCTTGTTTTAACCAACTTAATTG
AGCATTACAAAAACATAAAACTTGCATAA
Found at i:3623860 original size:22 final size:23
Alignment explanation
Indices: 3623814--3623867 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
3623804 AATATATGTA
3623814 TAATATTA-AAATAAAACATAGAT
1 TAAT-TTATAAATAAAACATAGAT
*
3623837 TAATTTATAAATAAAA-TTAGAT
1 TAATTTATAAATAAAACATAGAT
*
3623859 TAATATATA
1 TAATTTATA
3623868 CTAAATATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (23 bp):
TAATTTATAAATAAAACATAGAT
Found at i:3627399 original size:15 final size:15
Alignment explanation
Indices: 3627381--3627420 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3627371 AATAAATTTT
*
3627381 ATTTTTATTTTTAAA
1 ATTTATATTTTTAAA
*
3627396 ATTTATATTTTTCAA
1 ATTTATATTTTTAAA
*
3627411 ATTTAAATTT
1 ATTTATATTT
3627421 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTATATTTTTAAA
Found at i:3627418 original size:21 final size:20
Alignment explanation
Indices: 3627373--3627426 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
3627363 TTTTATTAAA
**
3627373 TAAATTT-TATTTTTATTTT
1 TAAATTTATATTTTTAAATT
3627392 TAAAATTTATATTTTTCAAATT
1 T-AAATTTATATTTTT-AAATT
*
3627414 TAAATTTAAATTT
1 TAAATTTATATTT
3627427 AAAATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 6 0.21
21 18 0.62
22 4 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TAAATTTATATTTTTAAATT
Found at i:3627918 original size:20 final size:20
Alignment explanation
Indices: 3627895--3627960 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 20
3627885 AAATAAAAAT
3627895 ATTTTTAAATATTTTTTATA
1 ATTTTTAAATATTTTTTATA
* *
3627915 A-TTTTATGATA-ATTTT-TA
1 ATTTTTA-AATATTTTTTATA
3627933 ATTTTTCAAAATATTTTTTATA
1 ATTTTT--AAATATTTTTTATA
3627955 ATTTTT
1 ATTTTT
3627961 TTATCCATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 3 0.08
19 13 0.36
20 7 0.19
21 5 0.14
22 8 0.22
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTTAAATATTTTTTATA
Found at i:3629849 original size:10 final size:10
Alignment explanation
Indices: 3629830--3629879 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
3629820 TTAAATTCTA
3629830 AAAGATAAAT
1 AAAGATAAAT
3629840 ACAA-ATAAAT
1 A-AAGATAAAT
*
3629850 AAAGATAATT
1 AAAGATAAAT
3629860 AAAGATAAAT
1 AAAGATAAAT
*
3629870 AAAAATAAAT
1 AAAGATAAAT
3629880 CCTAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:3629929 original size:14 final size:13
Alignment explanation
Indices: 3629893--3629930 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
3629883 AAATTTAAAT
3629893 CTAAATAATTATC
1 CTAAATAATTATC
*
3629906 CTTAATAATTATC
1 CTAAATAATTATC
3629919 CTAATATAATTA
1 CTAA-ATAATTA
3629931 AACATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (13 bp):
CTAAATAATTATC
Found at i:3631719 original size:15 final size:15
Alignment explanation
Indices: 3631699--3631727 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3631689 GTATAAAAAT
3631699 CCCCTTTCTATTATC
1 CCCCTTTCTATTATC
3631714 CCCCTTTCTATTAT
1 CCCCTTTCTATTAT
3631728 TTCACACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.38, G:0.00, T:0.48
Consensus pattern (15 bp):
CCCCTTTCTATTATC
Found at i:3631803 original size:21 final size:21
Alignment explanation
Indices: 3631769--3631812 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3631759 AAATCTCTAC
*
3631769 AATTTCTCCCTAAAGCTCTCA
1 AATTTCTCACTAAAGCTCTCA
* **
3631790 AATTTCTCATTAAATTTCTCA
1 AATTTCTCACTAAAGCTCTCA
3631811 AA
1 AA
3631813 GCTCTTTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTCTCACTAAAGCTCTCA
