Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 100 of 190
Found at i:30324308 original size:24 final size:24
Alignment explanation
Indices: 30324281--30324327 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
30324271 CATATTATTA
* * *
30324281 TTTATCCATAGTATATAAAATATG
1 TTTATCAAAAGTAGATAAAATATG
*
30324305 TTTATTAAAAGTAGATAAAATAT
1 TTTATCAAAAGTAGATAAAATAT
30324328 TCACCTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (24 bp):
TTTATCAAAAGTAGATAAAATATG
Found at i:30326113 original size:18 final size:18
Alignment explanation
Indices: 30326090--30326127 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
30326080 TAAATTTTTT
30326090 TATTTTTTAATTTTAAAA
1 TATTTTTTAATTTTAAAA
*
30326108 TATTTTTTATTTTTAAAA
1 TATTTTTTAATTTTAAAA
30326126 TA
1 TA
30326128 AATTTTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTTTTAATTTTAAAA
Found at i:30326133 original size:18 final size:18
Alignment explanation
Indices: 30326094--30326133 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30326084 TTTTTTTATT
**
30326094 TTTTAATTTTAAAATATT
1 TTTTAATTTTAAAATAAA
*
30326112 TTTTATTTTTAAAATAAA
1 TTTTAATTTTAAAATAAA
30326130 TTTT
1 TTTT
30326134 TGGTGTTTAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTAATTTTAAAATAAA
Found at i:30333776 original size:19 final size:20
Alignment explanation
Indices: 30333749--30333803 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
30333739 TTAGTGTCCT
*
30333749 TGTTCGCACTACGGTG-CCC
1 TGTTTGCACTACGGTGCCCC
*
30333768 TGTTTGCAC-ATCTGTGCCCC
1 TGTTTGCACTA-CGGTGCCCC
* *
30333788 TGTCTGCACTCCGGTG
1 TGTTTGCACTACGGTG
30333804 TTCTTGTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.04
19 12 0.43
20 15 0.54
ACGTcount: A:0.09, C:0.35, G:0.25, T:0.31
Consensus pattern (20 bp):
TGTTTGCACTACGGTGCCCC
Found at i:30335939 original size:22 final size:22
Alignment explanation
Indices: 30335911--30335953 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
30335901 TTTTTGGCTA
30335911 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
30335933 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
30335954 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:30337562 original size:25 final size:25
Alignment explanation
Indices: 30337524--30337594 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
30337514 CAGACCCATT
*
30337524 TCACAGCTCATGTGAGCATTTACAG
1 TCACAGCTCGTGTGAGCATTTACAG
*
30337549 TCACAGCTCGTGTGAGCATTTACTG
1 TCACAGCTCGTGTGAGCATTTACAG
* *
30337574 TCACAGCTTGTGTGAGTATTT
1 TCACAGCTCGTGTGAGCATTT
30337595 TCTCGTGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (25 bp):
TCACAGCTCGTGTGAGCATTTACAG
Found at i:30339029 original size:22 final size:21
Alignment explanation
Indices: 30338977--30339032 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
30338967 TTACAGAGTG
*
30338977 GGTCATGACATTGAGCTCTAG
1 GGTCATGACATTGAGCTCTAA
** *
30338998 GGTCGCGACATTGATCTCCTAA
1 GGTCATGACATTGAGCT-CTAA
30339020 GGTCATGACATTG
1 GGTCATGACATTG
30339033 TGTGCAGTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (21 bp):
GGTCATGACATTGAGCTCTAA
Found at i:30340018 original size:21 final size:21
Alignment explanation
Indices: 30339968--30340019 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
30339958 ATTTTCTGGT
30339968 AACTTCAAATCCAACAAAAAA
1 AACTTCAAATCCAACAAAAAA
*
30339989 AA-TTAAAATCCAACAAAAAA
1 AACTTCAAATCCAACAAAAAA
30340009 AACTTCAAATC
1 AACTTCAAATC
30340020 TAGACGGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (21 bp):
AACTTCAAATCCAACAAAAAA
Found at i:30340246 original size:21 final size:21
Alignment explanation
Indices: 30340221--30340289 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
30340211 ATTTTCTTAT
*
30340221 TGCCTCTGCTACCCTTGCTGT
1 TGCCTCTGCTACCCTTGCTGC
* *
30340242 TGCCTTTGCTACCCTTGTTGC
1 TGCCTCTGCTACCCTTGCTGC
* * *
30340263 TGCCTTTGCTTCCCTCGCTGC
1 TGCCTCTGCTACCCTTGCTGC
30340284 TGCCTC
1 TGCCTC
30340290 CGCTTTCAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.03, C:0.39, G:0.19, T:0.39
Consensus pattern (21 bp):
TGCCTCTGCTACCCTTGCTGC
Found at i:30345913 original size:50 final size:49
Alignment explanation
Indices: 30345788--30346086 Score: 221
Period size: 50 Copynumber: 6.0 Consensus size: 49
30345778 GATATTAACA
* * * ** * *
30345788 TGCCAAAGCCATGTTCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT-T-CGG
* * * * * * ** *
30345837 TGCAAATGCCATATCTCAGATATGGTCTTACATGAGAGTTTTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT-TCGG
* **
30345887 TGCCTATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT-TCGG
* * *
30345937 TGCCAACGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATTCGG
* **
30345986 TGCCAATGCCATGTCCTAGACATGGTCTTAC-GTGGGACCTCTCATAGCCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAG-GGGACCTCTCAT----TC---GG
*
30346042 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA--TCTCATTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATTC
30346087 CCTTAATGTC
Statistics
Matches: 204, Mismatches: 35, Indels: 21
0.78 0.13 0.08
Matches are distributed among these distances:
48 2 0.01
49 80 0.39
50 81 0.40
53 1 0.00
54 6 0.03
56 34 0.17
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATTCGG
Found at i:30345987 original size:99 final size:101
Alignment explanation
Indices: 30345884--30346072 Score: 265
Period size: 99 Copynumber: 1.9 Consensus size: 101
30345874 GTTTTCATAT
* * **
30345884 CGGTGCCTATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCAT-CTC-GGTGCCAACGCC
1 CGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATACTCAAATGCCAACGCC
30345947 ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATC
66 ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATC
* *
30345983 CGGTGCCAATGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATAGCCTCAATAATGCCAA
1 CGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATA--CTC-A-AATGCCAA
*
30346048 TGCCATGTCCCAGACATGGTCTTAC
62 CGCCATGTCCCAGACATGGTCTTAC
30346073 ATGGGATCTC
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
99 44 0.57
102 3 0.04
105 30 0.39
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.25
Consensus pattern (101 bp):
CGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATACTCAAATGCCAACGCC
ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATC
Found at i:30346007 original size:49 final size:50
Alignment explanation
Indices: 30345878--30346072 Score: 257
Period size: 50 Copynumber: 3.8 Consensus size: 50
30345868 ATGAGAGTTT
* * *
30345878 TCATATCGGTGCCTATGCCATGTCCCAGACATGGTCTTATGGGGGACCTC
1 TCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTC
*
30345928 TCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACGGGGGACCTC
1 TCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTC
* *
30345978 TCATC-CGGTGCCAATGCCATGTCCTAGACATGGTCTTACGTGGGACCTC
1 TCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTC
**
30346027 TCATAGCCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTAC
1 TCAT---CTC---GGTGCCAATGCCATGTCCCAGACATGGTCTTAC
30346073 ATGGGATCTC
Statistics
Matches: 128, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
49 45 0.35
50 51 0.40
52 1 0.01
53 1 0.01
56 30 0.23
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTC
Found at i:30352262 original size:24 final size:24
Alignment explanation
Indices: 30352234--30352285 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
30352224 TTGGGAAAGA
*
30352234 AAAAATTAAGTTAGGGAATTGGGG
1 AAAAATTAAGTTAGGGAATTGGAG
* *
30352258 AAAAATTTAGTTAGGGATTTGGAG
1 AAAAATTAAGTTAGGGAATTGGAG
30352282 AAAA
1 AAAA
30352286 TGATTTAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (24 bp):
AAAAATTAAGTTAGGGAATTGGAG
Found at i:30352788 original size:20 final size:20
Alignment explanation
Indices: 30352765--30352806 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
30352755 TTAATTTATT
*
30352765 AATTTAAAT-TTTGGGGACTA
1 AATTGAAATATTT-GGGACTA
*
30352785 AATTGAAATATTTTGGACTA
1 AATTGAAATATTTGGGACTA
30352805 AA
1 AA
30352807 CTAAATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (20 bp):
AATTGAAATATTTGGGACTA
Found at i:30360768 original size:27 final size:27
Alignment explanation
Indices: 30360738--30360794 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
30360728 AGGATAAGAT
30360738 TTATTCTTAACAGATCTCTTTAAAAAC
1 TTATTCTTAACAGATCTCTTTAAAAAC
30360765 TTATTCTTAACAGATCTCTTTAAAAAC
1 TTATTCTTAACAGATCTCTTTAAAAAC
30360792 TTA
1 TTA
30360795 CTCTGTACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.42
Consensus pattern (27 bp):
TTATTCTTAACAGATCTCTTTAAAAAC
Found at i:30363430 original size:22 final size:22
Alignment explanation
Indices: 30363402--30363473 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
30363392 TCCATTTATC
30363402 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
30363424 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
30363446 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
30363468 CTCATG
1 CTCATG
30363474 TTTGAACAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:30373065 original size:3 final size:3
Alignment explanation
Indices: 30373057--30373102 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
30373047 AGTGCATAAA
30373057 GAT GAT GAT -AT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
30373103 GATCTTTGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:30377274 original size:27 final size:26
