Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 188 of 189
Found at i:56091696 original size:36 final size:36
Alignment explanation
Indices: 56091656--56091728 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
56091646 CTAGAAGATA
56091656 TAATTATGGAATCTTAGAGTTCTAATTGTATATAGC
1 TAATTATGGAATCTTAGAGTTCTAATTGTATATAGC
*
56091692 TAATTATGTAATCTTAGAGTTCTAATTGTATATAGC
1 TAATTATGGAATCTTAGAGTTCTAATTGTATATAGC
56091728 T
1 T
56091729 TTTAATTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (36 bp):
TAATTATGGAATCTTAGAGTTCTAATTGTATATAGC
Found at i:56096837 original size:36 final size:36
Alignment explanation
Indices: 56096797--56096869 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
56096787 CTAAAAGATA
* * *
56096797 TAATTATGGAATCTTAGAGTTCTAATTGTATATAGC
1 TAATTATGGAAGCTTAGAGCTCTAATTGTATACAGC
*
56096833 TAATTATGTAAGCTTAGAGCTCTAATTGTATACAGC
1 TAATTATGGAAGCTTAGAGCTCTAATTGTATACAGC
56096869 T
1 T
56096870 TTTAATTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (36 bp):
TAATTATGGAAGCTTAGAGCTCTAATTGTATACAGC
Found at i:56097171 original size:49 final size:48
Alignment explanation
Indices: 56097095--56097191 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 48
56097085 TAAGGGAATT
** * *
56097095 CTGTTAAATCCTTTATCGTTGCGAGTTAAAGCTGACTTAGGCGTTTTTA
1 CTGTTAAATCCTTTATCACTGCAAGTT-AAGCTGAATTAGGCGTTTTTA
* *
56097144 CTGTTGAATCCTTTATCACTGCAAGTTAGGCTGAATTAGGCGTTTTTA
1 CTGTTAAATCCTTTATCACTGCAAGTTAAGCTGAATTAGGCGTTTTTA
56097192 AGCAAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
48 19 0.45
49 23 0.55
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (48 bp):
CTGTTAAATCCTTTATCACTGCAAGTTAAGCTGAATTAGGCGTTTTTA
Found at i:56098358 original size:62 final size:63
Alignment explanation
Indices: 56098282--56098407 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
56098272 GCGGTGATAA
*
56098282 AGAAACAGGTGAAGTTGCAATTT-GGGGGATATAGATATTGCTCCACTTCCAAACTTTAACTT
1 AGAAACAGGTGAAGTTGCAATTTGGGGGGATATAGATATTGCTCCACTTCCAAACGTTAACTT
56098344 AGAAACAGGTGAAGTTGCAATTTGGGGGGATATAGATATTGCTCCACTTCCAAACGTTAACTT
1 AGAAACAGGTGAAGTTGCAATTTGGGGGGATATAGATATTGCTCCACTTCCAAACGTTAACTT
56098407 A
1 A
56098408 CTTGATTCTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 23 0.37
63 39 0.63
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (63 bp):
AGAAACAGGTGAAGTTGCAATTTGGGGGGATATAGATATTGCTCCACTTCCAAACGTTAACTT
Found at i:56100760 original size:15 final size:16
Alignment explanation
Indices: 56100737--56100778 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
56100727 GGTCGGCAGC
56100737 AAAAA-AAAAGGGA-A
1 AAAAAGAAAAGGGAGA
*
56100751 AAAAAGAAAA-GAAGA
1 AAAAAGAAAAGGGAGA
56100766 AAAAAGAAAAGGG
1 AAAAAGAAAAGGG
56100779 CATCTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.30
15 15 0.65
16 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAGGGAGA
Found at i:56114682 original size:27 final size:27
Alignment explanation
Indices: 56114651--56114703 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
56114641 ATTTAATTAA
*
56114651 AATTTTAAAG-TTTTATACTTTTTAAAT
1 AATTTTAAAGATTTT-TAATTTTTAAAT
*
56114678 AATTTTAATGATTTTTAATTTTTAAA
1 AATTTTAAAGATTTTTAATTTTTAAA
56114704 AATAACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (27 bp):
AATTTTAAAGATTTTTAATTTTTAAAT
Found at i:56140665 original size:15 final size:15
Alignment explanation
Indices: 56140639--56140680 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
56140629 TTTCATTTTT
*
56140639 TTTCACTTTATTATTA
1 TTTCATTTTATTA-TA
56140655 TTTC-TTTTATTATA
1 TTTCATTTTATTATA
56140669 TTTCATTTTATT
1 TTTCATTTTATT
56140681 TCTTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 14 0.58
16 4 0.17
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCATTTTATTATA
Found at i:56148530 original size:29 final size:29
Alignment explanation
Indices: 56148464--56148542 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
56148454 TTTGCCTCAA
* *
56148464 TAGTT-TTTGAATTTTTAAAATTTAGTGC
1 TAGTTATTTTAATTTTTAAAAATTAGTGC
*
56148492 -ATTTACTTTTAATTTTTAAAAATTAGT-C
1 TAGTTA-TTTTAATTTTTAAAAATTAGTGC
*
56148520 TTAGTTATTTT-ATTTTAAAAAAT
1 -TAGTTATTTTAATTTTTAAAAAT
56148543 AAAATCCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
27 3 0.07
28 12 0.29
29 23 0.55
30 4 0.10
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (29 bp):
TAGTTATTTTAATTTTTAAAAATTAGTGC
Found at i:56151132 original size:19 final size:18
Alignment explanation
Indices: 56151098--56151160 Score: 81
Period size: 20 Copynumber: 3.3 Consensus size: 18
56151088 TTTTAAAAAT
*
56151098 AATTTTAACTTTGATTGAA
1 AATTTTAAC-TTGATTAAA
56151117 AATGTTTAACTTGATTTAAAA
1 AAT-TTTAACTTGA-TT-AAA
56151138 AATTTTAACTTGATTAAA
1 AATTTTAACTTGATTAAA
56151156 AATTT
1 AATTT
56151161 ATTCAAAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 8 0.20
19 9 0.22
20 18 0.45
21 5 0.12
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (18 bp):
AATTTTAACTTGATTAAA
Found at i:56153741 original size:41 final size:41
Alignment explanation
Indices: 56153684--56153833 Score: 239
Period size: 41 Copynumber: 3.7 Consensus size: 41
56153674 TTTAACATAT
*
56153684 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
56153725 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
56153766 TCACCGGCACTTAGCCTGCTAGG-TTCATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTT-ATAACCTGATTCAGA
*
56153807 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
56153834 AAGTCTAAAT
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
40 2 0.02
41 97 0.96
42 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:56153870 original size:82 final size:83
Alignment explanation
Indices: 56153682--56153858 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 83
56153672 AATTTAACAT
*
56153682 ATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACGTAGCCTGCTAG
1 ATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
** *
56153747 GTTTATAACCTGATTCAG
66 ACTTATAACCTAATTCAG
* *
56153765 A-TCACCGGCACTTAGCCTGCTAGG-TTCATAACCTGGTTCAGATCACCGGCACTTAGCCTGCTA
1 ATTCACCGGCACTTAGCCTGCTAGGCTT-ATAACCTGATTCAGATCACCGGCACGTAGCCTGCTA
*
56153828 GACTTA-AAGTCTAAATT-A-
65 GACTTATAA-CCT-AATTCAG
56153846 ATTCACCGGCACT
1 ATTCACCGGCACT
56153859 ACATCTGCTA
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
81 5 0.06
82 74 0.89
83 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (83 bp):
ATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
ACTTATAACCTAATTCAG
Found at i:56154284 original size:16 final size:15
Alignment explanation
Indices: 56154256--56154288 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
56154246 AACTTACAAA
56154256 ATTCGGCATATATAT
1 ATTCGGCATATATAT
56154271 ATTCGGCTATATATAT
1 ATTCGGC-ATATATAT
56154287 AT
1 AT
56154289 ATAGAATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (15 bp):
ATTCGGCATATATAT
Found at i:56158399 original size:28 final size:28
Alignment explanation
Indices: 56158363--56158460 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 28
56158353 ACAAATTTCA
*
56158363 AATAACGATAAGCATCAAAGTGCAAAAT
1 AATAACGATAAGCACCAAAGTGCAAAAT
* *
56158391 AATAACGATAAGCACCAAAGTACAAATTTT
1 AATAACGATAAGCACCAAAGTGCAAA--AT
* * * * *
56158421 TACAACGATAAGCACCGAAGCGCGAAAT
1 AATAACGATAAGCACCAAAGTGCAAAAT
56158449 AAT-ACGATAAGC
1 AATAACGATAAGC
56158461 GCGCTAATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
27 9 0.16
28 26 0.46
30 21 0.38
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.17
Consensus pattern (28 bp):
AATAACGATAAGCACCAAAGTGCAAAAT
Found at i:56162418 original size:13 final size:13
Alignment explanation
Indices: 56162400--56162425 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56162390 CGGTGCTTTG
56162400 GAGAATTTTCATT
1 GAGAATTTTCATT
56162413 GAGAATTTTCATT
1 GAGAATTTTCATT
56162426 TTCGAGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GAGAATTTTCATT
Found at i:56165991 original size:61 final size:61
Alignment explanation
Indices: 56165875--56165993 Score: 145
Period size: 61 Copynumber: 2.0 Consensus size: 61
56165865 TTTAATAATA
* * * *
56165875 ATTATAATAATTATATATTATTTTATTAGACTTTATTTAATAATAATTATGTTAAAATATG
1 ATTAAAATAATTATATATTATTTTATTAGAATTAATTTAATAATAATTATATTAAAATATG
*
56165936 ATTAAAATATTTAT-TATTATTATTATTA-AATATAATTTAATAATAATCT-TATTAAAAT
1 ATTAAAATAATTATATATTATT-TTATTAGAAT-TAATTTAATAATAAT-TATATTAAAAT
56165994 TTAATAACAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
60 9 0.18
61 40 0.80
62 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (61 bp):
ATTAAAATAATTATATATTATTTTATTAGAATTAATTTAATAATAATTATATTAAAATATG
Found at i:56166011 original size:21 final size:22
Alignment explanation
Indices: 56165969--56166016 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
56165959 TATTAAATAT
*
56165969 AATTTAATAATAATCTTATTAA
1 AATTTAATAATAATCTGATTAA
* *
56165991 AATTTAATAA-CATCTGCTTAA
1 AATTTAATAATAATCTGATTAA
56166012 AATTT
1 AATTT
56166017 TCTTTTGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTTAATAATAATCTGATTAA
Found at i:56166193 original size:16 final size:16
Alignment explanation
Indices: 56166171--56166239 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
56166161 TTTGGTTCGC
56166171 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
56166187 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
56166203 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
56166220 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
56166236 TGTA
1 TGTA
56166240 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:56166217 original size:33 final size:32
Alignment explanation
Indices: 56166171--56166239 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
56166161 TTTGGTTCGC
56166171 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
56166203 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
56166236 TGTA
1 TGTA
