Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_pilon, whole genome shotgun sequence
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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 23
Found at i:303157 original size:33 final size:33
Alignment explanation
Indices: 303115--303181 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
303105 TTTGGTCACC
303115 AAACCAAAGCATGGGAGCATGCAAAGAGAGAGA
1 AAACCAAAGCATGGGAGCATGCAAAGAGAGAGA
303148 AAACCAAAGCATGGGAGCATGCAAAGAGAGAGA
1 AAACCAAAGCATGGGAGCATGCAAAGAGAGAGA
303181 A
1 A
303182 TGTTTTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.15, G:0.30, T:0.06
Consensus pattern (33 bp):
AAACCAAAGCATGGGAGCATGCAAAGAGAGAGA
Found at i:306001 original size:16 final size:17
Alignment explanation
Indices: 305973--306004 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
305963 CTCAAATCCT
305973 CTCAAACCATCTCAAAG
1 CTCAAACCATCTCAAAG
305990 CTCAAA-CATCTCAAA
1 CTCAAACCATCTCAAA
306005 CCCGTCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.44, C:0.34, G:0.03, T:0.19
Consensus pattern (17 bp):
CTCAAACCATCTCAAAG
Found at i:307042 original size:20 final size:22
Alignment explanation
Indices: 307006--307052 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
306996 TACAATATTG
* *
307006 ATTTCGTATATTAATAA-TTTT
1 ATTTAGTATATTAATAAGATTT
307027 ATTTAGTATA-TAATAAGATTT
1 ATTTAGTATATTAATAAGATTT
307048 ATTTA
1 ATTTA
307053 ATTGAATAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (22 bp):
ATTTAGTATATTAATAAGATTT
Found at i:307984 original size:9 final size:9
Alignment explanation
Indices: 307966--307997 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
307956 GATGTCGGTC
*
307966 TTTTCTCAG
1 TTTTCCCAG
307975 TTTTCCCAG
1 TTTTCCCAG
307984 TTTTCCCAG
1 TTTTCCCAG
307993 TTTTC
1 TTTTC
307998 TATGAGCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.09, C:0.28, G:0.09, T:0.53
Consensus pattern (9 bp):
TTTTCCCAG
Found at i:308349 original size:38 final size:38
Alignment explanation
Indices: 308273--308354 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 38
308263 ATGACTTAAT
* * *
308273 TTATTTTGTTTATTACTTAATTCAAGTGAACAATTTTA
1 TTATTTTGATTATTACTTAATTCAAGCGAACAAGTTTA
* ***
308311 TTATTTTGATTATTACTTAATTGAAGCGAATGGGTTTA
1 TTATTTTGATTATTACTTAATTCAAGCGAACAAGTTTA
308349 TTATTT
1 TTATTT
308355 AGTGAATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.52
Consensus pattern (38 bp):
TTATTTTGATTATTACTTAATTCAAGCGAACAAGTTTA
Found at i:309250 original size:16 final size:17
Alignment explanation
Indices: 309231--309263 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
309221 TTTTATTAAA
309231 TATAAATA-ATATTTTT
1 TATAAATATATATTTTT
309247 TATAAATATATATTTTT
1 TATAAATATATATTTTT
309264 AGTTCGACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATAAATATATATTTTT
Found at i:315348 original size:12 final size:14
Alignment explanation
Indices: 315331--315369 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
315321 TTGTAGTATG
315331 AAGAG-TCTAG-GC
1 AAGAGTTCTAGAGC
315343 AAGAGTTCTAGAAGC
1 AAGAGTTCTAG-AGC
315358 AAGAGTTCTAGA
1 AAGAGTTCTAGA
315370 ATCATCTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 5 0.21
14 1 0.04
15 13 0.54
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (14 bp):
AAGAGTTCTAGAGC
Found at i:315361 original size:15 final size:15
Alignment explanation
Indices: 315341--315370 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
315331 AAGAGTCTAG
315341 GCAAGAGTTCTAGAA
1 GCAAGAGTTCTAGAA
315356 GCAAGAGTTCTAGAA
1 GCAAGAGTTCTAGAA
315371 TCATCTGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (15 bp):
GCAAGAGTTCTAGAA
Found at i:324803 original size:27 final size:29
Alignment explanation
Indices: 324762--324818 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
324752 AATTAGTATT
324762 TTATTTATTTATTTATTCA-T-ATATTTA
1 TTATTTATTTATTTATTCACTAATATTTA
324789 TTATTTATATT-TTTATTCACTAATATTTA
1 TTATTTAT-TTATTTATTCACTAATATTTA
324818 T
1 T
324819 ATGAAATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 16 0.59
28 3 0.11
29 8 0.30
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATTTATTTATTTATTCACTAATATTTA
Found at i:327062 original size:8 final size:7
Alignment explanation
Indices: 327038--327078 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
327028 TTTCCATATA
327038 TGCATTT
1 TGCATTT
327045 T-CATTT
1 TGCATTT
327051 TGCATCTT
1 TGCAT-TT
327059 TGCATTT
1 TGCATTT
327066 T-CATTTT
1 TGCA-TTT
327073 TGCATT
1 TGCATT
327079 CATACTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 8 0.27
7 13 0.43
8 9 0.30
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:327139 original size:22 final size:22
Alignment explanation
Indices: 327108--327150 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
327098 TTGAATTGCA
327108 CATTTTGCATTCTTAT-TTTTC
1 CATTTTGCATTCTTATATTTTC
*
327129 CATTTATGCATTTTTATATTTT
1 CATTT-TGCATTCTTATATTTT