Alignment explanation
Indices: 30377240--30377412 Score: 193
Period size: 27 Copynumber: 6.4 Consensus size: 26
30377230 CCCTAAAATA
* *
30377240 GGTAAAATAACAAAAATACCACCATAG
1 GGTAAAATGACCAAAATACC-CCATAG
30377267 GGTAAAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCC-ATAG
* * * *
30377294 GGTAAACTGATCGAAATACCCCTATAA
1 GGTAAAATGACCAAAATACCCC-ATAG
* *
30377321 GGTAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCAAAATA-CCCCATAG
*
30377348 GGTAGAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCAAAATA-CCCCATAG
* *
30377375 GGTAAAATGACCGAAATACCTCAATAG
1 GGTAAAATGACCAAAATACC-CCATAG
30377402 GGTAAAATGAC
1 GGTAAAATGAC
30377413 TGTTATACCC
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
26 4 0.03
27 121 0.94
28 4 0.03
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (26 bp):
GGTAAAATGACCAAAATACCCCATAG
Found at i:30377423 original size:81 final size:81
Alignment explanation
Indices: 30377239--30377412 Score: 240
Period size: 81 Copynumber: 2.1 Consensus size: 81
30377229 ACCCTAAAAT
* ** * * *
30377239 AGGTAAAATAACAAAAATACCACCATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAACTGA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGA
* *
30377304 TCGAAATACCCCTATA
66 CCGAAATACCCCAATA
* *
30377320 AGGTAGAATGACCGAAATACCCCCATAGGGTAGAATGACCAAAATACCCCCATAGGGTAAAATGA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGA
*
30377385 CCGAAATACCTCAATA
66 CCGAAATACCCCAATA
*
30377401 GGGTAAAATGAC
1 AGGTAAAATGAC
30377413 TGTTATACCC
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (81 bp):
AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGA
CCGAAATACCCCAATA
Found at i:30377439 original size:54 final size:54
Alignment explanation
Indices: 30377236--30377412 Score: 221
Period size: 54 Copynumber: 3.3 Consensus size: 54
30377226 GAGACCCTAA
* * * *
30377236 AATA-GGTAAAATAACAAAAATACCACCATAGGGTAAAATGACCAAAATACCCC
1 AATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCC
* * * * * * *
30377289 TATAGGGTAAACTGATCGAAATACCCCTATAAGGTAGAATGACCGAAATACCCC
1 AATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCC
* * *
30377343 CATAGGGTAGAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCTC
1 AATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCC
30377397 AATAGGGTAAAATGAC
1 AATAGGGTAAAATGAC
30377413 TGTTATACCC
Statistics
Matches: 101, Mismatches: 22, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
53 3 0.03
54 98 0.97
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.18
Consensus pattern (54 bp):
AATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCC
Found at i:30379970 original size:20 final size:21
Alignment explanation
Indices: 30379945--30379984 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
30379935 GGGTCAGAAG
30379945 AAAAAGTTTAGGAG-GAAAAT
1 AAAAAGTTTAGGAGAGAAAAT
*
30379965 AAAAAGTTTTGGAGAGAAAA
1 AAAAAGTTTAGGAGAGAAAA
30379985 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:30379998 original size:23 final size:23
Alignment explanation
Indices: 30379971--30380014 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
30379961 AAATAAAAAG
30379971 TTTTGGAGAGAAAAAGTTTAATA
1 TTTTGGAGAGAAAAAGTTTAATA
*
30379994 TTTTGGAGAGAAAATGTTTAA
1 TTTTGGAGAGAAAAAGTTTAA
30380015 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:30380321 original size:9 final size:9
Alignment explanation
Indices: 30380303--30380339 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
30380293 TATAATTTTA
30380303 TATTCGAAT
1 TATTCGAAT
*
30380312 TATTCTAAT
1 TATTCGAAT
*
30380321 TATTCGAGT
1 TATTCGAAT
30380330 TATTCGAAT
1 TATTCGAAT
30380339 T
1 T
30380340 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:30396108 original size:87 final size:87
Alignment explanation
Indices: 30396002--30396430 Score: 651
Period size: 87 Copynumber: 4.9 Consensus size: 87
30395992 AATTCAATCT
* *
30396002 GCTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTTCGATCTGTTTCGCTGTTAACGCAGGAAGG
1 GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
*
30396067 CAAGATCTGTTATCTTTAACAA
66 CAAGATCTGCTATCTTTAACAA
* * *
30396089 GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTCAATGCAGGAAGG
1 GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
* * * *
30396154 CAAGATATGTTATTTTTAACCA
66 CAAGATCTGCTATCTTTAACAA
* * * *
30396176 GCTCCACTGCAAACGATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGTTGTTAACGTAGGAAGG
1 GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
30396241 CAAGATCTGCTATCTTTAACAA
66 CAAGATCTGCTATCTTTAACAA
* * *
30396263 GCTCCACTGCAACAGATGGAGGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAACGCGGGAAGG
1 GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
*
30396328 CAAGATCTGCTATCTTTAACCA
66 CAAGATCTGCTATCTTTAACAA
* * * *
30396350 GCTCCACTACAACCGATAGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGG
1 GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
*
30396415 CAAGATCTGCTGTCTT
66 CAAGATCTGCTATCTT
30396431 CACTGATCTG
Statistics
Matches: 307, Mismatches: 35, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 307 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (87 bp):
GCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGG
CAAGATCTGCTATCTTTAACAA
Found at i:30396201 original size:44 final size:44
Alignment explanation
Indices: 30396064--30396375 Score: 122
Period size: 42 Copynumber: 7.2 Consensus size: 44
30396054 TAACGCAGGA
* * *
30396064 AGGCAAGATCTGTTATCTTTAACAAGCTCCACTGCAACCGATGG
1 AGGCAAGATCTGTTATTTTTAACCAGCTCCACTGCAAACGATGG
* * ** * * * *
30396108 AGGCAAG-GCT-TTGTTTTCGATCTGCTTCACTGTC-AATGCA-GG
1 AGGCAAGATCTGTTATTTTTAACCAGCTCCACTG-CAAACG-ATGG
*
30396150 AAGGCAAGATATGTTATTTTTAACCAGCTCCACTGCAAACGATGG
1 -AGGCAAGATCTGTTATTTTTAACCAGCTCCACTGCAAACGATGG
* * * * * * ** **
30396195 AGGCAAG-GCT-TTGTTTTTGATCTGCTTCGTTGTTAACG-TAGG
1 AGGCAAGATCTGTTATTTTTAACCAGCTCCACTGCAAACGAT-GG
* * *
30396237 AAGGCAAGATCTGCTATCTTTAACAAGCTCCACTGC-AACAGATGG
1 -AGGCAAGATCTGTTATTTTTAACCAGCTCCACTGCAAAC-GATGG
* * * * * * * ** **
30396282 AGGCAAG-GCT-TTGTTTTCAATCTGCTTCGCTGTTAACGCGGG
1 AGGCAAGATCTGTTATTTTTAACCAGCTCCACTGCAAACGATGG
* * * * *
30396324 AAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATAG
1 -AGGCAAGATCTGTTATTTTTAACCAGCTCCACTGCAAACGATGG
30396369 AGGCAAG
1 AGGCAAG
30396376 GCTTTGTTTT
Statistics
Matches: 179, Mismatches: 72, Indels: 34
0.63 0.25 0.12
Matches are distributed among these distances:
41 1 0.01
42 55 0.31
43 31 0.17
44 38 0.21
45 53 0.30
46 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (44 bp):
AGGCAAGATCTGTTATTTTTAACCAGCTCCACTGCAAACGATGG
Found at i:30397659 original size:7 final size:7
Alignment explanation
Indices: 30397640--30397694 Score: 78
Period size: 7 Copynumber: 8.0 Consensus size: 7
30397630 TTAGCCTCTC
30397640 CATTTTT
1 CATTTTT
30397647 -ATTTTTT
1 CA-TTTTT
30397654 CA-TTTT
1 CATTTTT
*
30397660 CACTTTT
1 CATTTTT
30397667 CATTTTT
1 CATTTTT
30397674 CATTTTT
1 CATTTTT
30397681 CATTTTT
1 CATTTTT
30397688 CATTTTT
1 CATTTTT
30397695 TTTACTCTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
6 7 0.16
7 36 0.82
8 1 0.02
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:30397666 original size:21 final size:21
Alignment explanation
Indices: 30397640--30397695 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
30397630 TTAGCCTCTC
30397640 CATTTTTATTTTTTCA-TTTT
1 CATTTTTATTTTTTCATTTTT
*
30397660 CACTTTTCA-TTTTTCATTTTT
1 CA-TTTTTATTTTTTCATTTTT
30397681 CATTTTTCATTTTTT
1 CATTTTT-ATTTTTT
30397696 TTACTCTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (21 bp):
CATTTTTATTTTTTCATTTTT
Found at i:30398600 original size:35 final size:34
Alignment explanation
Indices: 30398533--30398632 Score: 98
Period size: 35 Copynumber: 2.9 Consensus size: 34
30398523 CCTCTCCTTT
* * *
30398533 TTCTT-TTCATTTTGACTTTGATTTTGATTTTTTGC
1 TTCTTCTTCTTTTTGATTTTGATTTT--TTTTTTTC
*
30398568 TT-TTTTTGC-TTTTGATTTTGATTTTTTCTTTTTC
1 TTCTTCTT-CTTTTTGATTTTGATTTTTT-TTTTTC
*
30398602 TTCTTCTTCTTTTTGTTTTTGATTTTTTTTT
1 TTCTTCTTCTTTTTGATTTTGATTTTTTTTT
30398633 ACTCTAAACT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
33 2 0.04
34 13 0.23
35 40 0.71
36 1 0.02
ACGTcount: A:0.07, C:0.10, G:0.09, T:0.74
Consensus pattern (34 bp):
TTCTTCTTCTTTTTGATTTTGATTTTTTTTTTTC
Found at i:30398615 original size:29 final size:29
Alignment explanation
Indices: 30398553--30398630 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
30398543 TTTGACTTTG
*
30398553 ATTTTGATTTTTTGCTTTTTTTGCTTTTG
1 ATTTTGATTTTTTGCTTTTTTTGCTTTTC
30398582 ATTTTGATTTTTT-CTTTTTCTT-CTTCTTC
1 ATTTTGATTTTTTGCTTTTT-TTGCTT-TTC
* *
30398611 TTTTTG--TTTTTGATTTTTTT
1 ATTTTGATTTTTTGCTTTTTTT
30398631 TTACTCTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
27 7 0.16
28 14 0.33
29 22 0.51
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.76
Consensus pattern (29 bp):
ATTTTGATTTTTTGCTTTTTTTGCTTTTC
Found at i:30416441 original size:6 final size:6
Alignment explanation
Indices: 30416430--30416456 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30416420 ATCAAGGATG
30416430 GGGGAA GGGGAA GGGGAA GGGGAA GGG
1 GGGGAA GGGGAA GGGGAA GGGGAA GGG
30416457 AAATGGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:30418677 original size:13 final size:14
Alignment explanation
Indices: 30418640--30418676 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
30418630 CTCGTATCGA
30418640 TTTTCTTTTTGAAT