Found at i:3631983 original size:7 final size:7
Alignment explanation
Indices: 3631971--3632000 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3631961 GCAACAGTTT
3631971 ATTTTAA
1 ATTTTAA
3631978 ATTTTAA
1 ATTTTAA
3631985 ATTTTAA
1 ATTTTAA
3631992 ATTTTAA
1 ATTTTAA
3631999 AT
1 AT
3632001 ATTATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:3632055 original size:24 final size:23
Alignment explanation
Indices: 3632005--3632054 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
3631995 TTAAATATTA
*
3632005 TTTAATATTTTTTATTTATGTAAT
1 TTTAATAATTTTTATTTA-GTAAT
3632029 TTTAATTAATTTTTATTTA-TAAT
1 TTTAA-TAATTTTTATTTAGTAAT
3632052 TTT
1 TTT
3632055 TTATAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 5 0.21
25 12 0.50
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTAATAATTTTTATTTAGTAAT
Found at i:3633661 original size:18 final size:18
Alignment explanation
Indices: 3633621--3633655 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3633611 CCAGGTGTGT
*
3633621 ATCCTAGCCCTTATATGC
1 ATCCTAACCCTTATATGC
3633639 ATCCTAACCCTTATATG
1 ATCCTAACCCTTATATG
3633656 TTTCCTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
ATCCTAACCCTTATATGC
Found at i:3637367 original size:126 final size:126
Alignment explanation
Indices: 3637142--3637637 Score: 678
Period size: 126 Copynumber: 4.0 Consensus size: 126
3637132 GTCAATCATA
* * * *
3637142 AACTACTGTAGAAAAAGAGCGTCCACATGGGAGTTTTTTTCAGAAATTTTGCTAACATTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACATGGGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATCC
* *
3637207 TGCTTGAAGCATTTTTAACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAAG
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAAG
* * * * *
3637268 AACTACTGTAGAAAAAGAGCGTTCACGTAGTAGTTTTTTTCTGTAATTTTGCTGACAGTGCATCT
1 AACTACTGTAGAAAAAGAGCGTCCACATGGGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATCC
* *
3637333 TGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCATG
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAAG
* * ** * * *
3637394 AACTACTATAGAAAAAGAGCGTCCACGTGATAGCTTTTTTCTATAATTTTGTTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACATGGGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATCC
* * ** *
3637459 TACTTGAAGCGTTTTTGACACTA----TTCATAAATGTCTTCTCAAAATTATTTTTTCAGG
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAAG
* * *
3637516 AACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTT-TGTATTTTTGCTGACAGTGCATC
1 AACTACTGTAGAAAAAGAGCGTCCACATGGGAG-TTTTTTTCTGTAATTTTGCTGACAGTGCATC
**
3637580 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTT
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTT
3637638 TGGGGTACAA
Statistics
Matches: 326, Mismatches: 39, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
122 100 0.31
123 6 0.02
126 220 0.67
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (126 bp):
AACTACTGTAGAAAAAGAGCGTCCACATGGGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAAG
Found at i:3637587 original size:248 final size:249
Alignment explanation
Indices: 3637137--3637637 Score: 684
Period size: 248 Copynumber: 2.0 Consensus size: 249
3637127 CTAAGGTCAA
* * * *
3637137 TCATAAACTACTGTAGAAAAAGAGCGTCCACATGGGAGTTTTTTTCAGAAATTTTGCTAACATTG
1 TCATAAACTACTATAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGAAATTTTGCTAACAGTG
*
3637202 CATCCTGCTTGAAGCATTTTTAACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