56166240 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:56166496 original size:18 final size:17
Alignment explanation
Indices: 56166475--56166509 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56166465 TTATTATTAA
*
56166475 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56166493 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56166510 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56166698 original size:121 final size:120
Alignment explanation
Indices: 56166458--56166841 Score: 716
Period size: 120 Copynumber: 3.2 Consensus size: 120
56166448 ATCATATTTA
56166458 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
56166523 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* *
56166578 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGGA-T
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAA-T-AATT
56166642 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
64 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
56166699 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
56166764 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
56166819 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
56166842 AACTTGAAAA
Statistics
Matches: 256, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
119 1 0.00
120 138 0.54
121 116 0.45
122 1 0.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:56166737 original size:18 final size:17
Alignment explanation
Indices: 56166716--56166750 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56166706 TTATTATTAA
*
56166716 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56166734 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56166751 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56169896 original size:33 final size:33
Alignment explanation
Indices: 56169857--56169966 Score: 136
Period size: 33 Copynumber: 3.3 Consensus size: 33
56169847 ATTATAAAGC
56169857 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
56169890 ATGTATAATTGACCTAAAATTACTTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
56169923 AATGT-T-ATTGTCCCTAAAA-AACATTGTTGGTGT
1 -ATGTATAATTG-ACCTAAAATTA-ATTGTTGGTGT
56169956 ATGTATAATTG
1 ATGTATAATTG
56169967 TTGGTTTAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
32 9 0.14
33 49 0.74
34 8 0.12
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:56169973 original size:51 final size:50
Alignment explanation
Indices: 56169913--56170015 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 50
56169903 CTAAAATTAC
56169913 TTGTTGGTTTAATGTTATTGT-CCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATT-TACCCTAAAAAACATTGTTGGTGTATG-ATAA
56169964 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGATAA
56170014 TT
1 TT
56170016 TTTACGTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
50 7 0.14
51 44 0.86
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (50 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGATAA
Found at i:56170189 original size:86 final size:86
Alignment explanation
Indices: 56170082--56170262 Score: 355
Period size: 86 Copynumber: 2.1 Consensus size: 86
56170072 TTCTCTCCAC
56170082 ATAA-AATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
56170146 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
56170167 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
56170232 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
56170253 ATAATAATTA
1 ATAATAATTA
56170263 CAATTATATT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (86 bp):
ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
TTAATATTAAAGATAAAAATT
Found at i:56172622 original size:21 final size:22
Alignment explanation
Indices: 56172593--56172633 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
56172583 AGACTAACCG
56172593 ATGACGCAAATCGGCAGAAACT
1 ATGACGCAAATCGGCAGAAACT
*
56172615 ATGA-GCAAATCGGCCGAAA
1 ATGACGCAAATCGGCAGAAA
56172634 TAGAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (22 bp):
ATGACGCAAATCGGCAGAAACT
Found at i:56180911 original size:116 final size:116
Alignment explanation
Indices: 56180774--56181012 Score: 469
Period size: 116 Copynumber: 2.1 Consensus size: 116
56180764 TACACTCAAT
56180774 TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTGCCCTTCTAGTCCTTCCTCTATT
1 TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTGCCCTTCTAGTCCTTCCTCTATT
56180839 TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
66 TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
*
56180890 TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTTCCCTTCTAGTCCTTCCTCTATT
1 TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTGCCCTTCTAGTCCTTCCTCTATT
56180955 TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
66 TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
56181006 TTCAATA
1 TTCAATA
56181013 CTTTTCACTC
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 122 1.00
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (116 bp):
TTCAATATCCTCCACTATTTATTCTACTCTTTTCATATTATTGCCCTTCTAGTCCTTCCTCTATT
TCTCATTTATCTAATCAAGTCATTTCTTCTTTTTAATTTTCACACTTTTAC
Found at i:56181186 original size:20 final size:20
Alignment explanation
Indices: 56181157--56181196 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
56181147 ACATGTGTTT
56181157 AACCCAAAATGACACGGTCC
1 AACCCAAAATGACACGGTCC
*
56181177 AACCCGAAATGACACGGTCC
1 AACCCAAAATGACACGGTCC
56181197 CATTTTAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.35, G:0.17, T:0.10
Consensus pattern (20 bp):
AACCCAAAATGACACGGTCC
Found at i:56192992 original size:22 final size:24
Alignment explanation
Indices: 56192965--56193010 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
56192955 TTTTATAGTT
56192965 GTTGTTATAGA-TG-AAAAATAAA
1 GTTGTTATAGAGTGTAAAAATAAA
*
56192987 GTTGTTATGGAGTGTAAAAATAAA
1 GTTGTTATAGAGTGTAAAAATAAA
56193011 ACATGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
GTTGTTATAGAGTGTAAAAATAAA
Found at i:56193513 original size:21 final size:21
Alignment explanation
Indices: 56193489--56193532 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56193479 AAGATGTGAC
*
56193489 TTGTATTGAATTGAATG-TAAA
1 TTGTATTAAATTG-ATGTTAAA
56193510 TTGTATTAAATTGATGTTAAA
1 TTGTATTAAATTGATGTTAAA
56193531 TT
1 TT
56193533 TACTCGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (21 bp):
TTGTATTAAATTGATGTTAAA
Found at i:56194115 original size:24 final size:24
Alignment explanation
Indices: 56194081--56194131 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
56194071 GTGCTTCCCA
*
56194081 TTAATTGCTCTTCAGAGCTACCCG
1 TTAATTACTCTTCAGAGCTACCCG
**
56194105 TTAATTACTCTTTGGAGCTACCCG
1 TTAATTACTCTTCAGAGCTACCCG
56194129 TTA
1 TTA
56194132 TAGGCTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (24 bp):
TTAATTACTCTTCAGAGCTACCCG
Found at i:56194153 original size:25 final size:24
Alignment explanation
Indices: 56194095--56194158 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 24
56194085 TTGCTCTTCA
56194095 GAGCTACCCGTTAATTA--CTCTTTG
1 GAGCTACCCGTT-A-TAGGCTCTTTG
56194119 GAGCTACCCGTTATAGGCTCTTTG
1 GAGCTACCCGTTATAGGCTCTTTG
*
56194143 TGAGCTTCCCGTTATA
1 -GAGCTACCCGTTATA
56194159 TTGCCCAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 2 0.06
23 1 0.03
24 19 0.53
25 14 0.39
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (24 bp):
GAGCTACCCGTTATAGGCTCTTTG
Found at i:56195185 original size:24 final size:24
Alignment explanation
Indices: 56195158--56195204 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
56195148 ATTGAAATGG
56195158 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
56195182 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
56195205 GGAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:56195226 original size:21 final size:21
Alignment explanation
Indices: 56195175--56195226 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
56195165 TAGTATGTGA
* *
56195175 TGAATTTATT-GAATTTATAT
1 TGAATATATTGGAATATATAT
*
56195195 TGATTGA-ATTGGAATATATAT
1 TGAAT-ATATTGGAATATATAT
56195216 TGAATATATTG
1 TGAATATATTG
56195227 ATTATTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (21 bp):
TGAATATATTGGAATATATAT
Found at i:56195422 original size:39 final size:38
Alignment explanation
Indices: 56195360--56195435 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
56195350 CGACTTCAAG
* *
56195360 TCGATGAGACACTAGGTGTCAATTTAACTTCGGATTAAT
1 TCGATGAGACACTAGATGCCAATTT-ACTTCGGATTAAT
* *
56195399 TCGATGAGGCACTAGATGCCAATTTACTTCGGTTTAA
1 TCGATGAGACACTAGATGCCAATTTACTTCGGATTAA
56195436 CCAATGTGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 11 0.33
39 22 0.67
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (38 bp):
TCGATGAGACACTAGATGCCAATTTACTTCGGATTAAT
Found at i:56195662 original size:20 final size:20
Alignment explanation
Indices: 56195637--56195676 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56195627 TTGAATATGG
56195637 TATGGATAAAGCAATTGCAT
1 TATGGATAAAGCAATTGCAT
56195657 TATGGATAAAGCAATTGCAT
1 TATGGATAAAGCAATTGCAT
56195677 AAATGAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (20 bp):
TATGGATAAAGCAATTGCAT
Found at i:56201175 original size:37 final size:40
Alignment explanation
Indices: 56201114--56201208 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 40
56201104 ATCATAAGTG
*
56201114 TATAT-ATATTATAAATATTTAAAGTTAAAA-AA-TATATA
1 TATATAATATTAT-AATATTAAAAGTTAAAATAAGTATATA
56201152 T-TATAATATTATAATATTAAAAGTTAAAAGTTAAGTATATA
1 TATATAATATTATAATATTAAAAGTTAAAA--TAAGTATATA
*
56201193 TATATTATATTATAAT
1 TATATAATATTATAAT
56201209 GATAAAGTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
37 19 0.39
38 8 0.16
40 2 0.04
41 7 0.14
42 13 0.27
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (40 bp):
TATATAATATTATAATATTAAAAGTTAAAATAAGTATATA
Found at i:56201264 original size:25 final size:25
Alignment explanation