1 TTTTCTTTTTGAAT
30418654 TTTTCTTTTTGAAT
1 TTTTCTTTTTGAAT
30418668 TTTTCTTTT
1 TTTTCTTTT
30418677 GTTCTGCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTGAAT
Found at i:30419304 original size:17 final size:17
Alignment explanation
Indices: 30419282--30419314 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30419272 AAGAAAAGCA
*
30419282 TAAAAATTAAAACAAAT
1 TAAAAATCAAAACAAAT
30419299 TAAAAATCAAAACAAA
1 TAAAAATCAAAACAAA
30419315 ATTCCTATGT
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:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (17 bp):
TAAAAATCAAAACAAAT
Found at i:30431989 original size:39 final size:39
Alignment explanation
Indices: 30431896--30431995 Score: 132
Period size: 39 Copynumber: 2.6 Consensus size: 39
30431886 GAAATCCTTG
* *
30431896 TTATAATTATTGTAATTATAA-TTTATGATCGAATATTA
1 TTATAATTATTGTAATTATAATTTTATGATCAAACATTA
* * *
30431934 TTATAATTATTGTAATTGTAATTTTTTGGTCAAACATTA
1 TTATAATTATTGTAATTATAATTTTATGATCAAACATTA
30431973 TTATAATTA-TGATAATTATAATT
1 TTATAATTATTG-TAATTATAATT
30431996 ATTAAATTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
38 22 0.41
39 32 0.59
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (39 bp):
TTATAATTATTGTAATTATAATTTTATGATCAAACATTA
Found at i:30441234 original size:23 final size:23
Alignment explanation
Indices: 30441208--30441255 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
30441198 TTTGTGGCGT
30441208 TTCAGTAAT-GCCTATATGGCATA
1 TTCAGT-ATCGCCTATATGGCATA
* *
30441231 TTCAGTCTCGCCTTTATGGCATA
1 TTCAGTATCGCCTATATGGCATA
30441254 TT
1 TT
30441256 ATGATTTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (23 bp):
TTCAGTATCGCCTATATGGCATA
Found at i:30441354 original size:26 final size:26
Alignment explanation
Indices: 30441302--30441356 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
30441292 GGCGTATTTA
** **
30441302 GTTAGCCTTTATGATGTATCCTGTAT
1 GTTAGCCTTTATGACATATCCACTAT
*
30441328 GTTAGCCTTTATGACATATTCACTAT
1 GTTAGCCTTTATGACATATCCACTAT
30441354 GTT
1 GTT
30441357 TCCTTTGTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (26 bp):
GTTAGCCTTTATGACATATCCACTAT
Found at i:30442612 original size:23 final size:23
Alignment explanation
Indices: 30442598--30442649 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
30442588 CTTTATGGTG
*
30442598 TATTCTATGATGCCTATGTGGCA
1 TATTCTATGATGCCTATATGGCA
* **
30442621 TATTCTATGATGCCTGTGGGGCA
1 TATTCTATGATGCCTATATGGCA
30442644 TATTCT
1 TATTCT
30442650 GTAAAGCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (23 bp):
TATTCTATGATGCCTATATGGCA
Found at i:30448660 original size:6 final size:6
Alignment explanation
Indices: 30448644--30448682 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
30448634 TGATTTTCTC
* *
30448644 AAAATG GAAATG AAAATG ACAATG AAAATG AGAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG AA
30448683 TTCATTTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.62, C:0.03, G:0.21, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:30450081 original size:28 final size:28
Alignment explanation
Indices: 30450041--30450098 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
30450031 CATTTAGACC
30450041 ATCCATAGTTACGAATATGCCAAATTTT
1 ATCCATAGTTACGAATATGCCAAATTTT
30450069 ATCCATAGTTACGAATATGCCAAATTTT
1 ATCCATAGTTACGAATATGCCAAATTTT
30450097 AT
1 AT
30450099 GTACTAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (28 bp):
ATCCATAGTTACGAATATGCCAAATTTT
Found at i:30450344 original size:23 final size:23
Alignment explanation
Indices: 30450318--30450401 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
30450308 TTGCCTCAAG
*
30450318 GGCATTACAGAATACGCCATAAA
1 GGCATCACAGAATACGCCATAAA
* *
30450341 GGCATCATAGAATACGCCACAAA
1 GGCATCACAGAATACGCCATAAA
*
30450364 GGCATCACAGAATATGCCATAAA
1 GGCATCACAGAATACGCCATAAA
* *
30450387 GGAATCATAGAATAC
1 GGCATCACAGAATAC
30450402 ACCACAGAGC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (23 bp):
GGCATCACAGAATACGCCATAAA
Found at i:30450376 original size:46 final size:46
Alignment explanation
Indices: 30450318--30450407 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
30450308 TTGCCTCAAG
* * *
30450318 GGCATTACAGAATACGCCATAAAGGCATCATAGAATACGCCACAAA
1 GGCATCACAGAATACGCCATAAAGGAATCATAGAATACACCACAAA
*
30450364 GGCATCACAGAATATGCCATAAAGGAATCATAGAATACACCACA
1 GGCATCACAGAATACGCCATAAAGGAATCATAGAATACACCACA
30450408 GAGCGTGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (46 bp):
GGCATCACAGAATACGCCATAAAGGAATCATAGAATACACCACAAA
Found at i:30452818 original size:9 final size:9
Alignment explanation
Indices: 30452799--30452829 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
30452789 ATTTATTCTC
30452799 CTTTT-TTT
1 CTTTTCTTT
30452807 CTTTTCTTT
1 CTTTTCTTT
30452816 CTTTTCTTT
1 CTTTTCTTT
30452825 CTTTT
1 CTTTT
30452830 TTTTTTACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
CTTTTCTTT
Found at i:30452851 original size:9 final size:9
Alignment explanation
Indices: 30452800--30452851 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
30452790 TTTATTCTCC
30452800 TTTTTTTCT
1 TTTTTTTCT
*
30452809 TTTCTTTCT
1 TTTTTTTCT
*
30452818 TTTCTTTCT
1 TTTTTTTCT
30452827 TTTTTTT-T
1 TTTTTTTCT
**
30452835 TACCTTTTCT
1 T-TTTTTTCT
30452845 TTTTTTT
1 TTTTTTT
30452852 AATGGAAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 2 0.06
9 31 0.89
10 2 0.06
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:30462218 original size:48 final size:48
Alignment explanation
Indices: 30462159--30462355 Score: 252
Period size: 48 Copynumber: 4.1 Consensus size: 48
30462149 AACAAATTTC
* * * * * *
30462159 TCGGTGGCCTGCATACAGTCTGTACCACCTTTGTGTAATAACAGATTC
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
* * * * *
30462207 TCGGTGGCCTGCATATAGTCCGTTCCACCCTTGTATCCTAACA-AGTTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGA-TTA
* * *
30462255 TTGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCACAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
30462303 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
30462351 TCGGT
1 TCGGT
30462356 ACGCATAGTA
Statistics
Matches: 128, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
47 1 0.01
48 126 0.98
49 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (48 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
Found at i:30469506 original size:48 final size:49
Alignment explanation
Indices: 30469375--30469514 Score: 175
Period size: 48 Copynumber: 2.9 Consensus size: 49
30469365 CAGATTTCTC
* * *
30469375 GGTGGCCTGCACACAGTCCGTTCCACCCTTGTATC-CTAACAAGTTATT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCACTAACAAGATATT
30469423 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAC-AAC-AGAATATCT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCACTAACAAG-ATAT-T
* *
30469472 -GTGGCCTGCACACAGTCTGTGCCACCCTTATGTCA-TAA-AAGAT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCACTAACAAGAT
30469515 TATCGGTACA
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
47 4 0.05
48 76 0.93
49 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (49 bp):
GGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCACTAACAAGATATT
Found at i:30478542 original size:23 final size:23
Alignment explanation
Indices: 30478483--30478561 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
30478473 CACCTTAAGG
* ** *
30478483 GCATTACAGAATACACCACAAAG
1 GCATCACAGAATATGCCACAAAA
*
30478506 GCATCACAAAATATGCCACAAAA
1 GCATCACAGAATATGCCACAAAA
*
30478529 GCATCACAGAATATGCCACACAA
1 GCATCACAGAATATGCCACAAAA
*
30478552 GTATCACAGA
1 GCATCACAGA
30478562 GTGTAATACC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.47, C:0.27, G:0.13, T:0.14
Consensus pattern (23 bp):
GCATCACAGAATATGCCACAAAA
Found at i:30489718 original size:2 final size:2
Alignment explanation
Indices: 30489702--30489748 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
30489692 GAGAGCCTTA
*
30489702 AG AG -G AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30489743 AG AG AG
1 AG AG AG
30489749 TGTGTGTGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30489753 original size:2 final size:2
Alignment explanation
Indices: 30489748--30489772 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30489738 GAGAGAGAGA
30489748 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
30489773 AGTCAATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:30492945 original size:223 final size:229
Alignment explanation
Indices: 30492559--30493273 Score: 721
Period size: 223 Copynumber: 3.0 Consensus size: 229
30492549 AAGTAACACG
* * * *
30492559 TAATATATTAATCATTATCATATATTATCGTTTATTATTCTAGTTGAAATATGCTCTGAGTCCTT
1 TAATATATTAATTATTATCATAT-TT-T--TTTATTATACTAGTTGAAATATGCTCTAAGTCCCT
* * *
30492624 ATACTTTTCCTACATGTGAAAGTTAACCCTCCTACTATAATATATAATGTTATATCATATCATAC
62 ATACTTTTCATACATTTGAAAGTTAACCCT--TACTAT-ATATATAATGTTATATCATATCATAT
* * *
30492689 AGTGTATAATATATTAATATTTATATGTATGCATCAATGATTAAACATTATAATATCATGTAATA
124 AGTATATAATATATTAATAGTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATA
* *
30492754 CTATATCTTTTATTATATTCTATAATATAATAGTAGTGCAT-
189 CTATATCTTTTATTATAATCTATAATATAATA-TAGTACATA
30492795 T-ATATATTAATTATTATCATATTTTTTT-TTATACT-GATTGAAATATGCTCTAAGTCCCTATA
1 TAATATATTAATTATTATCATATTTTTTTATTATACTAG-TTGAAATATGCTCTAAGTCCCTATA
* * * * *
30492857 ATTTTCGTACATTTGAAAGTT-AGCCTT-C-GTAT-TATAATGTTAGATCATATCAT-TAGTATA