66 CATCCTACTTGAAGCATTTTTAACACTA--T-TTCAGAAACATCTTCTCAAAATTATTTTTTCAA
* * * * *
3637267 GAACTACTGTAGAAAAAGAGCGTTCACGTAGTAGTTTTTTTCTGTAATTTTGCTGACAGTGCATC
128 GAACTACTGTAGAAAAAGAACATCCACATAGGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATC
* *
3637332 TTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTT
193 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTT
* * * * * *
3637389 TCATGAACTACTATAGAAAAAGAGCGTCCACGTGATAGCTTTTTTCTA-TAATTTTGTTGACAGT
1 TCATAAACTACTATAGAAAAAGAGCGTCCACATGAGAGCTTTTTTC-AGAAATTTTGCTAACAGT
* * * ** *
3637453 GCATCCTACTTGAAGCGTTTTTGACACTA-TTCATAAATGTCTTCTCAAAATTATTTTTTCAGGA
65 GCATCCTACTTGAAGCATTTTTAACACTATTTCAGAAACATCTTCTCAAAATTATTTTTTCAAGA
* *
3637517 ACTACTGTAGAAAAAGAACATCCACATGGGAGCTTTTTTT-TGTATTTTTGCTGACAGTGCATCC
130 ACTACTGTAGAAAAAGAACATCCACATAGGAG-TTTTTTTCTGTAATTTTGCTGACAGTGCATCC
**
3637581 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTT
194 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTT
3637637 T
1 T
3637638 TGGGGTACAA
Statistics
Matches: 219, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
248 133 0.61
249 7 0.03
252 78 0.36
253 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (249 bp):
TCATAAACTACTATAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGAAATTTTGCTAACAGTG
CATCCTACTTGAAGCATTTTTAACACTATTTCAGAAACATCTTCTCAAAATTATTTTTTCAAGAA
CTACTGTAGAAAAAGAACATCCACATAGGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATCCTG
CTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTT
Found at i:3637780 original size:34 final size:29
Alignment explanation
Indices: 3637744--3637952 Score: 125
Period size: 34 Copynumber: 7.1 Consensus size: 29
3637734 ACCCTAATTT
3637744 AATTTATTTAAAACCCTAGAA-TCCTAAATTACTT
1 AATTTATTTAAAACCCTA-AACT-CT-AA-T--TT
*
3637778 AATTTATTTAAAAACCATAAACTCTAATTT
1 AATTTATTT-AAAACCCTAAACTCTAATTT
3637808 AATTTATTTAAAACCCT--A---T--TTT
1 AATTTATTTAAAACCCTAAACTCTAATTT
*
3637830 AATTTATTTAAAACCCTAAACCCTAATTTACTT
1 AATTTATTTAAAACCCTAAACTCTAA--T--TT
** * *
3637863 AATTTATTTAAAAACTATAAACCCTAAACCTT
1 AATTTATTT-AAAACCCTAAACTCT-AA-TTT
*
3637895 AATTTATTTAAAACCCT-AA-T-TTATTT
1 AATTTATTTAAAACCCTAAACTCTAATTT
* *
3637921 AATTTATTTAAAAACCATAAACCCTAATTT
1 AATTTATTT-AAAACCCTAAACTCTAATTT
3637951 AA
1 AA
3637953 ATAATTTTTA
Statistics
Matches: 142, Mismatches: 14, Indels: 42
0.72 0.07 0.21
Matches are distributed among these distances:
22 20 0.14
24 2 0.01
26 11 0.08
27 10 0.07
28 3 0.02
29 7 0.05
30 20 0.14
31 7 0.05
32 12 0.08
33 13 0.09
34 26 0.18
35 11 0.08
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.40
Consensus pattern (29 bp):
AATTTATTTAAAACCCTAAACTCTAATTT
Found at i:3637830 original size:22 final size:22
Alignment explanation
Indices: 3637796--3637848 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
3637786 TAAAAACCAT
*
3637796 AAACTCTAATTTAATTTATTTA
1 AAACCCTAATTTAATTTATTTA
*
3637818 AAACCCTATTTTAATTTATTTA
1 AAACCCTAATTTAATTTATTTA
3637840 AAACCCTAA
1 AAACCCTAA
3637849 ACCCTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (22 bp):
AAACCCTAATTTAATTTATTTA
Found at i:3637914 original size:17 final size:17
Alignment explanation
Indices: 3637888--3637922 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3637878 TATAAACCCT
*
3637888 AAACCTTAATTTATTTA
1 AAACCCTAATTTATTTA
3637905 AAACCCTAATTTATTTA
1 AAACCCTAATTTATTTA
3637922 A
1 A
3637923 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (17 bp):
AAACCCTAATTTATTTA