Indices: 56201210--56201284 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
56201200 TATTATAATG
* *
56201210 ATAAAGTAAAA-G-AAAAAGAAATAG
1 ATAAAG-AAAACGAAAAAAGAAAGAA
* *
56201234 AGAAAG-AAACGAAACAAAGAAGGAA
1 ATAAAGAAAACGAAA-AAAGAAAGAA
*
56201259 ATAAAGAAAAGGAAAAAAGAAAGAA
1 ATAAAGAAAACGAAAAAAGAAAGAA
56201284 A
1 A
56201285 GAAGGAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
22 3 0.08
23 1 0.03
24 7 0.17
25 22 0.55
26 7 0.17
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (25 bp):
ATAAAGAAAACGAAAAAAGAAAGAA
Found at i:56201986 original size:24 final size:24
Alignment explanation
Indices: 56201959--56202005 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
56201949 ATTGAAATAG
56201959 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
56201983 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
56202006 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:56202231 original size:38 final size:37
Alignment explanation
Indices: 56202187--56202264 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
56202177 TGTCAATTTA
*
56202187 TTACTTCGGATTAATTCAATAAGACACTGGGTGCCAAT
1 TTACTTCGGATTAA-CCAATAAGACACTGGGTGCCAAT
* * * *
56202225 TTACTTCGGTTTAACCGATGAGACACTGGGTGTCAAT
1 TTACTTCGGATTAACCAATAAGACACTGGGTGCCAAT
56202262 TTA
1 TTA
56202265 TTACTTTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 22 0.63
38 13 0.37
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (37 bp):
TTACTTCGGATTAACCAATAAGACACTGGGTGCCAAT
Found at i:56202283 original size:40 final size:40
Alignment explanation
Indices: 56202162--56202296 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
56202152 GACTTCGAGT
* *
56202162 CGATGAGAAACTAGGTGTCAATTTATTACTTCGGATTAATT
1 CGATGAGACACTAGGTGTCAATTTATTACTTCGGATT-ATC
* * * * * *
56202203 CAATAAGACACTGGGTGCCAA--T-TTACTTCGGTTTAAC
1 CGATGAGACACTAGGTGTCAATTTATTACTTCGGATTATC
* * *
56202240 CGATGAGACACTGGGTGTCAATTTATTACTTTGAATTATC
1 CGATGAGACACTAGGTGTCAATTTATTACTTCGGATTATC
*
56202280 CGATGAGGCACTAGGTG
1 CGATGAGACACTAGGTG
56202297 CCAAACTAGT
Statistics
Matches: 74, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 19 0.26
38 11 0.15
39 2 0.03
40 26 0.35
41 16 0.22
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (40 bp):
CGATGAGACACTAGGTGTCAATTTATTACTTCGGATTATC
Found at i:56206020 original size:21 final size:21
Alignment explanation
Indices: 56205996--56206041 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
56205986 TGTTTATTTT
56205996 TCAACAAAGATTCAAAA-TCTA
1 TCAACAAAGA-TCAAAACTCTA
* *
56206017 TCAACTAAGATCAAAACTCTT
1 TCAACAAAGATCAAAACTCTA
56206038 TCAA
1 TCAA
56206042 AATAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (21 bp):
TCAACAAAGATCAAAACTCTA
Found at i:56210934 original size:32 final size:32
Alignment explanation
Indices: 56210889--56210960 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
56210879 AGGAATATTG
* *
56210889 TATCATTTAACAAAAT-TAAAGTTGATAGTT-GT
1 TATCATTTAAC-AAATGAAAAGGTGATA-TTAGT
*
56210921 TATCATTTCACAAATGAAAAGGTGATATTAGT
1 TATCATTTAACAAATGAAAAGGTGATATTAGT
56210953 TATCATTT
1 TATCATTT
56210961 TATAGAACTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 6 0.17
32 29 0.83
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.40
Consensus pattern (32 bp):
TATCATTTAACAAATGAAAAGGTGATATTAGT
Found at i:56212046 original size:52 final size:52
Alignment explanation
Indices: 56211984--56212087 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
56211974 TAATAGTTAG
*
56211984 ACGCAACGTGCCTTAGACAATACCAATGGTATGTG-AGGTCCCAGAGGCTTCC
1 ACGCAACGTGCCTTAGACAATACCAATGGTATGTGCA-GTCCCAAAGGCTTCC
* * *
56212036 ACGCAACGTGCCTTAGACAGTACCAATGGTGTGTGCAGTCTCAAAGGCTTCC
1 ACGCAACGTGCCTTAGACAATACCAATGGTATGTGCAGTCCCAAAGGCTTCC
56212088 CCGTAATTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
52 46 0.98
53 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.25, T:0.22
Consensus pattern (52 bp):
ACGCAACGTGCCTTAGACAATACCAATGGTATGTGCAGTCCCAAAGGCTTCC
Found at i:56222640 original size:12 final size:13
Alignment explanation
Indices: 56222608--56222643 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
56222598 AAATTATCCA
56222608 ACCCAA-CCAATT
1 ACCCAACCCAATT
56222620 ACCCAACCCAATT
1 ACCCAACCCAATT
56222633 A-CCAACCCAAT
1 ACCCAACCCAAT
56222644 AAAACTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.42, C:0.44, G:0.00, T:0.14
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:56222730 original size:38 final size:38
Alignment explanation
Indices: 56222625--56222740 Score: 187
Period size: 39 Copynumber: 3.0 Consensus size: 38
56222615 CAATTACCCA
*
56222625 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTTT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
56222663 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTA-CCAACCCAATAAAACTAAAACTAAAGTCT
* * *
56222702 ACCCAATTATCAACCCAATAAAAATAAAATTAAAGTCT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
56222740 A
1 A
56222741 ACTCTAAGTC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 36 0.49
39 37 0.51
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.21
Consensus pattern (38 bp):
ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:56222893 original size:17 final size:17
Alignment explanation
Indices: 56222873--56222933 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
56222863 ATTTCAAGAC
56222873 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
56222890 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
56222909 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
56222927 TTATGTA
1 TTATGTA
56222934 GTGATCCAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 16 0.50
18 4 0.12
19 4 0.12
20 8 0.25
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:56222909 original size:37 final size:37
Alignment explanation
Indices: 56222868--56222938 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
56222858 TGTTAATTTC
*
56222868 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
56222905 AAGACTTATGTAATATTTTTAATTATGTAGTGAT
1 AAGACTTATGTAATATTTTTAATTATGTAGTGAT
56222939 CCAATTCGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.46
Consensus pattern (37 bp):
AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:56227667 original size:21 final size:22
Alignment explanation
Indices: 56227624--56227668 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
56227614 GGCCCGGCCC
56227624 ATTTTTTTAATAAACACAAAAA
1 ATTTTTTTAATAAACACAAAAA
*
56227646 ATTTATTTTAA-AAATA-AAAAA
1 ATTT-TTTTAATAAACACAAAAA
56227667 AT
1 AT
56227669 AAAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 8 0.38
23 6 0.29
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTTTTTAATAAACACAAAAA
Found at i:56232157 original size:41 final size:39
Alignment explanation
Indices: 56232048--56232157 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 39
56232038 TCAGATAATT
**
56232048 CGAAGTAATAATTTGACACCCAGTGTCTCATCGGCTAAAC
1 CGAAGTAA-AATTTGACACCCAGTGTCTCATCGAATAAAC
* * * *
56232088 CAAAGT-AAA-TTGGCACCCAGTGCCTCATCGAATATATC
1 CGAAGTAAAATTTGACACCCAGTGTCTCATCGAATA-AAC
*
56232126 CGAAGTAACAATTTGACACCTAGTGTCTCATC
1 CGAAGTAA-AATTTGACACCCAGTGTCTCATC
56232158 AACTCGAAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
37 21 0.38
38 9 0.16
39 2 0.04
40 7 0.12
41 17 0.30
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (39 bp):
CGAAGTAAAATTTGACACCCAGTGTCTCATCGAATAAAC
Found at i:56232337 original size:15 final size:15
Alignment explanation
Indices: 56232290--56232339 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
56232280 CAATTCAAAT
*
56232290 AATCAATATATATTC
1 AATCAATATAAATTC
56232305 AAT-ATATATACCAATTC
1 AATCA-ATATA--AATTC
56232322 AATCAATATAAATTC
1 AATCAATATAAATTC
56232337 AAT
1 AAT
56232340 AAATTCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCAATATAAATTC
Found at i:56232362 original size:24 final size:24
Alignment explanation
Indices: 56232317--56232363 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
56232307 TATATATACC
56232317 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
56232341 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
56232364 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:56236821 original size:3 final size:3
Alignment explanation
Indices: 56236813--56236853 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
56236803 TAATCATTAA
* * *
56236813 AAT AAT AAT AAT AAT TAT ATT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
56236854 AATTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:56237674 original size:5 final size:5
Alignment explanation
Indices: 56237666--56237706 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
56237656 TTTTTTACTT
*
56237666 ATATA ATATA ATACA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
56237707 AGCATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:56244274 original size:23 final size:23
Alignment explanation
Indices: 56244234--56244280 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
56244224 TTTACTTTTA
56244234 ATTATAATCATTAAAATAATAAT
1 ATTATAATCATTAAAATAATAAT
*
56244257 ATTATTAT-ATTAACAATAATAAT
1 ATTATAATCATTAA-AATAATAAT
56244280 A
1 A
56244281 ATAAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTATAATCATTAAAATAATAAT
Found at i:56245106 original size:5 final size:5
Alignment explanation
Indices: 56245098--56245138 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
56245088 TTTTTTACTT
* *
56245098 ATATA ATATA ATACA ATACA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
56245139 AGCATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (5 bp):
ATATA
Found at i:56250017 original size:2 final size:2
Alignment explanation
Indices: 56250012--56250082 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
56250002 TTTTTTTTGA
56250012 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
56250054 AC AC AC AC AC AC AC AT AC AT AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