65 CTTTTCATACATTTGAAAGTTAACCCTTACTATATATATAATGTTATATCATATCATATAGTATA
* *
30492917 TAATATATTAATAGCTTATATATATGCATCAATGATCAAACATTATAATATCATCTAATACTATA
130 TAATATATTAATAG-TTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATA
* *
30492982 TCTTTTATTATAGTCTATAATATAATAATAGTTATATA
194 TCTTTTATTATAATCTATAATATAAT-ATAG-TACATA
30493020 TAATAGTAGTATAGTATATATTATTTACTATATATTATTGTTTATTATTATACTAGTTGAAATAT
1 TAATA-TA-T-TA--AT-TATTA--T-C-----A-TATT-TTT-TTATTATACTAGTTGAAATAT
* * * * * * * *
30493085 GTTTTAAGTCTCTATACTTTTTATACATTTTAAAGTTAATCATCTTCCTATATTATATAATGCTA
49 GCTCTAAGTCCCTATACTTTTCATACATTTGAAAGTTAA-C-CCTTACTATA-TATATAATGTTA
* * * * * *
30493150 TATCATATCATGTAATATGTAATATATCAATAGTT-TATATTTGCATCAATAATTAAACATTATA
111 TATCATATCATATAGTATATAATATATTAATAGTTATATATATGCATCAATGATTAAACATTATA
* * *
30493214 ATACCATGTAATACTATATATTTTATTATAATCTATAATATAATATAGTTATATA
176 ATATCATGTAATACTATATCTTTTATTATAATCTATAATATAATATAG-TACATA
30493269 TAATA
1 TAATA
30493274 GTAGTACATT
Statistics
Matches: 405, Mismatches: 41, Indels: 53
0.81 0.08 0.11
Matches are distributed among these distances:
222 18 0.04
223 95 0.23
224 6 0.01
225 2 0.00
226 4 0.01
227 3 0.01
228 1 0.00
229 7 0.02
230 47 0.12
231 5 0.01
232 5 0.01
233 1 0.00
234 3 0.01
235 21 0.05
236 1 0.00
240 1 0.00
241 4 0.01
242 3 0.01
243 2 0.00
244 46 0.11
245 2 0.00
247 3 0.01
248 1 0.00
249 18 0.04
250 67 0.17
251 21 0.05
252 18 0.04
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.45
Consensus pattern (229 bp):
TAATATATTAATTATTATCATATTTTTTTATTATACTAGTTGAAATATGCTCTAAGTCCCTATAC
TTTTCATACATTTGAAAGTTAACCCTTACTATATATATAATGTTATATCATATCATATAGTATAT
AATATATTAATAGTTATATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATATC
TTTTATTATAATCTATAATATAATATAGTACATA
Found at i:30493022 original size:16 final size:17
Alignment explanation
Indices: 30492991--30493039 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
30492981 ATCTTTTATT
*
30492991 ATAGTCTATAATATAATA
1 ATAGTATAT-ATATAATA
30493009 ATAGT-TATATATAATA
1 ATAGTATATATATAATA
*
30493025 GTAGTATAGTATATA
1 ATAGTATA-TATATA
30493040 TTATTTACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.43
17 5 0.18
18 11 0.39
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (17 bp):
ATAGTATATATATAATA
Found at i:30497527 original size:50 final size:48
Alignment explanation
Indices: 30497470--30497605 Score: 166
Period size: 50 Copynumber: 2.7 Consensus size: 48
30497460 TCTAGAGTCA
* **
30497470 ATGCCATGTCCCAGACATCGTCTTACACTG-ACTCTTCTCTGTCCGTGTTG
1 ATGCCATGTCCCAGACAT-GTCTTACACTGCACTC--CTCGGTCCGTGCCG
*
30497520 ATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCTCGGTCTGTGCCG
1 ATGCCATGTCCCAGACAT-GTCTTACACT-GCACTCCTCGGTCCGTGCCG
30497570 ATGCCATGTCCCAGACATGCTCTTACACTGGCACTC
1 ATGCCATGTCCCAGACATG-TCTTACACT-GCACTC
30497606 ACCGATGCCA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
49 1 0.01
50 71 0.92
51 1 0.01
52 4 0.05
ACGTcount: A:0.18, C:0.34, G:0.19, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGTCTTACACTGCACTCCTCGGTCCGTGCCG
Found at i:30497622 original size:40 final size:40
Alignment explanation
Indices: 30497567--30497643 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
30497557 TCGGTCTGTG
30497567 CCGATGCCATGTCCCAGACATGCTCTTACACTGGCACTCA
1 CCGATGCCATGTCCCAGACATGCTCTTACACTGGCACTCA
30497607 CCGATGCCATGTCCCAGACATGCTCTTACACTGGCAC
1 CCGATGCCATGTCCCAGACATGCTCTTACACTGGCAC
30497644 ACTTACTACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.22
Consensus pattern (40 bp):
CCGATGCCATGTCCCAGACATGCTCTTACACTGGCACTCA
Found at i:30497718 original size:44 final size:44
Alignment explanation
Indices: 30497664--30497758 Score: 172
Period size: 44 Copynumber: 2.2 Consensus size: 44
30497654 ATGGTCCAAC
* *
30497664 CATGGTCTTTTCCGTCAATTCTTTCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
30497708 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
30497752 CATGGAC
1 CATGGAC
30497759 CTTGAGATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (44 bp):
CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
Found at i:30499725 original size:226 final size:227
Alignment explanation
Indices: 30499301--30499766 Score: 652
Period size: 226 Copynumber: 2.1 Consensus size: 227
30499291 ATGTCATATC
* * * *
30499301 ATATATATAATATATTAATAGCTTATATTTATGCATCAATGATTAAACATTATAATATTATGTAA
1 ATATATATAATATATTAATAGCTTATATATATGCATAAATAATTAAACATTATAATATCATGTAA
*
30499366 TATTATATATTTTATTATAATTGATAATATAATAATAGTTATATATAATAGTAGTACAATATATA
66 TACTATATATTTTATTATAATTGATAATATAATAATAGTTATATATAATAGTAGTACAATATATA
* *
30499431 TTACATATTATTATATATAATTGTTTATTAGTATACTAGTTGAAATATGCTCTAAGTCCCTATAC
131 TTACATATTATTATATATAATTATTTATTAGTATACTAGTTGAAATATGCTCAAAGTCCCTATAC
*
30499496 TTTTCGTACATTTGAAAA-TTAGCTTTCTTGCT
196 TTTTCATACATTT-AAAAGTTAGCTTTCTTGCT
*
30499528 ATATCATATCATATATTAATAG-TT-TATATATGCATAAATAATTAAACATTATAATATCATGTA
1 ATAT-ATATAATATATTAATAGCTTATATATATGCATAAATAATTAAACATTATAATATCATGTA
* * * *
30499591 ATACTATATCTTTTATTATAATCT-ATATTATAATAATAGTTATATATAATTGTAGTACACTATA
65 ATACTATATATTTTATTATAAT-TGATAATATAATAATAGTTATATATAATAGTAGTACAATATA
* * * * * ** *
30499655 TATTGCTTATTGTTATATATTATTATTTATTATTATACTAGTTGAAATATGCTCAAAGTCTTTTT
129 TATTACATATTATTATATATAATTATTTATTAGTATACTAGTTGAAATATGCTCAAAGTCCCTAT
* * *
30499720 ACTTTTCATACATTTAAAAGTTAGCTCTCCTACT
194 ACTTTTCATACATTTAAAAGTTAGCTTTCTTGCT
30499754 ATATTATATAATA
1 ATA-TATATAATA
30499767 CTATCGTATT
Statistics
Matches: 210, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
225 4 0.02
226 182 0.87
227 8 0.04
228 16 0.08
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (227 bp):
ATATATATAATATATTAATAGCTTATATATATGCATAAATAATTAAACATTATAATATCATGTAA
TACTATATATTTTATTATAATTGATAATATAATAATAGTTATATATAATAGTAGTACAATATATA
TTACATATTATTATATATAATTATTTATTAGTATACTAGTTGAAATATGCTCAAAGTCCCTATAC
TTTTCATACATTTAAAAGTTAGCTTTCTTGCT
Found at i:30499919 original size:5 final size:5
Alignment explanation
Indices: 30499909--30499995 Score: 140
Period size: 5 Copynumber: 17.2 Consensus size: 5
30499899 GTAATAGTTA
30499909 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
30499959 TATAT TATAT TATAT TAT-T AATAGT ATATAT TATAT T
1 TATAT TATAT TATAT TATAT TATA-T -TATAT TATAT T
30499996 TTTATTTTAT
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
4 3 0.04
5 69 0.90
6 2 0.03
7 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:30499924 original size:30 final size:31
Alignment explanation
Indices: 30499850--30499995 Score: 119
Period size: 30 Copynumber: 4.6 Consensus size: 31
30499840 CTATATCTTT
30499850 TATTATTATCTATATTATA--ATAATAGTTATA
1 TATTA-TAT-TATATTATATTATAATAGTTATA
*
30499881 TATGTAT-TAATATT-T-TTAGTAATAGTTATA
1 TAT-TATATTATATTATATTA-TAATAGTTATA
*
30499911 TATTATATTATATTATATTATATTA--TATTA
1 TATTATATTATATTATATTATAATAGTTA-TA
30499941 TATTATATTATATTATATTATATTATA-TTATA
1 TATTATATTATATTATATTATA--ATAGTTATA
30499973 TTATTAATAGTATATATTATATT
1 -TATT-ATA-T-TATATTATATT
30499996 TTTATTTTAT
Statistics
Matches: 96, Mismatches: 4, Indels: 25
0.77 0.03 0.20
Matches are distributed among these distances:
28 1 0.01
29 11 0.11
30 45 0.47
31 9 0.09
32 9 0.09
33 6 0.06
34 3 0.03
35 1 0.01
36 11 0.11
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (31 bp):
TATTATATTATATTATATTATAATAGTTATA
Found at i:30502256 original size:21 final size:21
Alignment explanation
Indices: 30502229--30502285 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
30502219 TGCTAAAGAA
30502229 AAACTCATAAGGGTTGAAC-G
1 AAACTCATAAGGGTTGAACGG
* *
30502249 AAAGCTCATAAGAGCTGAACGG
1 AAA-CTCATAAGGGTTGAACGG
*
30502271 AAACCCATAAGGGTT
1 AAACTCATAAGGGTT
30502286 AAATTGAAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 3 0.10
21 23 0.77
22 4 0.13
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.18
Consensus pattern (21 bp):
AAACTCATAAGGGTTGAACGG
Found at i:30502281 original size:42 final size:42
Alignment explanation
Indices: 30502229--30502340 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 42
30502219 TGCTAAAGAA
* * *
30502229 AAACTCATAAGGGTTGAA-CGAAAGCTCATAAGAGCTGAACGG
1 AAACCCATAAGGGTTAAATCG-AAGCTCAAAAGAGCTGAACGG
* * *
30502271 AAACCCATAAGGGTTAAATTGAAGCTCAAAATAGCTGAACTG
1 AAACCCATAAGGGTTAAATCGAAGCTCAAAAGAGCTGAACGG
* * *
30502313 AAACCCATTAGGGTTAAATGGAAACTCA
1 AAACCCATAAGGGTTAAATCGAAGCTCA
30502341 TATAAGTTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 59 0.98
43 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAATCGAAGCTCAAAAGAGCTGAACGG
Found at i:30503312 original size:20 final size:16
Alignment explanation
Indices: 30503266--30503302 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
30503256 CCTAGAAATC
*
30503266 TTTAGAATTCAATTTA
1 TTTAAAATTCAATTTA
30503282 TTTAAAATTCAATTTA
1 TTTAAAATTCAATTTA
30503298 TTTAA
1 TTTAA
30503303 GTTAATTTCA
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:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAAATTCAATTTA
Found at i:30507280 original size:32 final size:31
Alignment explanation
Indices: 30507227--30507287 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
30507217 TTTTAACTGC
* *
30507227 AATAATTAATTTAAAAAATTATATTAATTAG
1 AATAATTAATTAAAAAAATTATATCAATTAG
30507258 AATAATTAAATTAAAAAAATTATATCAATT
1 AATAATT-AATTAAAAAAATTATATCAATT
30507288 TAAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (31 bp):
AATAATTAATTAAAAAAATTATATCAATTAG
Found at i:30507297 original size:32 final size:32