Found at i:3637967 original size:92 final size:86
Alignment explanation
Indices: 3637732--3637951 Score: 309
Period size: 85 Copynumber: 2.5 Consensus size: 86
3637722 CATAAACCAT
* *
3637732 AAACCCTA-ATTTAATTTATTTAAAACCCTAGAATCCTAAATTACTTAATTTATTTAAAAACCAT
1 AAACCCTATATTTAATTTATTTAAAACCCTA-AACCCTAATTTACTTAATTTATTTAAAAACCAT
* *
3637796 AAACTCTAATTTAATTTATTTA
65 AAACCCTAACTTAATTTATTTA
*
3637818 AAACCCTAT-TTTAATTTATTTAAAACCCTAAACCCTAATTTACTTAATTTATTTAAAAACTATA
1 AAACCCTATATTTAATTTATTTAAAACCCTAAACCCTAATTTACTTAATTTATTTAAAAACCATA
3637882 AACCCTAAACCTTAATTTATTTA
66 AACCCT-AA-CTTAATTTATTTA
*
3637905 AAACCCTAATTTATTTAATTTATTTAAAAACCATAAACCCTAATTTA
1 AAACCCT-A--TATTTAATTTATTT-AAAACCCTAAACCCTAATTTA
3637952 AATAATTTTT
Statistics
Matches: 120, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
85 36 0.30
86 31 0.26
87 19 0.16
88 1 0.01
90 1 0.01
91 12 0.10
92 20 0.17
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (86 bp):
AAACCCTATATTTAATTTATTTAAAACCCTAAACCCTAATTTACTTAATTTATTTAAAAACCATA
AACCCTAACTTAATTTATTTA
Found at i:3638359 original size:24 final size:24
Alignment explanation
Indices: 3638313--3638359 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3638303 CTTAAATTTA
*
3638313 ATGTGAATTACCAAAATAAAAATT
1 ATGTGAATTACCAAAACAAAAATT
*
3638337 ATGTGAATTA-TAAAACAACAAAT
1 ATGTGAATTACCAAAACAA-AAAT
3638360 GGAACCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.28
Consensus pattern (24 bp):
ATGTGAATTACCAAAACAAAAATT
Found at i:3638438 original size:10 final size:10
Alignment explanation
Indices: 3638423--3638514 Score: 121
Period size: 10 Copynumber: 9.2 Consensus size: 10
3638413 ATTCAATGCG
*
3638423 TATATATACA
1 TATATATATA
3638433 TATATATATA
1 TATATATATA
*
3638443 CATATATATA
1 TATATATATA
*
3638453 CATATATATA
1 TATATATATA
*
3638463 TATGTATATA
1 TATATATATA
*
3638473 TATATATATG
1 TATATATATA
3638483 TATATATATA
1 TATATATATA
*
3638493 TGTATATATA
1 TATATATATA
*
3638503 TATATGTATA
1 TATATATATA
3638513 TA
1 TA
3638515 CACGCATTAC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 72 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (10 bp):
TATATATATA
Found at i:3638440 original size:12 final size:12
Alignment explanation
Indices: 3638423--3638514 Score: 121
Period size: 12 Copynumber: 7.7 Consensus size: 12
3638413 ATTCAATGCG
*
3638423 TATATATACATA
1 TATATATATATA
*
3638435 TATATATACATA
1 TATATATATATA
*
3638447 TATATACATATA
1 TATATATATATA
*
3638459 TATATATGTATA
1 TATATATATATA
*
3638471 TATATATATATG
1 TATATATATATA
*
3638483 TATATATATATG
1 TATATATATATA
3638495 TATATATATATA
1 TATATATATATA
*
3638507 TGTATATA
1 TATATATA
3638515 CACGCATTAC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 72 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (12 bp):
TATATATATATA
Found at i:3638442 original size:14 final size:14
Alignment explanation
Indices: 3638423--3638514 Score: 121
Period size: 14 Copynumber: 6.6 Consensus size: 14
3638413 ATTCAATGCG
*
3638423 TATATATACATATA
1 TATATATATATATA
*
3638437 TATATACATATATA
1 TATATATATATATA
*
3638451 TACATATATATATA
1 TATATATATATATA
*
3638465 TGTATATATATATA
1 TATATATATATATA
*
3638479 TATGTATATATATA
1 TATATATATATATA
*
3638493 TGTATATATATATA
1 TATATATATATATA
*
3638507 TGTATATA
1 TATATATA
3638515 CACGCATTAC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 68 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (14 bp):
TATATATATATATA
Found at i:3638648 original size:16 final size:16
Alignment explanation