56250083 TGTTCCCCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:56252381 original size:41 final size:41
Alignment explanation
Indices: 56252324--56252429 Score: 167
Period size: 41 Copynumber: 2.6 Consensus size: 41
56252314 AATGAGATAA
* * *
56252324 TTCAGACTTTACGTCTAGTAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
* *
56252365 TTCAGACTTTACGTCTAGCAGGCTTGACGCTGGTGAATTAT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
56252406 TTCAGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
56252430 AATTGCCAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
Found at i:56258996 original size:20 final size:20
Alignment explanation
Indices: 56258957--56259017 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
56258947 ATTTTATAAA
*
56258957 TTTTATAAAT-TCTT-AATT
1 TTTTATAAATATTTTGAATT
56258975 TTTTATAAATATTTTGAATT
1 TTTTATAAATATTTTGAATT
*
56258995 TTTGA-AAATTATTTTG-ATT
1 TTTTATAAA-TATTTTGAATT
56259014 TTTT
1 TTTT
56259018 TTTTGTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.27
19 12 0.32
20 15 0.41
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTATAAATATTTTGAATT
Found at i:56262002 original size:36 final size:36
Alignment explanation
Indices: 56261955--56262029 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
56261945 TTAACTCAAT
*
56261955 ATACATGGTATGAAACAGGGATATTATCTATTTCTA
1 ATACATGGTATGAAACAGAGATATTATCTATTTCTA
*
56261991 ATACATGGTATGAAACTGAGATATTATCTATTTCTA
1 ATACATGGTATGAAACAGAGATATTATCTATTTCTA
56262027 ATA
1 ATA
56262030 GTTTAATGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (36 bp):
ATACATGGTATGAAACAGAGATATTATCTATTTCTA
Found at i:56266509 original size:11 final size:11
Alignment explanation
Indices: 56266493--56266517 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56266483 AGGGAGTACC
56266493 AAACTATTAAT
1 AAACTATTAAT
56266504 AAACTATTAAT
1 AAACTATTAAT
56266515 AAA
1 AAA
56266518 TTAAGGGTGT
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
AAACTATTAAT
Found at i:56266815 original size:26 final size:26
Alignment explanation
Indices: 56266785--56266851 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
56266775 ATTAATTTTT
* *
56266785 AATATTATTTAATATACATAT-TTATT
1 AATATTATTTAATATA-ATATATAATA
* *
56266811 TATATT-TAATAATATAATATATAATA
1 AATATTAT-TTAATATAATATATAATA
56266837 AATATTATTTAATAT
1 AATATTATTTAATAT
56266852 TTTAACAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
25 5 0.16
26 26 0.81
27 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
AATATTATTTAATATAATATATAATA
Found at i:56266824 original size:36 final size:36
Alignment explanation
Indices: 56266784--56266894 Score: 101
Period size: 34 Copynumber: 3.1 Consensus size: 36
56266774 TATTAATTTT
56266784 TAATATTATTTAATATACATATTTATTT-ATA-TTTAA
1 TAATATTATTTAATATA-ATA-TTATTTAATATTTTAA
*
56266820 TAATATAATATATAATA-AATATTATTTAATATTTTAA
1 TAATAT--TATTTAATATAATATTATTTAATATTTTAA
*
56266857 CAA-ATTATTTAATATAA-A--ATTCTAATATTTATAA
1 TAATATTATTTAATATAATATTATT-TAATATTT-TAA
56266891 TAAT
1 TAAT
56266895 TTTAAATTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
32 3 0.05
33 8 0.13
34 14 0.22
35 8 0.13
36 14 0.22
37 8 0.13
38 8 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.50
Consensus pattern (36 bp):
TAATATTATTTAATATAATATTATTTAATATTTTAA
Found at i:56267650 original size:20 final size:19
Alignment explanation
Indices: 56267608--56267650 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
56267598 ATATTTTATT
*
56267608 ATTTCATAATTAAAAATAT
1 ATTTCATAATTAAAAATAC
* *
56267627 ATTTCATAAATTAGAATTAC
1 ATTTCAT-AATTAAAAATAC
56267647 ATTT
1 ATTT
56267651 TATTAGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTTCATAATTAAAAATAC
Found at i:56268494 original size:113 final size:114
Alignment explanation
Indices: 56268287--56268508 Score: 349
Period size: 113 Copynumber: 1.9 Consensus size: 114
56268277 GTAAAAAAAA
* * * *
56268287 TTTTACTTTTTTTTGTGTCAGTATCAGGTATCAGTATACGAAAAAAGTAAAAAAAAAAATTTGTG
1 TTTTACTTTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAGT-AAAAAAAAAATTGGTG
*
56268352 GTGGCCTGCCAATGGCCGGCACCACCTTTTTTGGTGGAAAAAAATATTTTT
65 GTGGCCTGCCAATGGCCGGCACCACC-TTTTTGGAGGAAAAAAATATTTTT
56268403 TTTTAC-TTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAGT-AAAAAAAAATTGGTGG
1 TTTTACTTTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAGTAAAAAAAAAATTGGTGG
* *
56268466 TGGCTTGTCAATGGCCGGCACCACCTTTTTGGAGGAAAAAAAT
66 TGGCCTGCCAATGGCCGGCACCACCTTTTTGGAGGAAAAAAAT
56268509 TTCGGGCATT
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
112 17 0.17
113 38 0.38
115 38 0.38
116 6 0.06
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (114 bp):
TTTTACTTTTTTTCGTGTCAATAGCAGGTATCAGTATACGAAAAAAGTAAAAAAAAAATTGGTGG
TGGCCTGCCAATGGCCGGCACCACCTTTTTGGAGGAAAAAAATATTTTT
Found at i:56269146 original size:54 final size:53
Alignment explanation
Indices: 56269031--56269213 Score: 289
Period size: 52 Copynumber: 3.5 Consensus size: 53
56269021 TAGAAACGAA
** * *
56269031 AATG-AAAAAAAGGGTGTTAGATGTATAAAAAAATCTGAAATAAATGAGATTG
1 AATGAAAAAAAAGGGTGTTAGATGTAGGAAAAAATTTAAAATAAATGAGATTG
56269083 AATG-AAAAAAAGGGTGTTAGATGTAGGAAAAAATTTAAAATAAATGAGATTG
1 AATGAAAAAAAAGGGTGTTAGATGTAGGAAAAAATTTAAAATAAATGAGATTG
56269135 AATGAAAAAAAAGGGTGTTAGATGTAGGAAAAAAATTTAAAATAAATGAGATTG
1 AATGAAAAAAAAGGGTGTTAGATGTAGG-AAAAAATTTAAAATAAATGAGATTG
*
56269189 AATGAAAAAAATAGAGTGTTAGATG
1 AATGAAAAAAA-AGGGTGTTAGATG
56269214 GCATTGTTCA
Statistics
Matches: 123, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
52 52 0.42
53 23 0.19
54 36 0.29
55 12 0.10
ACGTcount: A:0.52, C:0.01, G:0.22, T:0.25
Consensus pattern (53 bp):
AATGAAAAAAAAGGGTGTTAGATGTAGGAAAAAATTTAAAATAAATGAGATTG
Found at i:56271346 original size:13 final size:13
Alignment explanation
Indices: 56271328--56271352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56271318 GGTCGCGACG
56271328 ATTTTAATTTTTT
1 ATTTTAATTTTTT
56271341 ATTTTAATTTTT
1 ATTTTAATTTTT
56271353 ACTTTCTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTAATTTTTT
Found at i:56272070 original size:57 final size:57
Alignment explanation
Indices: 56271935--56272072 Score: 197
Period size: 57 Copynumber: 2.4 Consensus size: 57
56271925 AAAACTCAAA
* *
56271935 TTTTTTTTACTGTACTGGGTGCCAGCCATTGATAGGCCAGCACCCAAAAATTTTTTTC
1 TTTTTTTT-TTGTACTGGGTGCCGGCCATTGATAGGCCAGCACCCAAAAATTTTTTTC
** *
56271993 CCTTTTTTTCGTACTGGGTGCCGGCCATTGATAGGCCAGCACCC-AAAATTTTTTTC
1 TTTTTTTTTTGTACTGGGTGCCGGCCATTGATAGGCCAGCACCCAAAAATTTTTTTC
*
56272049 TTTTTTTTTTGTACTCTGGTGCCG
1 TTTTTTTTTTGTACT-GGGTGCCG
56272073 ACTAGACCTG
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
56 24 0.34
57 40 0.57
58 6 0.09
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (57 bp):
TTTTTTTTTTGTACTGGGTGCCGGCCATTGATAGGCCAGCACCCAAAAATTTTTTTC
Found at i:56272267 original size:13 final size:13
Alignment explanation
Indices: 56272251--56272275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56272241 AAAAATATTT
56272251 TAAAAATAAAAAA
1 TAAAAATAAAAAA
56272264 TAAAAATAAAAA
1 TAAAAATAAAAA
56272276 TATTTTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:56272303 original size:6 final size:6
Alignment explanation
Indices: 56272292--56272323 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
56272282 TAAAGTATTT
56272292 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
56272324 TATATGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:56277281 original size:22 final size:23
Alignment explanation
Indices: 56277256--56277300 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
56277246 ATAGCAACGT
56277256 ATTTATGATTA-ATTTA-TATAAA
1 ATTTATGA-TACATTTATTATAAA
*
56277278 ATTTATTATACATTTATTATAAA
1 ATTTATGATACATTTATTATAAA
56277301 GATCAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 12 0.60
23 6 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTATGATACATTTATTATAAA
Found at i:56282953 original size:41 final size:41
Alignment explanation
Indices: 56282891--56282974 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
56282881 CGGATGATCC
56282891 TTAAGCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
1 TTAAGCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
*
56282932 TTAATCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
1 TTAAGCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
56282973 TT
1 TT
56282975 GGGAAAGGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (41 bp):
TTAAGCTTGTTTTATTATATCTTGATTTCTACTTATTGAAA
Found at i:56295254 original size:22 final size:21
Alignment explanation
Indices: 56295226--56295283 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
56295216 ATGCAATCGT
*
56295226 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCTTAG
56295247 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TTTGTAATCTTAG
*
56295270 AGATTTGATTTGTA
1 AGATATGATTTGTA
56295284 GATACCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 6 0.18
22 15 0.45
23 12 0.36
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Found at i:56300368 original size:22 final size:23
Alignment explanation
Indices: 56300340--56300382 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56300330 GCAATCGTAG
*
56300340 ATATGA-TATGTAATCTTAGAAA
1 ATATGATTATGTAATATTAGAAA
*
56300362 ATATGATTTTGTAATATTAGA
1 ATATGATTATGTAATATTAGA
56300383 GATTTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (23 bp):
ATATGATTATGTAATATTAGAAA
Found at i:56304923 original size:21 final size:21
Alignment explanation
Indices: 56304898--56304939 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
56304888 TGGTCATTTT
56304898 ACCACCTAAGGTTAAACTATC
1 ACCACCTAAGGTTAAACTATC
56304919 ACCACCTAAGGTTAAACTATC
1 ACCACCTAAGGTTAAACTATC
56304940 CCAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.24
Consensus pattern (21 bp):
ACCACCTAAGGTTAAACTATC