327151 TTATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.63
Consensus pattern (22 bp):
CATTTTGCATTCTTATATTTTC
Found at i:334323 original size:22 final size:22
Alignment explanation
Indices: 334294--334348 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
334284 ATCTACACTC
*
334294 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
* *
334316 TTTAAAGATGACATATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
334338 TTCAAAGATGA
1 TTCAAAGATGA
334349 AAACTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:334947 original size:113 final size:113
Alignment explanation
Indices: 334749--335419 Score: 1039
Period size: 113 Copynumber: 6.0 Consensus size: 113
334739 TAGCAAAGAT
*
334749 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATTAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
334814 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
334862 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
334927 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
334975 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
335040 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
335088 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
335153 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
** * * * * *
335201 TTGAATTCATCAT-TCGATGGATTAGCATTTCCAG-AAGAGTTCATAATGAGAAGAACACATCTG
1 TCAAATCCATCATCT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * *
335264 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACATTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
** * * * ****
335313 TTGAATTCATCAT-TCGATGGATCAGCATTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATCT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
*
335377 AAG-AGG-AGAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTT
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTT
335420 GCATGACTCT
Statistics
Matches: 533, Mismatches: 23, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
110 30 0.06
111 5 0.01
112 109 0.20
113 389 0.73
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:336718 original size:4 final size:4
Alignment explanation
Indices: 336709--336757 Score: 57
Period size: 4 Copynumber: 12.5 Consensus size: 4
336699 AAATTAGTAT
* *
336709 TTTA TTTA TTTA TTTA TTTA TTCA TATA TTTA -TTA TTTA TATT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
336756 TT
1 TT
336758 CACTAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 5 0.13
4 31 0.82
5 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:339784 original size:13 final size:14
Alignment explanation
Indices: 339755--339787 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
339745 AAAAATGCGA
*
339755 GAAAAAAAGAGAGG
1 GAAAAAAAGAGAAG
339769 GAAAAAAAGA-AAG
1 GAAAAAAAGAGAAG
339782 GAAAAA
1 GAAAAA
339788 GACAAGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
GAAAAAAAGAGAAG
Found at i:350711 original size:24 final size:24
Alignment explanation
Indices: 350679--350737 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
350669 ATAGCCATCA
350679 AATTCCTAAAAAAAAGCTAAAGAT
1 AATTCCTAAAAAAAAGCTAAAGAT
*
350703 AATTCCTAAAAACAAGCTAAAGAT
1 AATTCCTAAAAAAAAGCTAAAGAT
350727 AATTCCTAAAA
1 AATTCCTAAAA
350738 TAATATCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (24 bp):
AATTCCTAAAAAAAAGCTAAAGAT
Found at i:350829 original size:85 final size:85
Alignment explanation
Indices: 350733--350916 Score: 234
Period size: 85 Copynumber: 2.2 Consensus size: 85
350723 AGATAATTCC
* *
350733 TAAAATAATATCTTTAATCCTAATT-AATACACTTAA-AACTATTTAAAATAAAATACCTAAAAC
1 TAAAATAATATCCTAAATCCTAATTGAA-ACAC-TAACAACTATTTAAAATAAAATACCTAAAAC
350796 AAAGATAAAATAAAATACTATT
64 AAAGATAAAATAAAATACTATT
* * * *
350818 TAAAATAATATCCTAAATCCTAATTGAAATACTAACATCTATTTAAACTAAAATACTTAAAACAA
1 TAAAATAATATCCTAAATCCTAATTGAAACACTAACAACTATTTAAAATAAAATACCTAAAACAA
* *
350883 AGATAAAAT---ATAATGTT
66 AGATAAAATAAAATACTATT
*
350900 TAAAATATTATCCTAAA
1 TAAAATAATATCCTAAA
350917 ACTTGAGTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
82 22 0.25
84 3 0.03
85 61 0.69
86 2 0.02
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (85 bp):
TAAAATAATATCCTAAATCCTAATTGAAACACTAACAACTATTTAAAATAAAATACCTAAAACAA
AGATAAAATAAAATACTATT
Found at i:352977 original size:35 final size:34
Alignment explanation
Indices: 352913--352978 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
352903 GAGAGCTTTA
*
352913 ATATTTTTTTAATAGATTCTATTTTTCAAAATAT
1 ATATTTTTTAAATAGATTCTATTTTTCAAAATAT
352947 ATATTTTTCTAAATAGGA-TCT-TTTTGTCAAAA
1 ATATTTTT-TAAATA-GATTCTATTTT-TCAAAA
352979 ACAATTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
34 12 0.43
35 14 0.50
36 2 0.07
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (34 bp):
ATATTTTTTAAATAGATTCTATTTTTCAAAATAT
Found at i:353144 original size:20 final size:20
Alignment explanation
Indices: 353119--353168 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