Alignment explanation
Indices: 30507230--30507303 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
30507220 TAACTGCAAT
* * *
30507230 AATT-AATTTAAAAAATTATATTAATTAGAAT
1 AATTAAATTAAAAAAATTATATCAATTAGAAA
30507261 AATTAAATTAAAAAAATTATATCAATTTA-AAA
1 AATTAAATTAAAAAAATTATATCAA-TTAGAAA
*
30507293 AATTATATTAA
1 AATTAAATTAA
30507304 TTAGAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 4 0.11
32 30 0.81
33 3 0.08
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (32 bp):
AATTAAATTAAAAAAATTATATCAATTAGAAA
Found at i:30507314 original size:18 final size:17
Alignment explanation
Indices: 30507231--30507321 Score: 80
Period size: 18 Copynumber: 5.3 Consensus size: 17
30507221 AACTGCAATA
*
30507231 ATTAATTTAAAAAATTAT
1 ATTAA-TTAAATAATTAT
*
30507249 ATTAATTAGAATAATTAA
1 ATTAATTA-AATAATTAT
30507267 ATTAA--AAA-AATTAT
1 ATTAATTAAATAATTAT
* *
30507281 ATCAATTTAAAAAATTAT
1 ATTAA-TTAAATAATTAT
*
30507299 ATTAATTAGAATAATTAA
1 ATTAATTA-AATAATTAT
30507317 ATTAA
1 ATTAA
30507322 AAAAACCATA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.15
15 2 0.03
16 1 0.02
17 9 0.15
18 39 0.65
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (17 bp):
ATTAATTAAATAATTAT
Found at i:30510319 original size:21 final size:21
Alignment explanation
Indices: 30510293--30510334 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
30510283 ATCCAGAAAG
*
30510293 TCTAGTACCAGTCAAAATTAA
1 TCTAGTACCAGCCAAAATTAA
30510314 TCTAGTACCAGCCAAAATTAA
1 TCTAGTACCAGCCAAAATTAA
30510335 CTTTTCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (21 bp):
TCTAGTACCAGCCAAAATTAA
Found at i:30512430 original size:31 final size:31
Alignment explanation
Indices: 30512389--30512453 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
30512379 GAAACAAGGA
* *
30512389 CAAGTTAGAAGGAATTGAAACTTCATTATTC
1 CAAGTCAGAAGAAATTGAAACTTCATTATTC
*
30512420 CAAGTCAGAAGAAATTGAAACTTCATTTTTC
1 CAAGTCAGAAGAAATTGAAACTTCATTATTC
30512451 CAA
1 CAA
30512454 AAATAGAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (31 bp):
CAAGTCAGAAGAAATTGAAACTTCATTATTC
Found at i:30513765 original size:14 final size:15
Alignment explanation
Indices: 30513743--30513773 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
30513733 TGTTTTTTGG
30513743 TTTCTTTTTTCTTTT
1 TTTCTTTTTTCTTTT
30513758 TTTC-TTTTTCTTTT
1 TTTCTTTTTTCTTTT
30513772 TT
1 TT
30513774 GAGCGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTCTTTTTTCTTTT
Found at i:30517059 original size:146 final size:146
Alignment explanation
Indices: 30516887--30517178 Score: 584
Period size: 146 Copynumber: 2.0 Consensus size: 146
30516877 AAAAATGGAT
30516887 CACGAATAATGTAGTGGGAAGGGTTCATAAAATAATTTCTCTATAGATGAGTGTATAATAATAAT
1 CACGAATAATGTAGTGGGAAGGGTTCATAAAATAATTTCTCTATAGATGAGTGTATAATAATAAT
30516952 TTCATGTCTCTAAAATTTGATGATGTGACGAAATTTTATTGGTGCCTAAAACCCTTAATTTTTAG
66 TTCATGTCTCTAAAATTTGATGATGTGACGAAATTTTATTGGTGCCTAAAACCCTTAATTTTTAG
30517017 AATTATCCTAATGTAA
131 AATTATCCTAATGTAA
30517033 CACGAATAATGTAGTGGGAAGGGTTCATAAAATAATTTCTCTATAGATGAGTGTATAATAATAAT
1 CACGAATAATGTAGTGGGAAGGGTTCATAAAATAATTTCTCTATAGATGAGTGTATAATAATAAT
30517098 TTCATGTCTCTAAAATTTGATGATGTGACGAAATTTTATTGGTGCCTAAAACCCTTAATTTTTAG
66 TTCATGTCTCTAAAATTTGATGATGTGACGAAATTTTATTGGTGCCTAAAACCCTTAATTTTTAG
30517163 AATTATCCTAATGTAA
131 AATTATCCTAATGTAA
30517179 GTTATTTTCG
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 146 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (146 bp):
CACGAATAATGTAGTGGGAAGGGTTCATAAAATAATTTCTCTATAGATGAGTGTATAATAATAAT
TTCATGTCTCTAAAATTTGATGATGTGACGAAATTTTATTGGTGCCTAAAACCCTTAATTTTTAG
AATTATCCTAATGTAA
Found at i:30521537 original size:24 final size:23
Alignment explanation
Indices: 30521461--30521543 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 23
30521451 CCTCGAGGTC
* * *
30521461 AAATGATTGTTTTGTCTGTGGTT
1 AAATGACTGATTTGTCTGTGTTT
30521484 AAATGACTGATTTGTCTGTGTTT
1 AAATGACTGATTTGTCTGTGTTT
**
30521507 GGTATGACTGATTTGTCTGTGATTT
1 -AAATGACTGATTTGTCTGTG-TTT
30521532 AAATGACTGATT
1 AAATGACTGATT
30521544 CTGAGCATGG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.39
24 28 0.55
25 3 0.06
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (23 bp):
AAATGACTGATTTGTCTGTGTTT
Found at i:30521645 original size:27 final size:27
Alignment explanation
Indices: 30521606--30521671 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
30521596 TATGGAGGAA
*
30521606 ATACTG-TACTGGTGGCTTTGCCACA-
1 ATACTGTTACTGGTGGCTTGGCCACAT
30521631 ATCACTGTTACTGGTGGCTTGGCCACAT
1 AT-ACTGTTACTGGTGGCTTGGCCACAT
30521659 ATACTGTTACTGG
1 ATACTGTTACTGG
30521672 CAGCTTTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.05
26 4 0.11
27 29 0.78
28 2 0.05
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (27 bp):
ATACTGTTACTGGTGGCTTGGCCACAT
Found at i:30521724 original size:26 final size:26
Alignment explanation
Indices: 30521669--30521724 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
30521659 ATACTGTTAC
* * * *
30521669 TGGCAGCTTTGTTGCGATACTGTTGC
1 TGGCAGCTTTGATGAGATACTATTGA
*
30521695 TGGCAGCTTTGATGAGATGCTATTGA
1 TGGCAGCTTTGATGAGATACTATTGA
30521721 TGGC
1 TGGC
30521725 TTTGTGCCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (26 bp):
TGGCAGCTTTGATGAGATACTATTGA
Found at i:30521754 original size:32 final size:32
Alignment explanation
Indices: 30521718--30521904 Score: 268
Period size: 32 Copynumber: 5.8 Consensus size: 32
30521708 GAGATGCTAT
30521718 TGATGGCTTTGTGCCGATCATATTACTATTAC
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
* * *
30521750 TGATGGCTGTGTGCCGATCATATTACCATTAT
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
* *
30521782 TGATGG-TTGTGTACCGATCATATTACTACTAC
1 TGATGGCTT-TGTGCCGATCATATTACTATTAC
*
30521814 TGATGGCTTTGTGCCGATCATACTACTATTAC
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
* * *
30521846 TGATGGCTTTGTGCCAATCATATTAGTACTAC
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
*
30521878 TGATGGCTTTGTGCCAATCATATTACT
1 TGATGGCTTTGTGCCGATCATATTACT
30521905 GTACTTGTGG
Statistics
Matches: 137, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
31 1 0.01
32 134 0.98
33 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATTACTATTAC
Found at i:30521939 original size:22 final size:22
Alignment explanation
Indices: 30521914--30521955 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
30521904 TGTACTTGTG
* *
30521914 GCTTGTAGCCATTCTGTTTATA
1 GCTTATAGCCATCCTGTTTATA
*
30521936 GCTTATAGCTATCCTGTTTA
1 GCTTATAGCCATCCTGTTTA
30521956 CGGCTCTTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (22 bp):
GCTTATAGCCATCCTGTTTATA
Found at i:30527750 original size:26 final size:26
Alignment explanation
Indices: 30527713--30527766 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
30527703 ATTGGATAAA
*
30527713 AAGGGGTCGCTAAGTGCAGATTCCCC
1 AAGGGGTCGCTAAGTACAGATTCCCC
* *
30527739 AAGGGGTTGCTAAGTACTGATTCCCC
1 AAGGGGTCGCTAAGTACAGATTCCCC
30527765 AA
1 AA
30527767 ATTATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (26 bp):
AAGGGGTCGCTAAGTACAGATTCCCC
Found at i:30531844 original size:38 final size:39
Alignment explanation
Indices: 30531792--30531900 Score: 177
Period size: 39 Copynumber: 2.8 Consensus size: 39
30531782 ATAAGCACAA
30531792 AAAAATTATTTTAAAAAT-AAAAAATAAAAAAAGTATCTT
1 AAAAA-TATTTTAAAAATAAAAAAATAAAAAAAGTATCTT
* *
30531831 AAAAATATTTTAAAATTAAAAAAATAAAAAAAGTATTTT
1 AAAAATATTTTAAAAATAAAAAAATAAAAAAAGTATCTT
30531870 AAAAATATTTT-AAAATAAAAAAATAAAAAAA
1 AAAAATATTTTAAAAATAAAAAAATAAAAAAA
30531901 TAAAAAAATA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
38 30 0.45
39 36 0.55
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (39 bp):
AAAAATATTTTAAAAATAAAAAAATAAAAAAAGTATCTT
Found at i:30531897 original size:7 final size:8
Alignment explanation
Indices: 30531881--30531910 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
30531871 AAAATATTTT
30531881 AAAATAAA
1 AAAATAAA
30531889 AAAATAAA
1 AAAATAAA
30531897 AAAATAAA
1 AAAATAAA
30531905 AAAATA
1 AAAATA
30531911 TATTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAATAAA
Found at i:30539438 original size:21 final size:22
Alignment explanation
Indices: 30539395--30539439 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
30539385 TTAAAATTTG
30539395 TGTTATGTATAGATTAAAATGAT
1 TGTTATGTATAGATT-AAATGAT
30539418 TGTTATGTGATA-ATT-AATGAT
1 TGTTATGT-ATAGATTAAATGAT
30539439 T
1 T
30539440 TGGATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (22 bp):
TGTTATGTATAGATTAAATGAT
Found at i:30539914 original size:21 final size:21
Alignment explanation
Indices: 30539874--30539914 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30539864 ATATGGATTC
*
30539874 TTGAAATGAAAATGTGTGATG
1 TTGAAATGAAAATGTATGATG
30539895 TTGAAA-GAAAATGATATGAT
1 TTGAAATGAAAATG-TATGAT
30539915 TGAGTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (21 bp):
TTGAAATGAAAATGTATGATG
Found at i:30543572 original size:23 final size:24
Alignment explanation
Indices: 30543528--30543573 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
30543518 CCACACACTT
*
30543528 TTTATCATCTTTTTAGGGTTTTAG
1 TTTATCAGCTTTTTAGGGTTTTAG
* *
30543552 TTTATCAGGTTTTT-GGTTTTTA
1 TTTATCAGCTTTTTAGGGTTTTA
30543574 CCTGTTAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.15, C:0.07, G:0.17, T:0.61
Consensus pattern (24 bp):
TTTATCAGCTTTTTAGGGTTTTAG
Found at i:30548047 original size:30 final size:30