Found at i:56305730 original size:19 final size:19
Alignment explanation
Indices: 56305682--56305732 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
56305672 ATATAATTTG
56305682 ATAATTTTACTAACAATTA
1 ATAATTTTACTAACAATTA
*
56305701 ATACA----ATTAACAATTA
1 ATA-ATTTTACTAACAATTA
56305717 ATAATTTTACTAACAA
1 ATAATTTTACTAACAA
56305733 AATGTTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
15 1 0.04
16 13 0.52
19 10 0.40
20 1 0.04
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAATTTTACTAACAATTA
Found at i:56305747 original size:93 final size:95
Alignment explanation
Indices: 56305650--56305836 Score: 281
Period size: 96 Copynumber: 2.0 Consensus size: 95
56305640 AACAATTAAT
*
56305650 ACAATTAACAATTAACATTTTGATATAATTTGATAA-TT-TTACTAACAATTAATA-CAATTAAC
1 ACAATTAACAATTAACAATTTGATATAATTTGATAATTTATTACTAACAATTAATATC-ATTAAC
56305712 AATTAATAATTTTACTAACAAAATGTTAGTA
65 AATTAATAATTTTACTAACAAAATGTTAGTA
* * *
56305743 ACAATTAATAATTAATAATTTGATATAATTTGATAATTTAATTAGTAACAATTAATATCATTAAC
1 ACAATTAACAATTAACAATTTGATATAATTTGATAATTT-ATTACTAACAATTAATATCATTAAC
* *
56305808 AATTACTAATTTTACTAGCAAAATGTTAG
65 AATTAATAATTTTACTAACAAAATGTTAG
56305837 ATTTTACAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
93 33 0.39
94 2 0.02
96 48 0.57
97 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (95 bp):
ACAATTAACAATTAACAATTTGATATAATTTGATAATTTATTACTAACAATTAATATCATTAACA
ATTAATAATTTTACTAACAAAATGTTAGTA
Found at i:56308232 original size:2 final size:2
Alignment explanation
Indices: 56308225--56308262 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56308215 AAAACAAGCA
56308225 AG AG AG 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
56308263 CTCAATTTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56311650 original size:16 final size:16
Alignment explanation
Indices: 56311629--56311670 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
56311619 AATCAAGTTG
*
56311629 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
56311645 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
56311661 --AAAATTAATT
1 AGAAAATTAATT
56311671 TATAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.40
16 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:56319302 original size:103 final size:106
Alignment explanation
Indices: 56319094--56319459 Score: 581
Period size: 103 Copynumber: 3.5 Consensus size: 106
56319084 AACCGTTATT
* ** *
56319094 GTGGATC-TCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GTGGATCATCGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
56319158 ATCAGCACATAGCAACCCCC-TTTC-CATTTCAAAGATATG
66 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATG
* *
56319197 GTGGAT-ATCGCACTTAGCACCA-CAATGAATC-GGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GTGGATCATCGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
56319259 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATG
66 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATG
56319300 GT-GATCATCGCACATAGCACCACCAATGAACC-GGGAATCAGCACTTAGCAACCCCTC-GGGGA
1 GTGGATCATCGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
56319362 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATG
66 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATG
* **
56319403 GTGGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCAGCACACAGCAACCCCT
1 GTGGATCATCGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCT
56319460 TTATATACAA
Statistics
Matches: 249, Mismatches: 7, Indels: 13
0.93 0.03 0.05
Matches are distributed among these distances:
101 51 0.20
102 14 0.06
103 124 0.50
104 60 0.24
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (106 bp):
GTGGATCATCGCACATAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATG
Found at i:56319817 original size:29 final size:29
Alignment explanation
Indices: 56319784--56319847 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
56319774 TAATCCACCA
56319784 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
56319813 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
56319843 CCCAA
1 CCCAA
56319848 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:56319821 original size:30 final size:30
Alignment explanation
Indices: 56319791--56319847 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56319781 CCACCCAACT
56319791 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
56319820 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
56319848 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:56326664 original size:26 final size:26
Alignment explanation
Indices: 56326634--56326685 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
56326624 CACCACTGAA
*
56326634 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
56326660 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
56326686 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:56326815 original size:104 final size:103
Alignment explanation
Indices: 56326602--56326867 Score: 453
Period size: 104 Copynumber: 2.6 Consensus size: 103
56326592 TAACCGTTAT
* *
56326602 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
56326667 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
56326705 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
56326770 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* **
56326809 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
56326868 TTATATACAA
Statistics
Matches: 154, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
103 57 0.37
104 96 0.62
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.18
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:56327226 original size:29 final size:29
Alignment explanation
Indices: 56327193--56327256 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
56327183 TAATCCACCA
56327193 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
56327222 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
56327252 CCCAA
1 CCCAA
56327257 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:56327230 original size:30 final size:30
Alignment explanation
Indices: 56327200--56327256 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56327190 CCACCCAACT
56327200 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
56327229 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
56327257 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:56332610 original size:16 final size:16
Alignment explanation
Indices: 56332589--56332621 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
56332579 ACTAGCCTTA
56332589 GTCAACAAGGGAAAAT
1 GTCAACAAGGGAAAAT
56332605 GTCAACAAGGGAAAAT
1 GTCAACAAGGGAAAAT
56332621 G
1 G
56332622 ATTGTCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.27, T:0.12
Consensus pattern (16 bp):
GTCAACAAGGGAAAAT
Found at i:56336013 original size:25 final size:25
Alignment explanation
Indices: 56335985--56336032 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
56335975 GGAAAGGATT
56335985 TTGTTAAATGAAATAATAAAAATAA
1 TTGTTAAATGAAATAATAAAAATAA
56336010 TTGTTAAATGAAATAATAAAAAT
1 TTGTTAAATGAAATAATAAAAAT
56336033 TGAGCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTGTTAAATGAAATAATAAAAATAA
Found at i:56336207 original size:28 final size:25
Alignment explanation
Indices: 56336155--56336217 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
56336145 AACTTACACA
56336155 GCGATGCAGCAGAGGAGTGTCGACG
1 GCGATGCAGCAGAGGAGTGTCGACG
*
56336180 GCGATGTAGCAGAGGAGTGTCGACG
1 GCGATGCAGCAGAGGAGTGTCGACG
* *
56336205 ACGATGCAACAGA
1 GCGATGCAGCAGA
56336218 TAGTCAGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.40, T:0.13
Consensus pattern (25 bp):
GCGATGCAGCAGAGGAGTGTCGACG
Found at i:56336404 original size:40 final size:40
Alignment explanation
Indices: 56336353--56336493 Score: 156
Period size: 40 Copynumber: 3.5 Consensus size: 40
56336343 AAAATGATAC
* *
56336353 TTTGTGGCATTTTTCTCATAGCGTCGCTAATGCTTGACTT
1 TTTGCGGCATTTTTCTCATAGCGTCGCTAATGCTTGACAT
*
56336393 TTTGCGGCATTTTTCTCATAGTGTCGCTAATGCTTGACAT
1 TTTGCGGCATTTTTCTCATAGCGTCGCTAATGCTTGACAT
** * * * * * *
56336433 TTTGCATCGTTTGTCTCGTAAACGTTGCTAATGCTTGACCT
1 TTTGCGGCATTTTTCTCAT-AGCGTCGCTAATGCTTGACAT
**
56336474 TTTGCGGTGTTTTTCTCATA
1 TTTGCGGCATTTTTCTCATA
56336494 AACGCCGCTG
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 52 0.63
41 31 0.37
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.45
Consensus pattern (40 bp):
TTTGCGGCATTTTTCTCATAGCGTCGCTAATGCTTGACAT
Found at i:56339301 original size:12 final size:12
Alignment explanation
Indices: 56339284--56339333 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
56339274 TTTTGTAAAA
56339284 TATATATTTAAT
1 TATATATTTAAT
56339296 TATATATTTAA-
1 TATATATTTAAT
56339307 TAT-TAATTT-AT
1 TATAT-ATTTAAT
*
56339318 TTTATATTTTAAT
1 TATATA-TTTAAT
56339331 TAT
1 TAT
56339334 TTTAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 2 0.06
11 10 0.32
12 15 0.48
13 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATATTTAAT
Found at i:56339308 original size:23 final size:24
Alignment explanation
Indices: 56339282--56339339 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
56339272 AATTTTGTAA
56339282 AATATATATTTAATTATATA-TTT
1 AATATATATTTAATTATATATTTT
*
56339305 AATAT-TAATTT-ATTTTATATTTT
1 AATATAT-ATTTAATTATATATTTT
56339328 AAT-TAT-TTTAAT
1 AATATATATTTAAT
56339340 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
21 3 0.10
22 11 0.37
23 16 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
AATATATATTTAATTATATATTTT
Found at i:56339341 original size:17 final size:17
Alignment explanation
Indices: 56339284--56339337 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 17
56339274 TTTTGTAAAA
56339284 TATATATTTAATTATATATT
1 TATAT-TTTAATT-TAT-TT
*
56339304 TA-ATATTAATTTATTT
1 TATATTTTAATTTATTT
56339320 TATATTTTAA-TTATTT
1 TATATTTTAATTTATTT
56339336 TA
1 TA