353109 TTTGAGTTAA
*
353119 TTAAAATATGTTT-AAGGTGT
1 TTAAAATATGTTTAAAGCT-T
*
353139 TTAAAATGTGTTTAAAGCTT
1 TTAAAATATGTTTAAAGCTT
353159 TTAAAATATG
1 TTAAAATATG
353169 AAAAATACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.44
Consensus pattern (20 bp):
TTAAAATATGTTTAAAGCTT
Found at i:354572 original size:116 final size:116
Alignment explanation
Indices: 354359--354572 Score: 252
Period size: 116 Copynumber: 1.8 Consensus size: 116
354349 AGAAAGAAAG
* * * *
354359 AAGCGTCCAAGGGAGAAGAAGTTCATATAGGAGAGTTTGTTTAACCTCAATGCGACATTTATGAG
1 AAGCGTCCAAGGGAGAAGAAATTCATATAGGAGAGCTTGTTCAACCTCAATGAGACATTTATGAG
* * * * *
354424 AGAATAGAGAGCTTACATAGGATAGCTTATCTACTCATTATGGAGAGGAGA
66 AGAACAAAGAGCTTACATAAGAGAGCTCATCTACTCATTATGGAGAGGAGA
* * * * * *
354475 AAGCTTCCAAGGGGGAAGAAATTCATATATGAGAGCTTGTTCGACCTCAAATTAG-CCTTTATGA
1 AAGCGTCCAAGGGAGAAGAAATTCATATAGGAGAGCTTGTTCAACCTC-AATGAGACATTTATGA
*
354539 GAGAACAAAGAG-TTCATATAAGAGAGCTCATCTA
65 GAGAACAAAGAGCTT-ACATAAGAGAGCTCATCTA
354573 ATAATTTCCA
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
115 2 0.03
116 74 0.93
117 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (116 bp):
AAGCGTCCAAGGGAGAAGAAATTCATATAGGAGAGCTTGTTCAACCTCAATGAGACATTTATGAG
AGAACAAAGAGCTTACATAAGAGAGCTCATCTACTCATTATGGAGAGGAGA
Found at i:354831 original size:8 final size:8
Alignment explanation
Indices: 354811--354856 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
354801 GAAAATAGAG
354811 AAAAAAAT
1 AAAAAAAT
*
354819 -GAAAAAT
1 AAAAAAAT
354826 AAAAAAAT
1 AAAAAAAT
*
354834 TAAAAAAT
1 AAAAAAAT
354842 AAAAAAAAT
1 -AAAAAAAT
354851 AAAAAA
1 AAAAAA
354857 GAAATAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 6 0.19
8 19 0.59
9 7 0.22
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:354856 original size:16 final size:16
Alignment explanation
Indices: 354811--354856 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
354801 GAAAATAGAG
*
354811 AAAAAAATGAAAAATA
1 AAAAAAATAAAAAATA
*
354827 AAAAAATTAAAAAATA
1 AAAAAAATAAAAAATA
354843 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
354857 GAAATAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.13
Consensus pattern (16 bp):
AAAAAAATAAAAAATA
Found at i:354865 original size:15 final size:15
Alignment explanation
Indices: 354809--354865 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
354799 TAGAAAATAG
*
354809 AGAAAAAAATGAAAA
1 AGAAAAAAATAAAAA
*
354824 ATAAAAAAATTAAAAA
1 AGAAAAAAA-TAAAAA
*
354840 ATAAAAAAAATAAAAA
1 A-GAAAAAAATAAAAA
*
354856 AGAAATAAAT
1 AGAAAAAAAT
354866 CTTTAGATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 15 0.43
16 13 0.37
17 7 0.20
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (15 bp):
AGAAAAAAATAAAAA
Found at i:358135 original size:3 final size:3
Alignment explanation
Indices: 358083--358125 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
358073 TTTTATTTTT
* * *
358083 TTA TTA TTA TTAA TAA TCA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
358126 ACTTTATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:359602 original size:17 final size:17
Alignment explanation
Indices: 359573--359606 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
359563 TATGGTTTTA
359573 TTCGTATTATTATATTT
1 TTCGTATTATTATATTT
359590 TTCGTCATT-TTATATTT
1 TTCGT-ATTATTATATTT
359607 CTTTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (17 bp):
TTCGTATTATTATATTT
Found at i:360440 original size:24 final size:24
Alignment explanation
Indices: 360413--360477 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
360403 AAGTTTTATA
360413 TATACTTATTATTTTCA-TAATATT
1 TATA-TTATTATTTTCATTAATATT
*
360437 TATATATATTATTTTTTATTAATATT
1 TATAT-TATTA-TTTTCATTAATATT
*
360463 TTTATT-TTATTTTCA
1 TATATTATTATTTTCA
360478 AGTATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
23 6 0.17
24 12 0.34
25 6 0.17
26 11 0.31
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (24 bp):
TATATTATTATTTTCATTAATATT
Found at i:360453 original size:26 final size:26
Alignment explanation
Indices: 360407--360475 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
360397 TTTCAAAAGT
360407 TTTATATATACTTATTATTTTCA-TAATA
1 TTTATATATA-TTATT-TTTT-ATTAATA
360435 TTTATATATATTATTTTTTATTAATA
1 TTTATATATATTATTTTTTATTAATA
*
360461 TTT-T-TATTTTATTTT
1 TTTATATATATTATTTT
360476 CAAGTATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
24 10 0.26
25 2 0.05
26 12 0.31
27 5 0.13
28 10 0.26
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTATATATATTATTTTTTATTAATA
Found at i:360935 original size:5 final size:5
Alignment explanation
Indices: 360925--360959 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
360915 TAAGCTCTAG
360925 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
360960 TCCTAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:370475 original size:22 final size:22