Alignment explanation
Indices: 30548011--30548069 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
30548001 AAAACCCTCA
30548011 TAGTATAGAATTAGTTCTAGTTTACTTTCG
1 TAGTATAGAATTAGTTCTAGTTTACTTTCG
*
30548041 TAGTATAGAATTAGTTTTAGTTTACTTTC
1 TAGTATAGAATTAGTTCTAGTTTACTTTC
30548070 TTTTTGGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.49
Consensus pattern (30 bp):
TAGTATAGAATTAGTTCTAGTTTACTTTCG
Found at i:30566369 original size:58 final size:60
Alignment explanation
Indices: 30566307--30566507 Score: 176
Period size: 68 Copynumber: 3.2 Consensus size: 60
30566297 AATCACTTTA
* * *
30566307 ATATTAAAATCATATAATACTTA-T-CAAGATAAATATTATATTAAATTTAATATTAAAT
1 ATATTAAAATAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAAT
* *
30566365 ATATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTATATTTAATATTAAGAT
1 ATATTAAAATAATAGAATACTTA-CTACAAGATAAATATTAAATTAAATTTAATATTAA-AT
* * ** * *
30566427 AGTCATTTTAATATTAA-ATTAATAAAATACTATCAAGATAAGTACTAAATTAAATTTAATATTA
1 A-T-A--TTAA-AATAATA-GAAT-ACTTACTA-CAAGATAAATATTAAATTAAATTTAATATTA
30566491 AA-
58 AAT
30566493 ACTATTAAAATAATA
1 A-TATTAAAATAATA
30566508 TTTTTGGAAT
Statistics
Matches: 117, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
58 20 0.17
60 1 0.01
61 30 0.26
62 7 0.06
63 6 0.05
64 1 0.01
65 1 0.01
66 7 0.06
67 12 0.10
68 32 0.27
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.39
Consensus pattern (60 bp):
ATATTAAAATAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAAT
Found at i:30566416 original size:61 final size:58
Alignment explanation
Indices: 30566307--30566507 Score: 181
Period size: 61 Copynumber: 3.2 Consensus size: 58
30566297 AATCACTTTA
* * *
30566307 ATATTAAAATCATATAATACTTATCAAGATAAATATTATATTAAATTTAATATTAAAT
1 ATATTAAAATAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAT
* *
30566365 ATATTAAATTAATAGAATACTTATCTACAAGATAAATATTAAATTATATTTAATATTAAGAT
1 ATATTAAAATAATAGAATACTTA--T-CAAGATAAATATTAAATTAAATTTAATATTAA-AT
* * *
30566427 AGTCATTTTAATATTAAATTAATAAAATAC-TATCAAGATAAGTACTAAATTAAATTTAATATTA
1 A-T-A---T--TA--AAA-TAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTA
30566491 AA-
56 AAT
30566493 ACTATTAAAATAATA
1 A-TATTAAAATAATA
30566508 TTTTTGGAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 29
0.75 0.07 0.18
Matches are distributed among these distances:
57 5 0.04
58 23 0.19
60 3 0.03
61 30 0.25
62 4 0.03
63 1 0.01
64 1 0.01
65 1 0.01
66 2 0.02
67 2 0.02
68 29 0.25
69 3 0.03
71 4 0.03
72 10 0.08
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.39
Consensus pattern (58 bp):
ATATTAAAATAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAT
Found at i:30581346 original size:22 final size:21
Alignment explanation
Indices: 30581297--30581346 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
30581287 AAACATCGAC
*
30581297 GTCATGACTTTGTTTTTTAAT
1 GTCATGACATTGTTTTTTAAT
*
30581318 GCCATGACATTGTTCTCTTT-AT
1 GTCATGACATTGTT-T-TTTAAT
30581340 GTCATGA
1 GTCATGA
30581347 TGTTGCCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 12 0.50
22 9 0.38
23 3 0.12
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (21 bp):
GTCATGACATTGTTTTTTAAT
Found at i:30581411 original size:26 final size:26
Alignment explanation
Indices: 30581382--30581443 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
30581372 TGACTTCTCA
*
30581382 TGTTTCAACGTCATGAATCCACTGAT
1 TGTTTCAACATCATGAATCCACTGAT
*
30581408 TGTTTCAACATCATGACTCCACTGAT
1 TGTTTCAACATCATGAATCCACTGAT
30581434 TGTTTCAACA
1 TGTTTCAACA
30581444 CAAGTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (26 bp):
TGTTTCAACATCATGAATCCACTGAT
Found at i:30588881 original size:81 final size:81
Alignment explanation
Indices: 30588746--30588902 Score: 305
Period size: 81 Copynumber: 1.9 Consensus size: 81
30588736 TTTTTTGCAG
*
30588746 AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCATAAGTCA
1 AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCAGAAGTCA
30588811 TTAGGGCTGAAGCAAA
66 TTAGGGCTGAAGCAAA
30588827 AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCAGAAGTCA
1 AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCAGAAGTCA
30588892 TTAGGGCTGAA
66 TTAGGGCTGAA
30588903 TTCTCAAGTG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (81 bp):
AAATCACACCACTTAAGACTTTTGTCCTTGCTGCCTCAGCTGGGCTTTATTGGCATCAGAAGTCA
TTAGGGCTGAAGCAAA
Found at i:30595507 original size:12 final size:12
Alignment explanation
Indices: 30595490--30595516 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30595480 TTTGTATGTG
30595490 AATATAGAAACA
1 AATATAGAAACA
30595502 AATATAGAAACA
1 AATATAGAAACA
30595514 AAT
1 AAT
30595517 GTATGTTTAA
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:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (12 bp):
AATATAGAAACA
Found at i:30597194 original size:25 final size:25
Alignment explanation
Indices: 30597147--30597194 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
30597137 GCTCTCTCTC
* *
30597147 GAGCCATATAACGAGAAGCTTATAT
1 GAGCCATATAACAAAAAGCTTATAT
* *
30597172 GAGCCATGTAACAAAAAGTTTAT
1 GAGCCATATAACAAAAAGCTTAT
30597195 CCAGGTTGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (25 bp):
GAGCCATATAACAAAAAGCTTATAT
Found at i:30597240 original size:24 final size:24
Alignment explanation
Indices: 30597204--30597372 Score: 125
Period size: 24 Copynumber: 6.9 Consensus size: 24
30597194 TCCAGGTTGT
*
30597204 ATAA-CGGGGAGCTCATAAGAGCC
1 ATAATCGGGAAGCTCATAAGAGCC
* *
30597227 ATAATCAGGAAGCTCATACGAGCC
1 ATAATCGGGAAGCTCATAAGAGCC
* *
30597251 AATAA-CGGGTAGCTC-TGAAAAGCC
1 -ATAATCGGGAAGCTCAT-AAGAGCC
* *
30597275 ATTAATCGGGAAGTTCA-AGCGAGCC
1 A-TAATCGGGAAGCTCATA-AGAGCC
30597300 AT-ATCGGGAAGCTCATAAAGAGCC
1 ATAATCGGGAAGCTCAT-AAGAGCC
* *
30597324 TTTAATCGGGAAGCTCACGAAGAGCC
1 -ATAATCGGGAAGCTCA-TAAGAGCC
*
30597350 ATAAAAT-GGGACGCTCATAAGAG
1 AT--AATCGGGAAGCTCATAAGAG
30597373 TTGCGGTGTG
Statistics
Matches: 114, Mismatches: 18, Indels: 26
0.72 0.11 0.16
Matches are distributed among these distances:
23 18 0.16
24 39 0.34
25 25 0.22
26 29 0.25
27 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (24 bp):
ATAATCGGGAAGCTCATAAGAGCC
Found at i:30597300 original size:49 final size:48
Alignment explanation
Indices: 30597204--30597340 Score: 154
Period size: 49 Copynumber: 2.8 Consensus size: 48
30597194 TCCAGGTTGT
* * *
30597204 ATAACGGGGAGCTCATAAGAGCCA-TAATCAGGAAGCTCATACGAGCC
1 ATAACGGGAAGCTCATAAAAGCCATTAATCGGGAAGCTCATACGAGCC
* *
30597251 AATAACGGGTAGCTC-TGAAAAGCCATTAATCGGGAAGTTCA-AGCGAGCC
1 -ATAACGGGAAGCTCAT-AAAAGCCATTAATCGGGAAGCTCATA-CGAGCC
* *
30597300 ATATCGGGAAGCTCATAAAGAGCCTTTAATCGGGAAGCTCA
1 ATAACGGGAAGCTCATAAA-AGCCATTAATCGGGAAGCTCA
30597341 CGAAGAGCCA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
47 1 0.01
48 36 0.47
49 39 0.51
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (48 bp):
ATAACGGGAAGCTCATAAAAGCCATTAATCGGGAAGCTCATACGAGCC
Found at i:30597360 original size:26 final size:26
Alignment explanation
Indices: 30597302--30597366 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
30597292 AGCGAGCCAT
* **
30597302 ATCGGGAAGCTCATAAAGAGCCTTTA
1 ATCGGGAAGCTCACAAAGAGCCTAAA
*
30597328 ATCGGGAAGCTCACGAAGAGCCATAAA
1 ATCGGGAAGCTCACAAAGAGCC-TAAA
*
30597355 AT-GGGACGCTCA
1 ATCGGGAAGCTCA
30597367 TAAGAGTTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 29 0.88
27 4 0.12
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (26 bp):
ATCGGGAAGCTCACAAAGAGCCTAAA
Found at i:30600510 original size:22 final size:22
Alignment explanation
Indices: 30600482--30600524 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30600472 ATCCCCATAT
*
30600482 TTTTTTTGTTTCAAGCTATTTA
1 TTTTTTTCTTTCAAGCTATTTA
* *
30600504 TTTTTTTCTTTTATGCTATTT
1 TTTTTTTCTTTCAAGCTATTT
30600525 GAACTTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTTTTTCTTTCAAGCTATTTA
Found at i:30601745 original size:22 final size:22
Alignment explanation
Indices: 30601717--30601787 Score: 90
Period size: 21 Copynumber: 3.2 Consensus size: 22
30601707 TCAATTGTTT
30601717 AATTAGGGTTTAGTGTTTATTA
1 AATTAGGGTTTAGTGTTTATTA
*
30601739 AATTAGGG-TTATTGTTTATTA
1 AATTAGGGTTTAGTGTTTATTA
* *
30601760 AATTAAGGTTTTAGTGTTTTATTT
1 AATT-AGGGTTTAGTG-TTTATTA
30601784 AATT
1 AATT
30601788 TTTTAAGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.38
22 11 0.26
23 5 0.12
24 10 0.24
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (22 bp):
AATTAGGGTTTAGTGTTTATTA
Found at i:30601800 original size:20 final size:19
Alignment explanation
Indices: 30601768--30601806 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
30601758 TAAATTAAGG
30601768 TTTTAGTGTTTTATTTAATT
1 TTTTAGTGTTTTA-TTAATT
30601788 TTTTAAGTG-TTTATTAATT
1 TTTT-AGTGTTTTATTAATT
30601807 AGTGTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (19 bp):
TTTTAGTGTTTTATTAATT
Found at i:30607674 original size:180 final size:180
Alignment explanation
Indices: 30607372--30607734 Score: 564
Period size: 180 Copynumber: 2.0 Consensus size: 180
30607362 GAATAGTTAA
*
30607372 TTCTAAATCAAATTCTCTGGTAGAGTCCCAATAGGAGTATAACTCTTTCACTACTCAATCAACAA
1 TTCTAAATCAAATTCTCTGGTAGAGTCCCAATAGGAGTATAACTCTTCCACTACTCAATCAACAA
* * * *
30607437 TGACCAATTGTCACCGGCCACTGGGACACCACCGTCCCAGCCACTAGCATCGCCGTGTCCGGTGA
66 TGACCAATCGCCACCGACCACTAGGACACCACCGTCCCAGCCACTAGCATCGCCGTGTCCGGTGA
* * *
30607502 TGCAGGTGCGACACCCTTACAGCACCCTGAGCCGGTTCGATTGCTACTAG