56339338 ATATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 12 0.39
17 9 0.29
18 6 0.19
19 2 0.06
20 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTTTAATTTATTT
Found at i:56354062 original size:59 final size:59
Alignment explanation
Indices: 56353985--56354103 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
56353975 CAAGAATAAC
56353985 TCAAACTCATCAATGGTATAATCTAAAATGTTTGATGATTTTACAAATTAGTCTTTGGG
1 TCAAACTCATCAATGGTATAATCTAAAATGTTTGATGATTTTACAAATTAGTCTTTGGG
56354044 TCAAACTCATCAATGGTATAATCTAAAATGTTTGATGATTTTACAAATTAGTCTTTGGG
1 TCAAACTCATCAATGGTATAATCTAAAATGTTTGATGATTTTACAAATTAGTCTTTGGG
56354103 T
1 T
56354104 TAGCTAAATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (59 bp):
TCAAACTCATCAATGGTATAATCTAAAATGTTTGATGATTTTACAAATTAGTCTTTGGG
Found at i:56362230 original size:43 final size:43
Alignment explanation
Indices: 56362166--56362249 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
56362156 GGTGCAGCCA
*
56362166 GGGTAAGAACAGGCTCGAAATTTTA-TCATGCTATCACTTAGTG
1 GGGTAAGAACAGGCTCAAAATTTTACT-ATGCTATCACTTAGTG
* *
56362209 GGGTAGGAACCGGCTCAAAATTTTACTATGCTATCACTTAG
1 GGGTAAGAACAGGCTCAAAATTTTACTATGCTATCACTTAG
56362250 GGCCCATCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (43 bp):
GGGTAAGAACAGGCTCAAAATTTTACTATGCTATCACTTAGTG
Found at i:56365715 original size:10 final size:10
Alignment explanation
Indices: 56365702--56365747 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
56365692 CTGTGACTAA
*
56365702 ATGTGATTGT
1 ATGTGATTAT
*
56365712 ATGTAATTAT
1 ATGTGATTAT
*
56365722 ATGTGCTTAT
1 ATGTGATTAT
56365732 ATGTGATTGAT
1 ATGTGATT-AT
56365743 ATGTG
1 ATGTG
56365748 TCGGAATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:56366546 original size:20 final size:21
Alignment explanation
Indices: 56366489--56366546 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
56366479 TTGATTTTCC
56366489 AGGCAGTATTGATACCATTTAA
1 AGGCAGTATTGATACCA-TTAA
* * *
56366511 AGGAAATATTGATACCA-TAG
1 AGGCAGTATTGATACCATTAA
*
56366531 AGGCAGTATCGATACC
1 AGGCAGTATTGATACC
56366547 TATGTAACAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 15 0.50
22 15 0.50
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (21 bp):
AGGCAGTATTGATACCATTAA
Found at i:56377972 original size:33 final size:33
Alignment explanation
Indices: 56377935--56377998 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
56377925 AATACATTGG
*
56377935 AAATCAGCATGCAGATGGTTTAAATACTATTCC
1 AAATCAGCATGCAGATGGTGTAAATACTATTCC
*
56377968 AAATCAGCATGCAGATGGTGTAAATAGTATT
1 AAATCAGCATGCAGATGGTGTAAATACTATT
56377999 TCAACTGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (33 bp):
AAATCAGCATGCAGATGGTGTAAATACTATTCC
Found at i:56388984 original size:17 final size:17
Alignment explanation
Indices: 56388962--56389002 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
56388952 ATCTCCGACA
* *
56388962 AGCTTCCAATCTAATTG
1 AGCTTCCAATCCAATCG
56388979 AGCTTCCAATCCAATCG
1 AGCTTCCAATCCAATCG
56388996 AGCTTCC
1 AGCTTCC
56389003 GATAATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (17 bp):
AGCTTCCAATCCAATCG
Found at i:56392646 original size:20 final size:19
Alignment explanation
Indices: 56392621--56392683 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
56392611 TTAGGGTTCA
56392621 AAGGTTAAAGGTTAAGGTTT
1 AAGGTT-AAGGTTAAGGTTT
56392641 AAGGTT-AGGATTAAGGGTTT
1 AAGGTTAAGG-TTAA-GGTTT
*
56392661 AAGGTTTAA-GTTAAGGGTT
1 AAGG-TTAAGGTTAAGGTTT
56392680 AAGG
1 AAGG
56392684 GTTTTGGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 3 0.08
19 12 0.32
20 19 0.50
21 3 0.08
22 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (19 bp):
AAGGTTAAGGTTAAGGTTT
Found at i:56392693 original size:27 final size:27
Alignment explanation
Indices: 56392632--56392687 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
56392622 AGGTTAAAGG
56392632 TTAAGGTTTAAGGTTAGGATTAAGGGT
1 TTAAGGTTTAAGGTTAGGATTAAGGGT
*
56392659 TTAAGGTTTAA-GTTAAGGGTTAAGGGT
1 TTAAGGTTTAAGGTT-AGGATTAAGGGT
56392686 TT
1 TT
56392688 TGGGTTGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (27 bp):
TTAAGGTTTAAGGTTAGGATTAAGGGT
Found at i:56392765 original size:14 final size:14
Alignment explanation
Indices: 56392739--56392780 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
56392729 GGTCAAGGTG
56392739 AAGGTTAAAGGCTTA
1 AAGGTT-AAGGCTTA
56392754 AAGGTTAAGGC-TA
1 AAGGTTAAGGCTTA
56392767 AA-GTTAATGGCTTA
1 AAGGTTAA-GGCTTA
56392781 GGGCTTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.20
13 7 0.28
14 7 0.28
15 6 0.24
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (14 bp):
AAGGTTAAGGCTTA
Found at i:56392925 original size:14 final size:14
Alignment explanation
Indices: 56392900--56392953 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
56392890 AGATTTCAAT
56392900 TTTTATGGTTTTGAG
1 TTTTA-GGTTTTGAG
*
56392915 TTTTAGGTTTTAAG
1 TTTTAGGTTTTGAG
* *
56392929 -TTTAGAGTTTAGTG
1 TTTTAG-GTTTTGAG
56392943 TTTTAGGTTTT
1 TTTTAGGTTTT
56392954 ATGGTTAGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 5 0.16
14 17 0.53
15 10 0.31
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (14 bp):
TTTTAGGTTTTGAG
Found at i:56392936 original size:21 final size:21
Alignment explanation
Indices: 56392907--56392952 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
56392897 AATTTTTATG
*
56392907 GTTTTGAGTTTTAG-GTTTTAA
1 GTTTAGAG-TTTAGTGTTTTAA
*
56392928 GTTTAGAGTTTAGTGTTTTAG
1 GTTTAGAGTTTAGTGTTTTAA
56392949 GTTT
1 GTTT
56392953 TATGGTTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (21 bp):
GTTTAGAGTTTAGTGTTTTAA
Found at i:56398932 original size:12 final size:11
Alignment explanation
Indices: 56398915--56398944 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
56398905 TGTGTTTGTA
56398915 AAAAAAAATAT
1 AAAAAAAATAT
56398926 GAAAAAAAATAT
1 -AAAAAAAATAT
56398938 AAAAAAA
1 AAAAAAA
56398945 CGTACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (11 bp):
AAAAAAAATAT
Found at i:56399154 original size:13 final size:14
Alignment explanation
Indices: 56399136--56399181 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
56399126 TAAATAAAAA
56399136 ATAATAATAATAGT
1 ATAATAATAATAGT
*
56399150 A-AATAATAATAGC
1 ATAATAATAATAGT
56399163 ATAAT-ATAATAGT
1 ATAATAATAATAGT
56399176 GATAAT
1 -ATAAT
56399182 GATATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAGT
Found at i:56400594 original size:44 final size:44
Alignment explanation
Indices: 56400553--56400663 Score: 152
Period size: 44 Copynumber: 2.5 Consensus size: 44
56400543 TCTGCTCCGT
* *
56400553 TGCAACCTCAGGGAGATAAGATCTGTGGT-TTTAATCCGCTCCAC
1 TGCAACTTCAGGGAGATAAGAT-TATGGTCTTTAATCCGCTCCAC
* * *
56400597 TGCAACTTCAGGGAGATAGGATTATTGTCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTATGGTCTTTAATCCGCTCCAC
*
56400641 TGCAACTTCAGAGAGATAAGATT
1 TGCAACTTCAGGGAGATAAGATT
56400664 CGCCATCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 4 0.07
44 55 0.93
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGATTATGGTCTTTAATCCGCTCCAC
Found at i:56400799 original size:44 final size:44
Alignment explanation
Indices: 56400741--56400904 Score: 256
Period size: 44 Copynumber: 3.7 Consensus size: 44
56400731 ACCAGTATGG
* * *
56400741 GAAGTCAAGATCTGCTATCTTTGATCTACTTCATGCCAATACAT
1 GAAGACAAGATCTGCCATCTTCGATCTACTTCATGCCAATACAT
56400785 GAAGACAAGATCTGCCATCTTCGATCTACTTCATGCCAATACAT
1 GAAGACAAGATCTGCCATCTTCGATCTACTTCATGCCAATACAT
56400829 GAAGACAAGATCTGCCATCTTCGATCTACTTCATGCCAATACAT
1 GAAGACAAGATCTGCCATCTTCGATCTACTTCATGCCAATACAT
* * ***
56400873 GAAGATAATATCTGTTTTCTTCGATCTACTTC
1 GAAGACAAGATCTGCCATCTTCGATCTACTTC
56400905 GCCACCAGTA
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 112 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.32
Consensus pattern (44 bp):
GAAGACAAGATCTGCCATCTTCGATCTACTTCATGCCAATACAT
Found at i:56400922 original size:133 final size:130
Alignment explanation
Indices: 56400741--56401780 Score: 956
Period size: 133 Copynumber: 7.9 Consensus size: 130
56400731 ACCAGTATGG
* ** **
56400741 GAAGTCAAGATCTGCTATCTTTGATCTACTTCATGCCAATACATGAAGACAAGATCTGCCATCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTT
* *
56400806 CGATCTACTTCATGCCAATACATGAAGACAAGATCTGCCATCTTCGATCTACTTCATGCCAATAC
66 CGATCTACTTC--GCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATAC
56400871 AT
129 AT
* * * * * * * *** * *
56400873 GAAGATAATATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGCTTCCT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTC-ACACCAATACATGAAGACAAGATCTGCTTTCT
* * * * * * ** * * *
56400938 TTGATCT-GTT-ACC--T--TTG-A-TCTACTTCATGC---CGTTCGATCTACTTCGCCACCAGT
65 TCGATCTACTTCGCCAATACATGAAGACAAGATC-TGCTATC-TTCGATCTACTTC-ACGCCAAT
* *
56400992 ATAG
127 ACAT
* * ** * *
56400996 GAAGACAAGATTTGCTATCTTTGATATACTTCATGCCAATATATGAAGACAAGATCTG-TCATCT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTGCT-TTCT
* * * * * *
56401060 TCGATCTACTTCATGCTAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACCAGT
65 TCGATCTACTTC--GCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAAT
* *
56401125 ATAG
127 ACAT
* **
56401129 GAAGACAAGATCTGCTACCTTTGATCTACTTCA-TGCAGATACATGAAGACAAGATCTGCTTTCT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCA-ATACATGAAGACAAGATCTGCTTTCT
*** *
56401193 TCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAAT
65 TCGATCTACTTCGCCA--A-TACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAAT
56401258 ACAT
127 ACAT
* *
56401262 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTT
** * * *
56401327 CGATCTACTTCGCCCCTAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCTAATG
66 CGATCTACTTCGCCAATA-CAT--GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATA
56401392 CAT
128 CAT
* * * * *
56401395 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAAGACATGAAGACAATATCTACTTTTTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTT
* * * *