Alignment explanation
Indices: 370452--370550 Score: 144
Period size: 22 Copynumber: 4.5 Consensus size: 22
370442 ATCTGCACTC
*
370452 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAGATTCTCTT
* *
370474 TTCAAAAATGATGGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
370496 TTCAAAGATGATGGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
370518 TTCAAAGATGATATATTTTCTT
1 TTCAAAGATGATAGATTCTCTT
370540 TTCAAAGATGA
1 TTCAAAGATGA
370551 AAGCTTTATT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:371076 original size:73 final size:73
Alignment explanation
Indices: 370989--371154 Score: 323
Period size: 73 Copynumber: 2.3 Consensus size: 73
370979 AGGAAGAAGA
370989 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTG
371054 CCAGGTAG
66 CCAGGTAG
*
371062 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATCAGCATTG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTG
371127 CCAGGTAG
66 CCAGGTAG
371135 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
371155 CATCTGAAGA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 92 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (73 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTG
CCAGGTAG
Found at i:371181 original size:113 final size:112
Alignment explanation
Indices: 371064--371319 Score: 388
Period size: 113 Copynumber: 2.3 Consensus size: 112
371054 CCAGGTAGAG
* * * *
371064 TTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATCAGCATTGCC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCC
* * *
371129 AG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA
66 AGAGGA-AGTTCATAATGAGAAAAACTCATCTGAAG-AGAAAGAAGAAA
* * *
371177 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCC
*
371242 AGAGGAAGTTCATAATGAGAAAAACTCATCTGAAGAGAAAGAAGAAG
66 AGAGGAAGTTCATAATGAGAAAAACTCATCTGAAGAGAAAGAAGAAA
371289 TTCATAATGAGAAGAACTTGTTCAACCTTTT
1 TTCATAATGAGAAGAACTTGTTCAACCTTTT
371320 TCTTGACTCT
Statistics
Matches: 130, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
112 40 0.31
113 88 0.68
114 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (112 bp):
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCC
AGAGGAAGTTCATAATGAGAAAAACTCATCTGAAGAGAAAGAAGAAA
Found at i:371254 original size:186 final size:185
Alignment explanation
Indices: 370928--371267 Score: 565
Period size: 186 Copynumber: 1.8 Consensus size: 185
370918 CAATCACTCA
*
370928 ATGGATCAACATGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 ATGGATCAACATGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATT
* * *
370993 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTGCCAG
66 CATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAG
* *
371058 GTAGAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCACTTG
131 GGAGAGTTCATAATGAGAAAAACTTGTTCAACCTTTTGTTTGAATTCATCACTTG
*
371113 ATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
1 ATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
* * *
371178 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCA
65 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCA
371243 GAGGA-AGTTCATAATGAGAAAAACT
130 G-GGAGAGTTCATAATGAGAAAAACT
371268 CATCTGAAGA
Statistics
Matches: 143, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
185 10 0.07
186 131 0.92
187 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (185 bp):
ATGGATCAACATGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATT
CATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAG
GGAGAGTTCATAATGAGAAAAACTTGTTCAACCTTTTGTTTGAATTCATCACTTG
Found at i:371589 original size:138 final size:137
Alignment explanation
Indices: 371355--371713 Score: 454
Period size: 138 Copynumber: 2.6 Consensus size: 137
371345 AGATCAGCAC
* * *
371355 CAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGGTCATAA
1 CAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAA
* * * * * * * *
371419 TAAGAAGAACTTGTTCGACCTTATCTTGATTCATCACCTA-TGGAGTTGAATGAAAGAAGAACCT
64 TGAGAAGAACTTGTTCAATCTTAGCTTAATTCATCACATATTGAAGTTGAAT-AAACAA-AACCT
*
371483 CTCTTGAGGAT
127 CTCTTGAAGAT
*
371494 CAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATG
1 CAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATG
* ** *
371559 AGAAGAACTTGTTCAATCTT-GCATTAATTCATCACATATTGAAGTTGAATTAACAATCCCTCTT
66 AGAAGAACTTGTTCAATCTTAGC-TTAATTCATCACATATTGAAGTTGAATAAACAAAACCTCTC
371623 TTGAAGAT
130 TTGAAGAT
* * *
371631 CAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAATAAGAAATTCATAAT
1 CAACATTTCCAGAA-GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAAT
*
371696 GAGAAGAATTTGTTCAAT
65 GAGAAGAACTTGTTCAAT
371714 TTTTTGCCAG
Statistics
Matches: 194, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
137 27 0.14
138 141 0.73
139 26 0.13
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (137 bp):
CAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAATCTTAGCTTAATTCATCACATATTGAAGTTGAATAAACAAAACCTCTCT