131 TGCAGGTGAGACACACTTACAGCACCCAGAGCCGGTTCGATTGCTACTAG
* * *
30607552 TTCTAAATCAAATTCTCTGGTAGAGTCCCAATATGAGTGTAACTCTTCCACTGCTCAATCAACAA
1 TTCTAAATCAAATTCTCTGGTAGAGTCCCAATAGGAGTATAACTCTTCCACTACTCAATCAACAA
* * * * *
30607617 TGATCAATCGCCGCCGACCATTAGGACACCACCGTCGCAGCCACTGGCATCGCCGTGTCCGGTGA
66 TGACCAATCGCCACCGACCACTAGGACACCACCGTCCCAGCCACTAGCATCGCCGTGTCCGGTGA
* *
30607682 TGCAGGTGAGACACACTTACAGCACTCAGAGCCGGTTCGATTGCTGCTAG
131 TGCAGGTGAGACACACTTACAGCACCCAGAGCCGGTTCGATTGCTACTAG
30607732 TTC
1 TTC
30607735 GGTCTGAGTC
Statistics
Matches: 165, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
180 165 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (180 bp):
TTCTAAATCAAATTCTCTGGTAGAGTCCCAATAGGAGTATAACTCTTCCACTACTCAATCAACAA
TGACCAATCGCCACCGACCACTAGGACACCACCGTCCCAGCCACTAGCATCGCCGTGTCCGGTGA
TGCAGGTGAGACACACTTACAGCACCCAGAGCCGGTTCGATTGCTACTAG
Found at i:30608378 original size:85 final size:86
Alignment explanation
Indices: 30608196--30608422 Score: 260
Period size: 85 Copynumber: 2.7 Consensus size: 86
30608186 TTTATTTGAA
* * * * * * *
30608196 AAACGCCGCTATAGAACATGACCTTTAGTGGCGCTTTTATAAAAAATGCTGCTAAAGAACATGGC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATGAC
30608261 CTTTAGCGACGCTTTACCCAC
66 CTTTAGCGACGCTTTACCCAC
* * * * *
30608282 AAATGCCGCTAAAGAACATGACCTTTAGCAGCGC-TTTACCCCAAACGCCGCTAAAGAGCATGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATGAC
*** *
30608346 CTTTAGCGACGCTTTTTTCAT
66 CTTTAGCGACGCTTTACCCAC
* * *
30608367 AAACGTCGCTAAAAAACAAT-ACCTTTAGCGGCGCTTTTATCACAAACGACGCTAAA
1 AAACGCCGCTAAAGAAC-ATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAA
30608423 AGTACCGTTT
Statistics
Matches: 116, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
85 66 0.57
86 50 0.43
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATGAC
CTTTAGCGACGCTTTACCCAC
Found at i:30608423 original size:43 final size:43
Alignment explanation
Indices: 30608196--30608422 Score: 235
Period size: 43 Copynumber: 5.3 Consensus size: 43
30608186 TTTATTTGAA
* * * *
30608196 AAACGCCGCTATAGAACATGACCTTTAGTGGCGCTTTTATAAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
* * * * *
30608239 AAATGCTGCTAAAGAACATGGCCTTTAGCGACGC-TTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA-TCAC
* * * *
30608282 AAATGCCGCTAAAGAACATGACCTTTAGCAGCGC-TTTACCCC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
* * * *
30608324 AAACGCCGCTAAAGAGCATGACCTTTAGCGACGCTTTTTTCAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
* *
30608367 AAACGTCGCTAAAAAACAAT-ACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAAC-ATGACCTTTAGCGGCGCTTTTATCAC
*
30608410 AAACGACGCTAAA
1 AAACGCCGCTAAA
30608423 AGTACCGTTT
Statistics
Matches: 152, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
42 37 0.24
43 113 0.74
44 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
Found at i:30611312 original size:9 final size:9
Alignment explanation
Indices: 30611298--30611328 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30611288 GTTAAACGAA
30611298 TCGAGTTAT
1 TCGAGTTAT
*
30611307 TCGAGTTAA
1 TCGAGTTAT
30611316 TCGAGTTAT
1 TCGAGTTAT
30611325 TCGA
1 TCGA
30611329 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:30611398 original size:9 final size:9
Alignment explanation
Indices: 30611381--30611417 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
30611371 TGAGTTTTCG
30611381 AATTCGAAT
1 AATTCGAAT
*
30611390 AACTCGAAT
1 AATTCGAAT
30611399 AATTCGAAT
1 AATTCGAAT
30611408 AATTCGAAT
1 AATTCGAAT
30611417 A
1 A
30611418 TCAAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:30611511 original size:29 final size:30
Alignment explanation
Indices: 30611459--30611516 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
30611449 AACTCCCAAA
* * *
30611459 CCTTTTTACTTTTCCCTCAGAACTTTTACT
1 CCTTCTTACTTTTCCCCCAAAACTTTTACT
30611489 CCTTCTTAC-TTTCCCCCAAAACTTTTAC
1 CCTTCTTACTTTTCCCCCAAAACTTTTAC
30611517 CCCCTCCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.19, C:0.34, G:0.02, T:0.45
Consensus pattern (30 bp):
CCTTCTTACTTTTCCCCCAAAACTTTTACT
Found at i:30614588 original size:15 final size:15
Alignment explanation
Indices: 30614548--30614588 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
30614538 CCCTTAAGCC
30614548 ATAATCCCT-AATCT
1 ATAATCCCTAAATCT
*
30614562 ATAATCTCTAAATCT
1 ATAATCCCTAAATCT
*
30614577 ATACTCCCTAAA
1 ATAATCCCTAAA
30614589 CCTTAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAATCCCTAAATCT
Found at i:30614894 original size:15 final size:14
Alignment explanation
Indices: 30614852--30614900 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
30614842 TCCCAACCCT
*
30614852 TAAACCATAATACC
1 TAAACCATAATCCC
30614866 TAAACCATAATCCC
1 TAAACCATAATCCC
*
30614880 TAAATCCATACTCCC
1 TAAA-CCATAATCCC
30614895 TAAACC
1 TAAACC
30614901 TTAAAATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:30615306 original size:41 final size:41
Alignment explanation
Indices: 30615246--30615685 Score: 465
Period size: 41 Copynumber: 10.8 Consensus size: 41
30615236 TAAAAAAAAT
*
30615246 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCCAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
* * *
30615287 TTAGCGGTGCTTTTCCAAAAACGCCGCTAAAGCCCCCAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
* * * *
30615328 TTAGCAGTGCTTTTCCAAAAACGCAGCTAAAGCCCC-AGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
* * * * *
30615368 TTAGAGGCGCTTTTTCAGAAACGCCACTAAAACCTCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
* *
30615409 TTAGCGGCGC-TTTTAAAAAACGCCGCTAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
* * * *
30615449 TTAGCAGCACTTTTTCAAAAACGCCGCTAAAG-CCCTAACA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
* * * *
30615489 TTAGTGACGCTTTTTCAAAAACGCTGCTAACA-CCCCGAGAA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAA-AGCCCCGAGCA
* * * *
30615530 TTAGCGGCGCTTTTTAAAAAACACCGCTAAAACACCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
* ** * * *
30615571 TTAGTGTTGCTTTTTCAAAAACGCAGCTAAAACCTCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
* * *
30615612 TTAGCGGTGCATTTTCAAAAATGCCGCTAAAGCCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
* * * ** *
30615653 TTGGTGGCCCTTTTTTGAAAACGCTGCTAAAGC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGC
30615686 TCATAAAGGT
Statistics
Matches: 331, Mismatches: 63, Indels: 10
0.82 0.16 0.02
Matches are distributed among these distances:
40 97 0.29
41 234 0.71
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCA
Found at i:30615392 original size:81 final size:81
Alignment explanation
Indices: 30615253--30615683 Score: 427
Period size: 81 Copynumber: 5.3 Consensus size: 81
30615243 AATTTAGCGG
* * * *
30615253 CGCTTTTTCAAAAACGCCGCTAAAGCCCCCAGCATTAGCGGTGCTTTTCCAAAAACGCCGCTAAA
1 CGCTTTTTCAAAAACGCAGCTAAA-ACCCCAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
* *
30615318 GCCCCCAGCATTAG-CA
65 GCCCCGAGCATTAGTGA
* * * * * *
30615334 GTGCTTTTCCAAAAACGCAGCTAAAGCCCCAGCATTAGAGGCGCTTTTTCAGAAACGCCACTAAA
1 -CGCTTTTTCAAAAACGCAGCTAAAACCCCAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
* * * *
30615399 ACCTCGAGCATTAGCGG
65 GCCCCGAGCATTAGTGA
* * * *
30615416 CGC-TTTTAAAAAACGCCGCTAAAACCCCGAGCATTAGCAGCACTTTTTCAAAAACGCCGCTAAA
1 CGCTTTTTCAAAAACGCAGCTAAAACCCC-AGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
* *
30615480 G-CCCTAACATTAGTGA
65 GCCCCGAGCATTAGTGA
* * * * *
30615496 CGCTTTTTCAAAAACGCTGCTAACACCCCGAGAATTAGCGGCGCTTTTTAAAAAACACCGCTAAA
1 CGCTTTTTCAAAAACGCAGCTAAAACCCC-AGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
* * *
30615561 ACACCGAGCATTAGTGT
65 GCCCCGAGCATTAGTGA
* * * * *
30615578 TGCTTTTTCAAAAACGCAGCTAAAACCTCGAGCATTAGCGGTGCATTTTCAAAAATGCCGCTAAA
1 CGCTTTTTCAAAAACGCAGCTAAAACC-CCAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
* *
30615643 GCCCCGAGCATTGGTGG
65 GCCCCGAGCATTAGTGA
* ** *
30615660 CCCTTTTTTGAAAACGCTGCTAAA
1 CGCTTTTTCAAAAACGCAGCTAAA
30615684 GCTCATAAAG
Statistics
Matches: 282, Mismatches: 62, Indels: 10
0.80 0.18 0.03
Matches are distributed among these distances:
80 34 0.12
81 130 0.46
82 117 0.41
83 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (81 bp):
CGCTTTTTCAAAAACGCAGCTAAAACCCCAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG
CCCCGAGCATTAGTGA
Found at i:30618905 original size:20 final size:20
Alignment explanation
Indices: 30618869--30618911 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
30618859 CATTAATTAC
30618869 TATTTTTGTATTAAGCAA-A
1 TATTTTTGTATTAAGCAACA
* *
30618888 TATTTTTTTATTTCAGCAACA
1 TATTTTTGTA-TTAAGCAACA
30618909 TAT
1 TAT
30618912 CAATAATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (20 bp):
TATTTTTGTATTAAGCAACA
Found at i:30620784 original size:26 final size:26
Alignment explanation
Indices: 30620755--30620833 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
30620745 TAATCACTTA
30620755 AATATTAAATTAATATAATATTTATC
1 AATATTAAATTAATATAATATTTATC
* * *
30620781 AATATTAGATTAATTTTAATATTAAATC
1 AATATTAAATTAA-TATAATATT-TATC
* * *
30620809 -TTATTAAAATAATAGAATATTTATC
1 AATATTAAATTAATATAATATTTATC
30620834 TTGTAGATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
25 3 0.07
26 19 0.45
27 17 0.40
28 3 0.07
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (26 bp):
AATATTAAATTAATATAATATTTATC
Found at i:30620888 original size:37 final size:33
Alignment explanation