56401460 CGATCTACTTCGCTACTAGTATGGGAAGACAAGATTTGCTATCTTCGATCTACTTCACGCCAATA
66 CGATCTACTTCGCCAATA-CAT--GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATA
56401525 CAT
128 CAT
* * *
56401528 GAAGACAAGATCTGCTATCTTTAATTTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTT
* * *
56401593 CGATCTACTTCGCCACTAGAATGGGAAGACAAGATCTGCTAT-TTCTGATCTACTTCATGCCAAT
66 CGATCTACTTCGCCAATA-CAT--GAAGACAAGATCTGCTATCTTC-GATCTACTTCACGCCAAT
*
56401657 ACAA
127 ACAT
* * * * * **
56401661 GAAGACAAGATCCGTTTTCTTTGATCTATTTCACGCCAATACATGAAGACAAGATCTGCTACCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTT
* * * * *
56401726 TGATCTACTTCATGCCGATACATGAAGACAAGATTTTCTTTCTTCGATCTACTTC
66 CGATCTACTTC--GCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC
56401781 GCCACTAGTA
Statistics
Matches: 756, Mismatches: 121, Indels: 62
0.81 0.13 0.07
Matches are distributed among these distances:
121 2 0.00
122 40 0.05
123 37 0.05
124 4 0.01
125 2 0.00
126 1 0.00
127 1 0.00
128 1 0.00
129 2 0.00
130 4 0.01
131 7 0.01
132 62 0.08
133 550 0.73
134 38 0.05
135 5 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (130 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTT
CGATCTACTTCGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:56401045 original size:44 final size:44
Alignment explanation
Indices: 56400996--56401780 Score: 837
Period size: 44 Copynumber: 17.7 Consensus size: 44
56400986 ACCAGTATAG
* * * * *
56400996 GAAGACAAGATTTGCTATCTTTGATATACTTCATGCCAATATAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
56401040 GAAGACAAGATCTG-TCATCTTCGATCTACTTCATGCTAATACAT
1 GAAGACAAGATCTGCT-ATCTTCGATCTACTTCACGCCAATACAT
* * * * * * *
56401084 GAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACCAGTATAG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
* * *
56401129 GAAGACAAGATCTGCTACCTTTGATCTACTTCATG-CAGATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCA-ATACAT
* * * * ***
56401173 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
*
56401218 GAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
56401262 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * ***
56401306 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCCCTAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC-AATACAT
* *
56401351 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCTAATGCAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
56401395 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAAGACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * * * *
56401439 GAAGACAATATCTACTTTTTTCGATCTACTT--CGCTACTAGTAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATA-CAT
*
56401482 GGGAAGACAAGATTTGCTATCTTCGATCTACTTCACGCCAATACAT
1 --GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
** *
56401528 GAAGACAAGATCTGCTATCTTTAATTTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * *
56401572 GAAGACAAGATCTGCTTTCTTCGATCTACTT--CGCCACTAGAAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATA-CAT
* *
56401615 GGGAAGACAAGATCTGCTAT-TTCTGATCTACTTCATGCCAATACAA
1 --GAAGACAAGATCTGCTATCTTC-GATCTACTTCACGCCAATACAT
* * * * *
56401661 GAAGACAAGATCCGTTTTCTTTGATCTATTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * *
56401705 GAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * *
56401749 GAAGACAAGATTTTCTTTCTTCGATCTACTTC
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC
56401781 GCCACTAGTA
Statistics
Matches: 610, Mismatches: 112, Indels: 38
0.80 0.15 0.05
Matches are distributed among these distances:
42 12 0.02
43 7 0.01
44 417 0.68
45 157 0.26
46 5 0.01
47 12 0.02
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:56401133 original size:89 final size:89
Alignment explanation
Indices: 56400996--56401780 Score: 755
Period size: 89 Copynumber: 8.9 Consensus size: 89
56400986 ACCAGTATAG
* * * *** *
56400996 GAAGACAAGATTTGCTATCTTTGATATACTTC-ATGCCAATATATGAAGACAAGATCTG-TCATC
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATACATGAAGACAAGATCTGCT-ATC
* *
56401059 TTCGATCTACTTCATGCTAATACAT
65 TTCGATCTACTTCACGCCAATACAT
* * * * * *
56401084 GAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTACCT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATACATGAAGACAAGATCTGCTATCT
* *
56401149 TTGATCTACTTCATG-CAGATACAT
66 TCGATCTACTTCACGCCA-ATACAT
* * ***
56401173 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATACATGAAGACAAGATCTGCTATCT
*
56401238 TCGATCTACTTCACACCAATACAT
66 TCGATCTACTTCACGCCAATACAT
* * *
56401262 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTTCT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATACATGAAGACAAGATCTGCTATCT
* * * ***
56401326 TCGATCTACTTCGCCCCTAGTATGG
66 TCGATCTACTTCACGCC-AATACAT
* * * *
56401351 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCTAATGCATGAAGACAAGATCTGCTATCT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATACATGAAGACAAGATCTGCTATCT
* *
56401415 TTGATCTACTTCACGCCAAGACAT
66 TCGATCTACTTCACGCCAATACAT
* * * * * * * *** *
56401439 GAAGACAATATCTACTTTTTTCGATCTACTTCGCTACTAGTATGGGAAGACAAGATTTGCTATCT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATACATGAAGACAAGATCTGCTATCT
56401504 TCGATCTACTTCACGCCAATACAT
66 TCGATCTACTTCACGCCAATACAT
** * * * *
56401528 GAAGACAAGATCTGCTATCTTTAATTTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTTCT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATACATGAAGACAAGATCTGCTATCT
* *
56401592 TCGATCTACTT--CGCCACTAGAAT
66 TCGATCTACTTCACGCCAATA-CAT
*** * * * *
56401615 GGGAAGACAAGATCTGCTAT-TTCTGATCTACTTC-ATGCCAATACAAGAAGACAAGATCCGTTT
1 --GAAGACAAGATCTGCTATCTTC-GATCTACTTCGCCACCAATACATGAAGACAAGATCTGCTA
* *
56401678 TCTTTGATCTATTTCACGCCAATACAT
63 TCTTCGATCTACTTCACGCCAATACAT
* * *** * * * *
56401705 GAAGACAAGATCTGCTACCTTTGATCTACTTC-ATGCCGATACATGAAGACAAGATTTTCTTTCT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATACATGAAGACAAGATCTGCTATCT
56401769 TCGATCTACTTC
66 TCGATCTACTTC
56401781 GCCACTAGTA
Statistics
Matches: 585, Mismatches: 99, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
86 7 0.01
87 2 0.00
88 196 0.34
89 368 0.63
90 5 0.01
91 7 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (89 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATACATGAAGACAAGATCTGCTATCT
TCGATCTACTTCACGCCAATACAT
Found at i:56401800 original size:266 final size:264
Alignment explanation
Indices: 56400713--56401805 Score: 1065
Period size: 266 Copynumber: 4.2 Consensus size: 264
56400703 AAGACTTGTG
* * * *
56400713 TCTTCGATCTACTTCGCCACCAGTATGGGAAGTCAAGATCTGCTATCTTTGATCTACTTCATGCC
1 TCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTTGATATACTTCACGCC
** * *
56400778 AATACATGAAGACAAGATCTGCCATCTTCGATCTACTTCATGCCAATA-CAT--GAAGACAAGAT
66 AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC--GCCACTAGAATGGGAAGACAAGAT
* * * * * * *
56400840 CTGCCATCTTCGATCTACTTCATGCCAATACATGAAGATAATATCTGTTTTCTTCGATCTACTTC
129 CTGCTATCTTCGATCTACTTCA-GCCAATACAAGAAGACAAGATCTGCTATCTTTGATCTACTTC
* * * *** * * * *
56400905 GCCACCAGTATGGGAAGACAATATCTGCTTCCTTTGATCT-GTT--AC-CT--T-T-G-A-TC--
193 -ACGCCAATACATGAAGACAAGATCTGCTT-CTTTGATCTACTTCGCCACTAGTATGGAAGACAA
* *
56400958 TACTT-C-A
256 GATTTGCTA
* *
56400965 TGCCGTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATTTGCTATCTTTGATATACTTCAT
1 T--C-TTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTTGATATACTTCAC
* * * * *
56401030 GCCAATATATGAAGACAAGATCTG-TCATCTTCGATCTACTTCATGCTAATA-CAT--GAAGACA
63 GCCAATACATGAAGACAAGATCTGCT-TTCTTCGATCTACTTC--GCCACTAGAATGGGAAGACA
* * * * *
56401091 AGATCTACTTTCTTCGATCTACTTC-GCCACCAGTATAGGAAGACAAGATCTGCTACCTTTGATC
125 AGATCTGCTATCTTCGATCTACTTCAGCCA--A-TACAAGAAGACAAGATCTGCTATCTTTGATC
* * *
56401155 TACTTCATG-CAGATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGG
187 TACTTCACGCCA-ATACATGAAGACAAGATCTGC-TTCTTTGATCTACTTCGCCACTAGTAT-GG
*
56401219 AAGACAAGATCTGCTA
249 AAGACAAGATTTGCTA
* * * * * *
56401235 TCTTCGATCTACTTC-ACACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTTGATATACTTCACGCC
* *
56401299 AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCCCTAGTATGGGAAGACAAGATCT
66 AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACTAGAATGGGAAGACAAGATCT
* * *
56401364 GCTATCTTCGATCTACTTCACGCTAATGCATGAAGACAAGATCTGCTATCTTTGATCTACTTCAC
131 GCTATCTTCGATCTACTTCA-GCCAATACAAGAAGACAAGATCTGCTATCTTTGATCTACTTCAC
* * * * *
56401429 GCCAAGACATGAAGACAATATCTACTTTTTTCGATCTACTTCGCTACTAGTATGGGAAGACAAGA
195 GCCAATACATGAAGACAAGATCTGCTTCTTT-GATCTACTTCGCCACTAGTAT-GGAAGACAAGA
56401494 TTTGCTA
258 TTTGCTA
* * * * * * *
56401501 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTATCTTTAATTTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTTGATATACTTCACGCC
56401565 AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACTAGAATGGGAAGACAAGATCT
66 AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACTAGAATGGGAAGACAAGATCT
* * * *
56401630 GCTAT-TTCTGATCTACTTCATGCCAATACAAGAAGACAAGATCCGTTTTCTTTGATCTATTTCA
131 GCTATCTTC-GATCTACTTCA-GCCAATACAAGAAGACAAGATCTGCTATCTTTGATCTACTTCA
* *
56401694 CGCCAATACATGAAGACAAGATCTGCTACCTTTGATCTACTTCATGCCGA-TA-CAT-GAAGACA
194 CGCCAATACATGAAGACAAGATCTGCT-TCTTTGATCTACTTC--GCC-ACTAGTATGGAAGACA
* *
56401756 AGATTTTCTT
255 AGATTTGCTA
* *
56401766 TCTTCGATCTACTTCGCCACTAGTATGGGAAGACAAGATC
1 TCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATC
56401806 AAGAATGCCA
Statistics
Matches: 709, Mismatches: 94, Indels: 62
0.82 0.11 0.07
Matches are distributed among these distances:
252 1 0.00
253 4 0.01
254 3 0.00
255 160 0.23
256 33 0.05
258 1 0.00
259 1 0.00
261 1 0.00
262 1 0.00
264 5 0.01
265 40 0.06
266 393 0.55
267 52 0.07
268 7 0.01
269 5 0.01
270 2 0.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (264 bp):
TCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTTGATATACTTCACGCC
AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACTAGAATGGGAAGACAAGATCT
GCTATCTTCGATCTACTTCAGCCAATACAAGAAGACAAGATCTGCTATCTTTGATCTACTTCACG
CCAATACATGAAGACAAGATCTGCTTCTTTGATCTACTTCGCCACTAGTATGGAAGACAAGATTT
GCTA
Found at i:56403926 original size:4 final size:4
Alignment explanation
Indices: 56403919--56403945 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
56403909 TATAAATAAC
56403919 ATGA ATGA ATGA ATGA ATGA ATGA ATG
1 ATGA ATGA ATGA ATGA ATGA ATGA ATG
56403946 GTTTGGCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
ATGA
Found at i:56403980 original size:18 final size:18
Alignment explanation
Indices: 56403954--56403996 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
56403944 TGGTTTGGCA
*
56403954 GAAAAAATCCTAAAGAAT
1 GAAAGAATCCTAAAGAAT
*
56403972 GAAAGAATCGTAAAGAAT
1 GAAAGAATCCTAAAGAAT
56403990 GAAAGAA
1 GAAAGAA
56403997 CATTTGCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.60, C:0.07, G:0.19, T:0.14
Consensus pattern (18 bp):
GAAAGAATCCTAAAGAAT
Found at i:56411139 original size:17 final size:17
Alignment explanation
Indices: 56411117--56411153 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
56411107 TACTTCACTT
*
56411117 GAAAAAAGAAACGAAAA
1 GAAAAAAGAAAAGAAAA
56411134 GAAAAAAGAAAAGAAAA
1 GAAAAAAGAAAAGAAAA
56411151 GAA
1 GAA
56411154 TAGCAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAAAGAAAA
Found at i:56411145 original size:22 final size:23
Alignment explanation
Indices: 56411120--56411169 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
56411110 TTCACTTGAA
*
56411120 AAAAGAAACGAAAAG-AAAAAAG
1 AAAAGAAAAGAAAAGCAAAAAAG
* *
56411142 AAAAGAAAAGAATAGCAAAAAGG
1 AAAAGAAAAGAAAAGCAAAAAAG
56411165 AAAAG
1 AAAAG
56411170 GAGAGGCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.74, C:0.04, G:0.20, T:0.02
Consensus pattern (23 bp):
AAAAGAAAAGAAAAGCAAAAAAG
Found at i:56412557 original size:50 final size:50
Alignment explanation
Indices: 56412503--56413016 Score: 285
Period size: 50 Copynumber: 10.3 Consensus size: 50
56412493 CGCAACAGAA
* * *
56412503 AATCTTACTTTCCTGGCGATGTAGTGGATCAGATTGAAGCTACAACGGCG
1 AATCTTACTTCCCTGGCGATGCAGTGGAACAGATTGAAGCTACAACGGCG
* * * ** * * *
56412553 AATCTT-GTTCCCTGAC-ATTGCAATTAAAGAGATTGAAGCCACAACGGCA
1 AATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTGAAGCTACAACGGCG
* * * ** * * *
56412602 AATCTCACTTTCCTGG-GAGTACAGTGGAGTAGATTAAAGCTACGACGGCA
1 AATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTGAAGCTACAACGGCG
* * * * * * **
56412652 AATCTTGCTTCCCTAG-TATTGCAAT-TAAAAGGATTGAAGCCGCAACGGCG
1 AATCTTACTTCCCTGGCGA-TGCAGTGGAACA-GATTGAAGCTACAACGGCG
* * * * *
56412702 AATCTTTCTTTCCTGGCGATGAAGTGGATCAGATTGAAGCTACAACGACG
1 AATCTTACTTCCCTGGCGATGCAGTGGAACAGATTGAAGCTACAACGGCG
** * * ** * *
56412752 AAT-TTTGTTCCCTGAC-ATTGCAATTAAAGAGATTGAAGCCACAACGGCG
1 AATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTGAAGCTACAACGGCG
* * * * *
56412801 AATCTCACTTCCCTGGC-AGTACAGTGGAGCAGATTAAAGCTACAACGGCA
1 AATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTGAAGCTACAACGGCG
* * * ** * **
56412851 AATCTTGCTTCCCTGG-TACTGCAATTAAAAAGATTGAAGCCGCAACGGCG
1 AATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTGAAGCTACAACGGCG
* * * *
56412901 AATCTTACTTTCCTGGCGATGCAGTGGATCAAATTGAAGCTACAACGGTG
1 AATCTTACTTCCCTGGCGATGCAGTGGAACAGATTGAAGCTACAACGGCG
* * * * ** * *
56412951 AATCTT-GTTCCCCGAC-ATTGCAATTAAAGAGATTGAAGCCACAACGGCG
1 AATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTGAAGCTACAACGGCG
*
56413000 AATCTCACTTCCCTGGC
1 AATCTTACTTCCCTGGC
56413017 AGATTAAAGC
Statistics
Matches: 333, Mismatches: 119, Indels: 24
0.70 0.25 0.05
Matches are distributed among these distances:
48 3 0.01
49 107 0.32
50 219 0.66
51 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (50 bp):
AATCTTACTTCCCTGGCGATGCAGTGGAACAGATTGAAGCTACAACGGCG
Found at i:56412762 original size:199 final size:198
Alignment explanation
Indices: 56412410--56413419 Score: 1406
Period size: 199 Copynumber: 5.1 Consensus size: 198
56412400 ATGAAGTTAC
* * * * * *
56412410 CTTTCCTAGCAGTATAGTGGAGCAGATTAAAGCTACGATGGTGAATCTTGCTTCCTTGGTATTGT
1 CTTTCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGGTATTGC
* ** *
56412475 AATTAAATAGATTGAAGCCGCAACAGAAAATCTTACTTTCCTGGCGATGTAGTGGATCAGATTGA
66 AATTAAA-AGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
* *
56412540 AGCTACAACGGCGAATCTTGTTCCCTGACATTGCAATTAAAGAGATTGAAGCCACAACGGCAAAT
130 AGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAAT
56412605 CTCA
195 CTCA
* * * *
56412609 CTTTCCTGGGAGTACAGTGGAGTAGATTAAAGCTACGACGGCAAATCTTGCTTCCCTAGTATTGC
1 CTTTCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGGTATTGC
* *
56412674 AATTAAAAGGATTGAAGCCGCAACGGCGAATCTTTCTTTCCTGGCGATGAAGTGGATCAGATTGA
66 AATTAAAA-GATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
* * *
56412739 AGCTACAACGACGAATTTTGTTCCCTGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAAT
130 AGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAAT
56412804 CTCA
195 CTCA
* * * *
56412808 CTTCCCTGGCAGTACAGTGGAGCAGATTAAAGCTACAACGGCAAATCTTGCTTCCCTGGTACTGC
1 CTTTCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGGTATTGC
*
56412873 AATTAAAAAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAAATTGA
66 AATT-AAAAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
*
56412938 AGCTACAACGGTGAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAAT
130 AGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAAT
56413003 CTCA
195 CTCA
*
56413007 C-TT-C---C----C--T-G-GCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGGTATTGT
1 CTTTCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGGTATTGC
* *
56413059 AATTAAAAAGATTGAAGCCGCAACGGCAAATCTTACTTTCCTGGCAATGCAGTGGATCAGATTGA
66 AATT-AAAAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
* * *
56413124 AGCTACAACGGCGAATCTTATTCCCCAACATTGCAATTAAAGAGATTGAAGCCGCAACGGCGAAT
130 AGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAAT
56413189 CTCA
195 CTCA
* * **
56413193 CTTCCCTGGTAGTACAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTAATATTGC
1 CTTTCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGGTATTGC
* * * *
56413258 AATTTAAAAGATTGAAGCCGCAACGGTGAATCTTAC-TTCCTTGGTGGTGCAGTCGGA-CTGATT
66 AA-TTAAAAGATTGAAGCCGCAACGGCGAATCTTACTTTCC-TGGCGATGCAGT-GGATCAGATT
* * *
56413321 GAAGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAAAGATTAAAGCCACAACGGTGA
128 GAAGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGA
56413386 ATCTCA
193 ATCTCA
*
56413392 CTTCTCCCTAAGCAGT--AGTGGAGCAGAT
1 CTT-T-CCT-GGCAGTACAGTGGAGCAGAT
56413420 CACATCCAGT
Statistics
Matches: 727, Mismatches: 63, Indels: 41
0.87 0.08 0.05
Matches are distributed among these distances:
186 168 0.23
187 2 0.00
188 2 0.00
190 1 0.00
194 1 0.00
195 1 0.00
197 2 0.00
198 7 0.01
199 515 0.71
200 21 0.03
201 3 0.00
202 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (198 bp):
CTTTCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGGTATTGC
AATTAAAAGATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGAA
GCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAATC
TCA
Found at i:56413035 original size:37 final size:37
Alignment explanation
Indices: 56412980--56413052 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
56412970 GCAATTAAAG
*
56412980 AGATTGAAGCCACAACGGCGAATCTCACTTCCCTGGC
1 AGATTAAAGCCACAACGGCGAATCTCACTTCCCTGGC
* * **
56413017 AGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGG
1 AGATTAAAGCCACAACGGCGAATCTCACTTCCCTGG
56413053 TATTGTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (37 bp):
AGATTAAAGCCACAACGGCGAATCTCACTTCCCTGGC
Found at i:56413071 original size:87 final size:86
Alignment explanation
Indices: 56412937--56413104 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 86
56412927 GATCAAATTG
* * *
56412937 AAGCTACAACGGTGAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGCGAA
1 AAGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGGCAAA
56413002 TCTCACTTCCCTGGCAGATTA
66 TCTCACTTCCCTGGCAGATTA
* * ** * *
56413023 AAGCTACGACGGCGAATCTTGCTTCCCTGGTATTGTAATTAAAAAGATTGAAGCCGCAACGGCAA
1 AAGCTACAACGGCGAATCTTG-TTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGGCAA
* *
56413088 ATCTTACTTTCCTGGCA
65 ATCTCACTTCCCTGGCA
56413105 ATGCAGTGGA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
86 19 0.27
87 51 0.73
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (86 bp):
AAGCTACAACGGCGAATCTTGTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGGCAAA
TCTCACTTCCCTGGCAGATTA
Found at i:56413092 original size:50 final size:50
Alignment explanation
Indices: 56413031--56413395 Score: 230
Period size: 50 Copynumber: 7.3 Consensus size: 50
56413021 TAAAGCTACG
* *
56413031 ACGGCGAATCTTGCTTCCCTGGTATTGTAATTAAAAAGATTGAAGCCGCA
1 ACGGCGAATCTTACTTCCCTGGTATTGCAATTAAAAAGATTGAAGCCGCA
* * * * * ** ** **
56413081 ACGGCAAATCTTACTTTCCTGGCAATGCAGTGGATCAGATTGAAGCTACA
1 ACGGCGAATCTTACTTCCCTGGTATTGCAATTAAAAAGATTGAAGCCGCA
**** *
56413131 ACGGCGAATCTTA-TTCCCCAACATTGCAATTAAAGAGATTGAAGCCGCA
1 ACGGCGAATCTTACTTCCCTGGTATTGCAATTAAAAAGATTGAAGCCGCA
* * * * ** ** * ** *
56413180 ACGGCGAATCTCACTTCCCTGGTAGTACAGTGGAGCAGATTAAAGCTACG
1 ACGGCGAATCTTACTTCCCTGGTATTGCAATTAAAAAGATTGAAGCCGCA
* ** *
56413230 ACGGCGAATCTTGCTTCCCTAATATTGCAATTTAAAAGATTGAAGCCGCA
1 ACGGCGAATCTTACTTCCCTGGTATTGCAATTAAAAAGATTGAAGCCGCA
* * ** * *** ** **
56413280 ACGGTGAATCTTACTTCCTTGGTGGTGCAGTCGGACTGATTGAAGCTACA
1 ACGGCGAATCTTACTTCCCTGGTATTGCAATTAAAAAGATTGAAGCCGCA
* * ** * *
56413330 ACGGCGAATCTT-GTTCCCCGACATTGCAATTAAAAAGATTAAAGCCACA
1 ACGGCGAATCTTACTTCCCTGGTATTGCAATTAAAAAGATTGAAGCCGCA
* *
56413379 ACGGTGAATCTCACTTC
1 ACGGCGAATCTTACTTC
56413396 TCCCTAAGCA
Statistics
Matches: 222, Mismatches: 91, Indels: 4
0.70 0.29 0.01
Matches are distributed among these distances:
49 68 0.31
50 154 0.69
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (50 bp):
ACGGCGAATCTTACTTCCCTGGTATTGCAATTAAAAAGATTGAAGCCGCA
Done.