TGAAGAT
Found at i:371966 original size:22 final size:22
Alignment explanation
Indices: 371938--371997 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
371928 GTTTTTATTT
371938 TTATTATTATTATTAATAATCA
1 TTATTATTATTATTAATAATCA
* * *
371960 TTATTATTATTATTATTTATTA
1 TTATTATTATTATTAATAATCA
371982 TTATTATTATTATTAA
1 TTATTATTATTATTAA
371998 ATTTATTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTATTATTATTAATAATCA
Found at i:371991 original size:19 final size:19
Alignment explanation
Indices: 371932--371995 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
371922 CCATTCGTTT
371932 TTATT-TTTATTATTATTA
1 TTATTATTTATTATTATTA
* * *
371950 TTAATAATCATTATTATTA
1 TTATTATTTATTATTATTA
371969 TTATTATTTATTATTATTA
1 TTATTATTTATTATTATTA
371988 TTATTATT
1 TTATTATT
371996 AAATTTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
18 4 0.10
19 35 0.90
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTATTTATTATTATTA
Found at i:372006 original size:3 final size:3
Alignment explanation
Indices: 371932--371996 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
371922 CCATTCGTTT
* * *
371932 TTA TTT TTA TTA TTA TTA TTAA TAA TCA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA
371979 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
371997 AATTTATTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
3 50 0.91
4 5 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:373312 original size:11 final size:11
Alignment explanation
Indices: 373296--373321 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
373286 TAAATTAGTA
373296 ATTTAATTATT
1 ATTTAATTATT
373307 ATTTAATTATT
1 ATTTAATTATT
373318 ATTT
1 ATTT
373322 TAGTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTAATTATT
Found at i:373374 original size:2 final size:2
Alignment explanation
Indices: 373367--373404 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
373357 TATAAAACAA
373367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
373405 GGTTTTATTC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:375794 original size:136 final size:138
Alignment explanation
Indices: 375434--375800 Score: 381
Period size: 139 Copynumber: 2.7 Consensus size: 138
375424 CCCTAAACAT
* * * * * * * *
375434 TTTAATTTA-GGTGAATTTTTAATTTGGTGACCACATT-TATGCCCGAGGATCCATATTAATTAT
1 TTTAATTTACGG-AAATTTTTAATTTGATCATCAC-TTGTATGCTCGAGGTTCAATTTTAATTAT
* * *
375497 TTGATCCAATAATTTGTTAAAATTTCTTAGGATTAATAATTAGAGACTTCATTTTAGTTTAATTG
64 TAGATCCAATAATTTG-TAAAATTTATTAGGATTAATAATTAGAGACTTCATTTTAGATTAATTG
*
375562 CACTTTAGTCC
128 CACTATAGTCC
* * *
375573 TTTAATTTACGTAAATTTTTAATTTGCTCATCACTTGTATGCTCGAGGTTCAATTTTAATTATTC
1 TTTAATTTACGGAAATTTTTAATTTGATCATCACTTGTATGCTCGAGGTTCAATTTTAATTATTA
* * *
375638 GATCCAATAATTTGTAAAAATTGATTAGGATTAATAATTA-A-ATTTCATTTTAGATTAATTTCA
66 GATCCAATAATTTGT-AAAATTTATTAGGATTAATAATTAGAGACTTCATTTTAGATTAATTGCA
*
375701 CTATATTCC
130 CTATAGTCC
** *
375710 TTTAATTTA-GGAGAA-TTTTAATTTGATCATCTTTTTTATGCAT-GAGGTTTC-ATTTTAATTA
1 TTTAATTTACGGA-AATTTTTAATTTGATCATCACTTGTATGC-TCGAGG-TTCAATTTTAATTA
* * *
375771 CTAGATTCAATAAATTGCTAAAATTTATTA
63 TTAGATCCAATAATTTG-TAAAATTTATTA
375801 AGTTGATATT
Statistics
Matches: 194, Mismatches: 27, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
136 61 0.31
137 42 0.22
138 4 0.02
139 86 0.44
140 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (138 bp):
TTTAATTTACGGAAATTTTTAATTTGATCATCACTTGTATGCTCGAGGTTCAATTTTAATTATTA
GATCCAATAATTTGTAAAATTTATTAGGATTAATAATTAGAGACTTCATTTTAGATTAATTGCAC
TATAGTCC
Found at i:376634 original size:17 final size:17
Alignment explanation
Indices: 376604--376642 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
376594 CCTCCGTGTT
* *
376604 TATTATTATTATTATTA
1 TATTAATATCATTATTA
376621 TATTAATATCATTATTA
1 TATTAATATCATTATTA
376638 -ATTAA
1 TATTAA
376643 ATTGAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAATATCATTATTA
Found at i:376668 original size:86 final size:86
Alignment explanation
Indices: 376547--376720 Score: 348
Period size: 86 Copynumber: 2.0 Consensus size: 86
376537 AAATTAAAAC
376547 TATTAATTAAATTGAAAAATAATTTAATTATCCTTGACACCAATTTTCCTCCGTGTTTATTATTA
1 TATTAATTAAATTGAAAAATAATTTAATTATCCTTGACACCAATTTTCCTCCGTGTTTATTATTA
376612 TTATTATTATATTAATATCAT
66 TTATTATTATATTAATATCAT
376633 TATTAATTAAATTGAAAAATAATTTAATTATCCTTGACACCAATTTTCCTCCGTGTTTATTATTA
1 TATTAATTAAATTGAAAAATAATTTAATTATCCTTGACACCAATTTTCCTCCGTGTTTATTATTA
376698 TTATTATTATATTAATATCAT
66 TTATTATTATATTAATATCAT
376719 TA
1 TA
376721 ATATATTTTA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (86 bp):
TATTAATTAAATTGAAAAATAATTTAATTATCCTTGACACCAATTTTCCTCCGTGTTTATTATTA
TTATTATTATATTAATATCAT
Found at i:377830 original size:17 final size:17
Alignment explanation
Indices: 377787--377831 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
377777 TCCTTCATGC
*
377787 TTGTTACATGTTAGAAA
1 TTGTTACATTTTAGAAA