Indices: 3638627--3638663 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3638617 ATGCGTATAT
3638627 ATATATATATACACAC
1 ATATATATATACACAC
*
3638643 ATATATATATACATAC
1 ATATATATATACACAC
3638659 ATATA
1 ATATA
3638664 CATACATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATATATATACACAC
Found at i:3638662 original size:14 final size:14
Alignment explanation
Indices: 3638629--3638671 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
3638619 GCGTATATAT
*
3638629 ATATATATACACAC
1 ATATATATACATAC
3638643 ATATATAT--ATAC
1 ATATATATACATAC
*
3638655 ATACATATACATAC
1 ATATATATACATAC
3638669 ATA
1 ATA
3638672 ATGTATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 10 0.40
14 15 0.60
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATATATACATAC
Found at i:3638730 original size:4 final size:4
Alignment explanation
Indices: 3638723--3638785 Score: 63
Period size: 4 Copynumber: 15.8 Consensus size: 4
3638713 ATTCAATGCG
* * * * * *
3638723 TATA TATA TATA TATA CACA TATA TATA TGTA TATG TATG TATA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
3638771 TGTA TATA TATA TAT
1 TATA TATA TATA TAT
3638786 GTCTATATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (4 bp):
TATA
Found at i:3638734 original size:6 final size:6
Alignment explanation
Indices: 3638723--3638785 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
3638713 ATTCAATGCG
* * * * * *
3638723 TATATA TATATA TATACA CATATA TATATG TATATG TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
3638771 TGTATA TATATA TAT
1 TATATA TATATA TAT
3638786 GTCTATATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (6 bp):
TATATA
Found at i:3638738 original size:10 final size:10
Alignment explanation
Indices: 3638723--3638785 Score: 63
Period size: 10 Copynumber: 6.3 Consensus size: 10
3638713 ATTCAATGCG
3638723 TATATATATA
1 TATATATATA
* *
3638733 TATATACACA
1 TATATATATA
*
3638743 TATATATATG
1 TATATATATA
* *
3638753 TATATGTATG
1 TATATATATA
* *
3638763 TATATGTATG
1 TATATATATA
3638773 TATATATATA
1 TATATATATA
3638783 TAT
1 TAT
3638786 GTCTATATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 45 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (10 bp):
TATATATATA
Found at i:3638774 original size:14 final size:14
Alignment explanation
Indices: 3638723--3638793 Score: 70
Period size: 14 Copynumber: 5.1 Consensus size: 14
3638713 ATTCAATGCG
*
3638723 TATATATATATATA
1 TATATATGTATATA
* * *
3638737 TACACATATATATA
1 TATATATGTATATA
* *
3638751 TGTATATGTATGTA
1 TATATATGTATATA
*
3638765 TATGTATGTATATA
1 TATATATGTATATA
*
3638779 TATATATGTCTATA
1 TATATATGTATATA
3638793 T
1 T
3638794 TTTTTTTGGT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 45 1.00
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.48
Consensus pattern (14 bp):
TATATATGTATATA
Found at i:3652111 original size:43 final size:43
Alignment explanation
Indices: 3652050--3652136 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
3652040 TGTTAATAAG
3652050 TTAGTATTAAAGTTTCGTTAAGAAATTTTACTATTTTGATAGC
1 TTAGTATTAAAGTTTCGTTAAGAAATTTTACTATTTTGATAGC
3652093 TTAGTATTAAAGTTTCGTTAAGAAATTTTACTATTTTGATAGC
1 TTAGTATTAAAGTTTCGTTAAGAAATTTTACTATTTTGATAGC
3652136 T
1 T
3652137 AATTGAAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (43 bp):
TTAGTATTAAAGTTTCGTTAAGAAATTTTACTATTTTGATAGC
Found at i:3653273 original size:52 final size:53
Alignment explanation
Indices: 3653213--3653401 Score: 231
Period size: 53 Copynumber: 3.6 Consensus size: 53