Indices: 30620846--30620936 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 33
30620836 GTAGATAAAC
30620846 ATTAAATTAAATTTAATATTAAGATAATCACTTTAA-T
1 ATTAAATTAAATTTAATATTAA-ATAAT-A---TAAGT
* * *
30620883 ATTAAATT-AATTAAATACT-ATTAATATAAGT
1 ATTAAATTAAATTTAATATTAAATAATATAAGT
30620914 ATTAAATTAAATTTAATATTAAA
1 ATTAAATTAAATTTAATATTAAA
30620937 CTATTAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
30 3 0.07
31 9 0.20
32 9 0.20
33 2 0.04
34 4 0.09
35 1 0.02
36 9 0.20
37 8 0.18
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (33 bp):
ATTAAATTAAATTTAATATTAAATAATATAAGT
Found at i:30620893 original size:20 final size:18
Alignment explanation
Indices: 30620846--30620936 Score: 65
Period size: 17 Copynumber: 5.3 Consensus size: 18
30620836 GTAGATAAAC
30620846 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
30620863 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
*
30620883 ATTAAATT-A-ATTAAAT
1 ATTAAATTAATATTTAAT
*
30620899 ACT--ATTAATA--TAAGT
1 ATTAAATTAATATTTAA-T
30620914 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
30620931 ATTAAA
1 ATTAAA
30620937 CTATTAAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 24
0.67 0.05 0.28
Matches are distributed among these distances:
14 5 0.09
15 4 0.07
16 9 0.16
17 21 0.36
18 4 0.07
19 3 0.05
20 12 0.21
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:30620940 original size:37 final size:36
Alignment explanation
Indices: 30620878--30620953 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
30620868 GATAATCACT
*
30620878 TTAATATTAAATTAATTAAATACTATTAATATAAGTA
1 TTAATATTAAATTAATTAAATACTATTAAAATAA-TA
*
30620915 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAAT-TAAATACTATTAAAATAATA
30620951 TTA
1 TTA
30620954 TTTTTGTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 11 0.31
37 21 0.60
38 3 0.09
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (36 bp):
TTAATATTAAATTAATTAAATACTATTAAAATAATA
Found at i:30625709 original size:22 final size:22
Alignment explanation
Indices: 30625684--30625727 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
30625674 AAATATATTT
*
30625684 AAAATTTATTAAAA-AT-TAGAA
1 AAAAATTA-TAAAATATATAGAA
30625705 AAAAATTATAAAATATATAGAA
1 AAAAATTATAAAATATATAGAA
30625727 A
1 A
30625728 TATAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (22 bp):
AAAAATTATAAAATATATAGAA
Found at i:30625717 original size:9 final size:9
Alignment explanation
Indices: 30625620--30625807 Score: 50
Period size: 10 Copynumber: 20.0 Consensus size: 9
30625610 GACAAGTGAC
*
30625620 AAAAATGAT
1 AAAAATTAT
30625629 AAAAA--AT
1 AAAAATTAT
*
30625636 AAAAATCAAT
1 AAAAAT-TAT
*
30625646 AAAAGTTA-
1 AAAAATTAT
30625654 AAAAATTACT
1 AAAAATTA-T
**
30625664 AAATTTTAAT
1 AAAAATT-AT
30625674 AAATATATT-T
1 AAA-A-ATTAT
*
30625684 AAAATTTATT
1 AAAAATTA-T
*
30625694 AAAAATTAGAA
1 AAAAATT--AT
30625705 AAAAATTAT
1 AAAAATTAT
30625714 -AAAATATAT
1 AAAAAT-TAT
* *
30625723 AGAAATATAGA
1 AAAAAT-TA-T
30625734 AAAAATTAT
1 AAAAATTAT
*
30625743 -AAAATTTT
1 AAAAATTAT
*
30625751 ATAAAGTCGTA-
1 A-AAAAT--TAT
30625762 AGAAAATTAT
1 A-AAAATTAT
* *
30625772 AAAAAATGT
1 AAAAATTAT
*
30625781 AAAAAATAT
1 AAAAATTAT
30625790 -AAAATTCAT
1 AAAAATT-AT
30625799 AAAAATTAT
1 AAAAATTAT
30625808 CGTACAAAAA
Statistics
Matches: 133, Mismatches: 24, Indels: 44
0.66 0.12 0.22
Matches are distributed among these distances:
7 7 0.05
8 26 0.20
9 31 0.23
10 47 0.35
11 18 0.14
12 4 0.03
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:30625718 original size:30 final size:29
Alignment explanation
Indices: 30625683--30625755 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 29
30625673 TAAATATATT
30625683 TAAAATTTATTAAAAAT-TAGAAAAAAATTA
1 TAAAATTTA-TAAAAATATAG-AAAAAATTA
* *
30625713 TAAAATATATAGAAATATAGAAAAAATTA
1 TAAAATTTATAAAAATATAGAAAAAATTA
30625742 TAAAATTTTATAAA
1 TAAAA-TTTATAAA
30625756 GTCGTAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (29 bp):
TAAAATTTATAAAAATATAGAAAAAATTA
Found at i:30626009 original size:19 final size:20
Alignment explanation
Indices: 30625977--30626014 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
30625967 GTAAATGGCC
30625977 TTTTTGATGCATTTTATAAT
1 TTTTTGATGCATTTTATAAT
*
30625997 TTTTTTATG-ATTTTATAA
1 TTTTTGATGCATTTTATAA
30626015 CATTTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTTTGATGCATTTTATAAT
Found at i:30626020 original size:19 final size:21
Alignment explanation
Indices: 30625977--30626020 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
30625967 GTAAATGGCC
*
30625977 TTTTTGATGCATTTTATAA-T
1 TTTTTGATGCATTTTATAACA
*
30625997 TTTTTTATG-ATTTTATAACA
1 TTTTTGATGCATTTTATAACA
30626017 TTTT
1 TTTT
30626021 ACAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTTTGATGCATTTTATAACA
Found at i:30626029 original size:9 final size:9
Alignment explanation
Indices: 30626017--30626059 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
30626007 TTTTATAACA
30626017 TTTTACAATT
1 TTTTACAA-T
*
30626027 TTTTACGAT
1 TTTTACAAT
30626036 TTTTACAAT
1 TTTTACAAT
*
30626045 TTTGTATAAT
1 TTT-TACAAT
30626055 TTTTA
1 TTTTA
30626060 ATAAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTACAAT
Found at i:30626029 original size:19 final size:21
Alignment explanation
Indices: 30626007--30626053 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
30625997 TTTTTTATGA
30626007 TTTTATAAC-A-TTTTACAAT
1 TTTTATAACGATTTTTACAAT
30626026 TTTT-T-ACGATTTTTACAAT
1 TTTTATAACGATTTTTACAAT
30626045 TTTGTATAA
1 TTT-TATAA
30626054 TTTTTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 16 0.70
20 1 0.04
21 1 0.04
22 1 0.04
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTATAACGATTTTTACAAT
Found at i:30626056 original size:19 final size:19
Alignment explanation
Indices: 30626017--30626059 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
30626007 TTTTATAACA
* *
30626017 TTTTACAATTTTTTACGAT
1 TTTTACAATTTTGTACAAT
*
30626036 TTTTACAATTTTGTATAAT
1 TTTTACAATTTTGTACAAT
30626055 TTTTA
1 TTTTA
30626060 ATAAAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTACAATTTTGTACAAT
Found at i:30626088 original size:10 final size:9
Alignment explanation
Indices: 30626075--30626131 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
30626065 ATTTAAATAT
30626075 TTTTATTAAA
1 TTTTATT-AA
30626085 TTTTATTAA
1 TTTTATTAA
* *
30626094 ATTTATTGA
1 TTTTATTAA
*
30626103 TTTTATTGA
1 TTTTATTAA
*
30626112 TTTTATT-T
1 TTTTATTAA
30626120 TTTTA-TAA
1 TTTTATTAA
30626128 TTTT
1 TTTT
30626132 TTGCCACAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 1 0.02
8 9 0.22
9 24 0.59
10 7 0.17
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (9 bp):
TTTTATTAA
Found at i:30627401 original size:56 final size:56
Alignment explanation
Indices: 30627334--30627452 Score: 211
Period size: 56 Copynumber: 2.1 Consensus size: 56
30627324 ATCAATAATC
30627334 TAAAAATATTAAACCAAGAATTAAAGACACATAACTGAGAACAAGATTTCGCAAAA
1 TAAAAATATTAAACCAAGAATTAAAGACACATAACTGAGAACAAGATTTCGCAAAA
* *
30627390 TAAAAATATTAAACCAAGAATTAAGGACACATAACTGAGAACAAGATTTTGCAAAA
1 TAAAAATATTAAACCAAGAATTAAAGACACATAACTGAGAACAAGATTTCGCAAAA
*
30627446 TAGAAAT
1 TAAAAAT
30627453 CAAATGACAG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.55, C:0.13, G:0.12, T:0.21
Consensus pattern (56 bp):
TAAAAATATTAAACCAAGAATTAAAGACACATAACTGAGAACAAGATTTCGCAAAA
Found at i:30629623 original size:6 final size:6
Alignment explanation
Indices: 30629596--30629649 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
30629586 AAAGTGTCAC
* * * * *
30629596 AAAT-A AAATAA AAACAA CAATAA AAATAA AAGTAC AACTAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
30629643 AAATAA A
1 AAATAA A
30629650 TAAAACAGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
5 4 0.10
6 35 0.90
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:30634247 original size:6 final size:6
Alignment explanation
Indices: 30634238--30634293 Score: 103
Period size: 6 Copynumber: 9.3 Consensus size: 6
30634228 TAAGAATAAC
*
30634238 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACGT
1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT
30634286 AAACAT AA
1 AAACAT AA
30634294 TAATAATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.66, C:0.16, G:0.02, T:0.16
Consensus pattern (6 bp):
AAACAT
Found at i:30634298 original size:3 final size:3
Alignment explanation
Indices: 30634290--30634362 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
30634280 AAACGTAAAC
30634290 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30634338 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
30634363 CAACAACAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30634367 original size:3 final size:3
Alignment explanation
Indices: 30634361--30634389 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30634351 TAATAATAAT
30634361 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
30634390 AGGAAGTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:30636872 original size:22 final size:22
Alignment explanation
Indices: 30636844--30636889 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
30636834 TTTAGTTAAC
30636844 TTCTCCTTAAGGTTTGATTTCT
1 TTCTCCTTAAGGTTTGATTTCT
30636866 TTCTCCTTAAGGTTTGATTTCT
1 TTCTCCTTAAGGTTTGATTTCT
30636888 TT
1 TT
30636890 TCTTACTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (22 bp):
TTCTCCTTAAGGTTTGATTTCT
Done.