377804 TTGTTACATTTTAGAAA
1 TTGTTACATTTTAGAAA
377821 TTGTTACATTT
1 TTGTTACATTT
377832 ATGCTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (17 bp):
TTGTTACATTTTAGAAA
Found at i:382097 original size:20 final size:20
Alignment explanation
Indices: 382072--382145 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
382062 ATGGCTTTCG
382072 TTCATGCCTTAATGCATCCT
1 TTCATGCCTTAATGCATCCT
* *
382092 TTCATGCATTTTAAATTATGGCATCCG
1 TTCATGC--CTT--A--AT-GCATCCT
*
382119 TTCATGCCTTTATGCATCCT
1 TTCATGCCTTAATGCATCCT
382139 TTCATGC
1 TTCATGC
382146 ATTTTCAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
20 20 0.48
21 2 0.05
22 2 0.05
24 1 0.02
25 2 0.05
26 2 0.05
27 13 0.31
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (20 bp):
TTCATGCCTTAATGCATCCT
Found at i:382116 original size:27 final size:27
Alignment explanation
Indices: 382085--382172 Score: 75
Period size: 27 Copynumber: 3.5 Consensus size: 27
382075 ATGCCTTAAT
*
382085 GCATCCTTTCATGCATTTTAAATTATG
1 GCATCCGTTCATGCATTTTAAATTATG
*
382112 GCATCCGTTCATGC---CT---TTAT-
1 GCATCCGTTCATGCATTTTAAATTATG
*
382132 GCATCCTTTCATGCATTTTCAAA-TATG
1 GCATCCGTTCATGCATTTT-AAATTATG
*
382159 ACATCCGTTCATGC
1 GCATCCGTTCATGC
382173 CTTTATGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
20 13 0.28
21 4 0.09
23 1 0.02
24 1 0.02
26 3 0.06
27 25 0.53
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (27 bp):
GCATCCGTTCATGCATTTTAAATTATG
Found at i:382206 original size:47 final size:47
Alignment explanation
Indices: 382050--382206 Score: 233
Period size: 47 Copynumber: 3.3 Consensus size: 47
382040 CCATTTTCGA
* * * * *
382050 GCATTTCCAATTATGGCTTTCGTTCATGCCTTAATGCATCCTTTCAT
1 GCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCCTTTCAT
* *
382097 GCATTTTAAATTATGGCATCCGTTCATGCCTTTATGCATCCTTTCAT
1 GCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCCTTTCAT
* *
382144 GCATTTTCAAATATGACATCCGTTCATGCCTTTATGCATCCTTTCTT
1 GCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCCTTTCAT
382191 GCATTTTCAATTATGA
1 GCATTTTCAATTATGA
382207 AATTGATTTA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 100 1.00
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.43
Consensus pattern (47 bp):
GCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCCTTTCAT
Found at i:387962 original size:59 final size:59
Alignment explanation
Indices: 387870--387988 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
387860 GCAGGGGGAG
387870 GTTGAAACCGAGTAAAGATGACGTCTAGAGCTTGCATGAAAGTTCCAAACTCATGCACT
1 GTTGAAACCGAGTAAAGATGACGTCTAGAGCTTGCATGAAAGTTCCAAACTCATGCACT
387929 GTTGAAACCGAGTAAAGATGACGTCTAGAGCTTGCATGAAAGTTCCAAACTCATGCACT
1 GTTGAAACCGAGTAAAGATGACGTCTAGAGCTTGCATGAAAGTTCCAAACTCATGCACT
387988 G
1 G
387989 AAATCCTAGA
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:0.20, G:0.23, T:0.24
Consensus pattern (59 bp):
GTTGAAACCGAGTAAAGATGACGTCTAGAGCTTGCATGAAAGTTCCAAACTCATGCACT
Found at i:388949 original size:47 final size:47
Alignment explanation
Indices: 388884--389127 Score: 273
Period size: 47 Copynumber: 5.5 Consensus size: 47
388874 AATACACCCT
* * *
388884 TTTCAAGCATTTCCAATTATGACATCCGTTCATGCCTTAATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* * *
388931 TTTCATGCATTTTAAATTATG----GC-TT--TG--TTCATG---CC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
*
388966 TTT-ATGCATTTTCAATTATGGCATCCGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* *
389012 TTTCATTCATTTTCAATTATGGA-ATCTGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTAT-GACATCCGTTCATGCCTTTATGCATCC
* *
389059 TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTTATGCATCA
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
*
389106 TTTCTTGCATTTTCAATTATGA
1 TTTCATGCATTTTCAATTATGA
389128 AATTGATTTA
Statistics
Matches: 165, Mismatches: 17, Indels: 30
0.78 0.08 0.14
Matches are distributed among these distances:
34 16 0.10
35 5 0.03
38 6 0.04
39 2 0.01
40 2 0.01
41 2 0.01
42 2 0.01
43 6 0.04
46 6 0.04
47 117 0.71
48 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (47 bp):
TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
Found at i:388973 original size:34 final size:35
Alignment explanation
Indices: 388929--389009 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
388919 CTTAATGCAT
**
388929 CCTTTCATGCATTTTAAATTATGGC-TTTGTTCATG
1 CCTTT-ATGCATTTTAAATTATGGCATCCGTTCATG
*
388964 CCTTTATGCATTTTCAATTATGGCATCCGTTCATG
1 CCTTTATGCATTTTAAATTATGGCATCCGTTCATG
388999 CCTTTATGCAT
1 CCTTTATGCAT
389010 CCTTTCATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
34 18 0.43
35 24 0.57
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.46
Consensus pattern (35 bp):
CCTTTATGCATTTTAAATTATGGCATCCGTTCATG
Found at i:388985 original size:81 final size:82
Alignment explanation
Indices: 388890--389056 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 82
388880 CCCTTTTCAA
*
388890 GCATTTCCAATTATGACATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGG-C
1 GCATTTCCAATTATGACATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGAA
*
388954 TTTGTTCATGCCTTTAT
66 TCTGTTCATGCCTTTAT
* * * * *
388971 GCATTTTCAATTATGGCATCCGTTCATGCCTTTATGCATCCTTTCATTCATTTTCAATTATGGAA
1 GCATTTCCAATTATGACATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGAA
389036 TCTGTTCATGCCTTTAT
66 TCTGTTCATGCCTTTAT
389053 GCAT
1 GCAT
389057 CCTTTCATGC
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 58 0.74
82 20 0.26
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (82 bp):
GCATTTCCAATTATGACATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTAAATTATGGAA
TCTGTTCATGCCTTTAT
Found at i:389090 original size:27 final size:27
Alignment explanation
Indices: 388969--389093 Score: 89
Period size: 27 Copynumber: 5.1 Consensus size: 27
388959 TCATGCCTTT
388969 ATGCATTTTCAATTATGGCATCCGTTC
1 ATGCATTTTCAATTATGGCATCCGTTC
* *
388996 ATGC-----C-TTTAT-GCATCCTTTC
1 ATGCATTTTCAATTATGGCATCCGTTC
* * *
389016 ATTCATTTTCAATTATGGAATCTGTTC
1 ATGCATTTTCAATTATGGCATCCGTTC
* *
389043 ATGC-----C-TTTAT-GCATCCTTTC
1 ATGCATTTTCAATTATGGCATCCGTTC
389063 ATGCATTTTCAATTATGGCATCCGTTC
1 ATGCATTTTCAATTATGGCATCCGTTC
389090 ATGC
1 ATGC
389094 CTTTATGCAT
Statistics
Matches: 70, Mismatches: 14, Indels: 28
0.62 0.12 0.25
Matches are distributed among these distances:
20 23 0.33
21 8 0.11
22 2 0.03
25 2 0.03
26 8 0.11
27 27 0.39
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (27 bp):
ATGCATTTTCAATTATGGCATCCGTTC
Found at i:389735 original size:96 final size:95
Alignment explanation
Indices: 389517--389741 Score: 242
Period size: 95 Copynumber: 2.4 Consensus size: 95
389507 TAAGACCCTT
* * * * *
389517 TGGTATCGATACTACCCTATTAGGGTATTGATACCCCCTTCATGTATCGATACCAAAATTAGTTT
1 TGGTATCGATACTACCTTGTTAGGGTACTGATACCCCCTTCAGGTATCGATACCAAAATTAGATT
* *
389582 CGATGTAGCCTGGTATTGATACCTTCACCA
66 CGATGTAGACTGGTATCGATACCTTCACCA
* * *
389612 TGGTATCGATACT-CCTATGTTATGGTACTGATACCCCC-TCTAGGTATCGATATCTAAATTAGA
1 TGGTATCGATACTACCT-TGTTAGGGTACTGATACCCCCTTC-AGGTATCGATACCAAAATTAGA
* **
389675 TTCGATATTTTACTGGTATCGATACCCTT-ACCA
64 TTCGAT-GTAGACTGGTATCGATA-CCTTCACCA
* *
389708 TGGTATCGATACTACATTGCTT-GGGTACCGATAC
1 TGGTATCGATACTACCTTG-TTAGGGTACTGATAC
389742 TGGTTGAATC
Statistics
Matches: 108, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
94 4 0.04
95 55 0.51
96 41 0.38
97 8 0.07
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (95 bp):
TGGTATCGATACTACCTTGTTAGGGTACTGATACCCCCTTCAGGTATCGATACCAAAATTAGATT
CGATGTAGACTGGTATCGATACCTTCACCA
Found at i:391207 original size:19 final size:18
Alignment explanation
Indices: 391179--391234 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
391169 TTTTTTTATT
391179 AAAAATAAAAAAACCAAAG
1 AAAAA-AAAAAAACCAAAG
* *
391198 AAAAAGAAAAAAGCCAAAT
1 AAAAA-AAAAAAACCAAAG
*
391217 AAATAAAAAAAATCCAAA
1 AAA-AAAAAAAAACCAAA
391235 ATTTTGCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 30 0.94
20 2 0.06
ACGTcount: A:0.77, C:0.11, G:0.05, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAAAACCAAAG
Found at i:392847 original size:157 final size:157
Alignment explanation
Indices: 392561--392874 Score: 628
Period size: 157 Copynumber: 2.0 Consensus size: 157
392551 TGGTACACAC
392561 TAAAACAAGCAATGAGAAAATATTTTCTCTTGACACACTATATTTGTGAAGTTAAACAACAACTT
1 TAAAACAAGCAATGAGAAAATATTTTCTCTTGACACACTATATTTGTGAAGTTAAACAACAACTT
392626 CGCCGACTTCGAAAAAAAAGAAGTTTAGTCGAAAACTACTACAAGGAGATGACATTTTTAATGAA
66 CGCCGACTTCGAAAAAAAAGAAGTTTAGTCGAAAACTACTACAAGGAGATGACATTTTTAATGAA
392691 TCGTACAGATATATATGAAGCATACGG
131 TCGTACAGATATATATGAAGCATACGG
392718 TAAAACAAGCAATGAGAAAATATTTTCTCTTGACACACTATATTTGTGAAGTTAAACAACAACTT
1 TAAAACAAGCAATGAGAAAATATTTTCTCTTGACACACTATATTTGTGAAGTTAAACAACAACTT
392783 CGCCGACTTCGAAAAAAAAGAAGTTTAGTCGAAAACTACTACAAGGAGATGACATTTTTAATGAA
66 CGCCGACTTCGAAAAAAAAGAAGTTTAGTCGAAAACTACTACAAGGAGATGACATTTTTAATGAA
392848 TCGTACAGATATATATGAAGCATACGG
131 TCGTACAGATATATATGAAGCATACGG
392875 ATATATAGTG
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (157 bp):
TAAAACAAGCAATGAGAAAATATTTTCTCTTGACACACTATATTTGTGAAGTTAAACAACAACTT
CGCCGACTTCGAAAAAAAAGAAGTTTAGTCGAAAACTACTACAAGGAGATGACATTTTTAATGAA
TCGTACAGATATATATGAAGCATACGG
Found at i:393858 original size:12 final size:12
Alignment explanation
Indices: 393824--393859 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
393814 ATTAGGATAG
*
393824 TATTGTTATTAT
1 TATTGTTATTTT
393836 TATTGTTATTTT
1 TATTGTTATTTT
*
393848 TATTATTATTTT
1 TATTGTTATTTT
393860 CAAGCATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (12 bp):
TATTGTTATTTT
Found at i:394198 original size:17 final size:16
Alignment explanation
Indices: 394173--394211 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
394163 TTCCACAACT
394173 CCATCATCTTCAAATCA
1 CCATCATCTTC-AATCA
* *
394190 CCATTATCTTCCATCA
1 CCATCATCTTCAATCA
394206 CCATCA