3653203 TGTGCGCCCT
* ** *
3653213 TATAAGACCATAGTTGGGCTATGGCATCTGTGCAATGTGAT-ACGTG-TTCCCG
1 TATAAGACCATAGTTGGGCTATGGCATCGGTGTGATGTGATAATGTGATT-CCG
* * *
3653265 TATAAGACCATAGTTGGGCTATGGCTTCGGTATGATGTGATAATGTGATTCCA
1 TATAAGACCATAGTTGGGCTATGGCATCGGTGTGATGTGATAATGTGATTCCG
* * *
3653318 TATAAGACCATAGCTGAGCTATGGCGTCGGTGTGATGTGATAATGTGATTCCG
1 TATAAGACCATAGTTGGGCTATGGCATCGGTGTGATGTGATAATGTGATTCCG
* *
3653371 TATAAAACCATA-TCTGGGATATGGCATCGGT
1 TATAAGACCATAGT-TGGGCTATGGCATCGGT
3653402 ATTATATGTG
Statistics
Matches: 117, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
52 36 0.31
53 79 0.68
54 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (53 bp):
TATAAGACCATAGTTGGGCTATGGCATCGGTGTGATGTGATAATGTGATTCCG
Found at i:3654978 original size:22 final size:22
Alignment explanation
Indices: 3654950--3655004 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
3654940 TTCTTCTTTG
3654950 TTTTCTCCTTTTCTCCAAAATT
1 TTTTCTCCTTTTCTCCAAAATT
*
3654972 TTTTCTCCTCTTCTCCAAAATT
1 TTTTCTCCTTTTCTCCAAAATT
*
3654994 TATT-TCCTTTT
1 TTTTCTCCTTTT
3655005 TCCTTATCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTCTCCTTTTCTCCAAAATT
Found at i:3662164 original size:4 final size:4
Alignment explanation
Indices: 3662155--3662180 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3662145 AACAAAACAA
3662155 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
3662181 ACGTAAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:3665599 original size:16 final size:14
Alignment explanation
Indices: 3665576--3665615 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 14
3665566 CGTCTTTCCC
3665576 TCTTTCTTTTCTCAT
1 TCTTTCTTTTCTC-T
3665591 TCTTTTCTTTTTCTCT
1 TC-TTTC-TTTTCTCT
3665607 TCTTTCTTT
1 TCTTTCTTT
3665616 AACCAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 6 0.26
16 7 0.30
17 7 0.30
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTTTCTTTTCTCT
Found at i:3667644 original size:31 final size:31
Alignment explanation
Indices: 3667606--3667669 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3667596 TTTCTGTGAA
3667606 TTTTGTCATAAATGAGTATTTGCTTCAATGG
1 TTTTGTCATAAATGAGTATTTGCTTCAATGG
3667637 TTTTGTCATAAATGAGTATTTGCTTCAATGG
1 TTTTGTCATAAATGAGTATTTGCTTCAATGG
3667668 TT
1 TT
3667670 AAGTGTTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (31 bp):
TTTTGTCATAAATGAGTATTTGCTTCAATGG
Found at i:3669477 original size:42 final size:42
Alignment explanation
Indices: 3669411--3669537 Score: 161
Period size: 42 Copynumber: 3.0 Consensus size: 42
3669401 CTTCGTTTTC
** * * *
3669411 TCGATGCCATAGTTCAACTGTGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
3669454 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
3669495 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
3669536 TC
1 TC
3669538 TCACTGATGC
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 10 0.13
42 63 0.84
43 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:3669600 original size:47 final size:46
Alignment explanation
Indices: 3669496--3669619 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
3669486 ATTCATATAT
* * * * *
3669496 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * * *
3669542 TGATGCTATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
3669589 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
3669620 GAAATCACTT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 26 0.39
47 40 0.61
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Done.