1 CCATCA
394212 AAACCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (16 bp):
CCATCATCTTCAATCA
Found at i:394285 original size:19 final size:18
Alignment explanation
Indices: 394261--394300 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
394251 TATGTCTTCT
* *
394261 TTTATTTTCTTATTATATA
1 TTTATTATCTTAATAT-TA
394280 TTTATTATCTTAATATTA
1 TTTATTATCTTAATATTA
394298 TTT
1 TTT
394301 CCTTTGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATCTTAATATTA
Found at i:396335 original size:25 final size:25
Alignment explanation
Indices: 396285--396439 Score: 169
Period size: 25 Copynumber: 6.4 Consensus size: 25
396275 AAGTAAGGGG
*
396285 AAACATTTTTC-AAA--ATTTCATC
1 AAACATTTTTCAAAATTATTTCATT
396307 AAACATTTTTCAAAATTATTTCATT
1 AAACATTTTTCAAAATTATTTCATT
** * *
396332 AAACATTTTTTGAAATTCTTTCATC
1 AAACATTTTTCAAAATTATTTCATT
*
396357 AAACATTTCTCAAAATTCA-TTCATT
1 AAACATTTTTCAAAATT-ATTTCATT
* *
396382 AAACATTTTTCAAAATTCTTTCATA
1 AAACATTTTTCAAAATTATTTCATT
396407 AAACA-TTTTCAAAACTTATTT-ATT
1 AAACATTTTTCAAAA-TTATTTCATT
*
396431 GAACATTTT
1 AAACATTTT
396440 CACCTTTTGA
Statistics
Matches: 110, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
22 11 0.10
23 3 0.03
24 15 0.14
25 81 0.74
ACGTcount: A:0.39, C:0.15, G:0.01, T:0.45
Consensus pattern (25 bp):
AAACATTTTTCAAAATTATTTCATT
Found at i:396364 original size:50 final size:50
Alignment explanation
Indices: 396285--396439 Score: 205
Period size: 50 Copynumber: 3.2 Consensus size: 50
396275 AAGTAAGGGG
396285 AAACATTTTTCAAAA---TTTCATCAAACATTTTTCAAAATTATTTCATT
1 AAACATTTTTCAAAATTCTTTCATCAAACATTTTTCAAAATTATTTCATT
** *
396332 AAACATTTTTTGAAATTCTTTCATCAAACATTTCTCAAAATTCA-TTCATT
1 AAACATTTTTCAAAATTCTTTCATCAAACATTTTTCAAAATT-ATTTCATT
*
396382 AAACATTTTTCAAAATTCTTTCATAAAACA-TTTTCAAAACTTATTT-ATT
1 AAACATTTTTCAAAATTCTTTCATCAAACATTTTTCAAAA-TTATTTCATT
*
396431 GAACATTTT
1 AAACATTTT
396440 CACCTTTTGA
Statistics
Matches: 94, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
47 13 0.14
49 20 0.21
50 60 0.64
51 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.01, T:0.45
Consensus pattern (50 bp):
AAACATTTTTCAAAATTCTTTCATCAAACATTTTTCAAAATTATTTCATT
Found at i:396802 original size:30 final size:30
Alignment explanation
Indices: 396766--396847 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
396756 ACTAAGTACC
*
396766 AAATAGTACATGGACTTGGCCACCAAGGTT
1 AAATAGTACAAGGACTTGGCCACCAAGGTT
*
396796 AAATAGTACAAGGACTTAGCCACCAAGGTT
1 AAATAGTACAAGGACTTGGCCACCAAGGTT
* *
396826 AAATAGTATAGGGACTTGGCCA
1 AAATAGTACAAGGACTTGGCCA
396848 TTATTGTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (30 bp):
AAATAGTACAAGGACTTGGCCACCAAGGTT
Found at i:397142 original size:88 final size:88
Alignment explanation
Indices: 396993--397169 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
396983 ACATTAATCA
396993 CAATCGCATTAGATTATTTTTAGGATATATCGCACATGACACATATGAAATCATAGCATATGACC
1 CAATCGCATTAGATTATTTTTAGGATATATCGCACATGACACATATGAAATCATAGCATATGACC
397058 TTTTCAAACATGATCTATGAAAT
66 TTTTCAAACATGATCTATGAAAT
397081 CAATCGCATTAGATTATTTTTAGGATATATCGCACATGACACATATGAAATCATAGCATATGACC
1 CAATCGCATTAGATTATTTTTAGGATATATCGCACATGACACATATGAAATCATAGCATATGACC
397146 TTTTCAAACATGATCTATGAAAT
66 TTTTCAAACATGATCTATGAAAT
397169 C
1 C
397170 CATCTCAATA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (88 bp):
CAATCGCATTAGATTATTTTTAGGATATATCGCACATGACACATATGAAATCATAGCATATGACC
TTTTCAAACATGATCTATGAAAT
Found at i:398016 original size:17 final size:17
Alignment explanation
Indices: 397994--398026 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
397984 TTATGACATT
397994 ATAAATTATAAAACAAC
1 ATAAATTATAAAACAAC
*
398011 ATAAATTTTAAAACAA
1 ATAAATTATAAAACAA
398027 AAGTTGAAAC
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:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAATTATAAAACAAC
Found at i:399677 original size:3 final size:3
Alignment explanation
Indices: 399669--399780 Score: 134
Period size: 3 Copynumber: 37.0 Consensus size: 3
399659 GTCCCTGTAC
*
399669 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
399717 TAT TAT TAT TAT TAT GTAG TAG TAG TAT TAG TAT TAG TAT TAG TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
399763 TAG TAT TAG TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
399781 ATAAGTATTT
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
3 92 0.98
4 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:402592 original size:42 final size:42
Alignment explanation
Indices: 402533--402616 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
402523 ACGCCAACAT
402533 TCAATTAATATATTATTAAATCAGTAAAGATTGTTAATGGTG
1 TCAATTAATATATTATTAAATCAGTAAAGATTGTTAATGGTG
*
402575 TCAATTACTATATTATTAAATCAGTAAAGATTGTTAATGGTG
1 TCAATTAATATATTATTAAATCAGTAAAGATTGTTAATGGTG
402617 AGTGACTGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.40
Consensus pattern (42 bp):
TCAATTAATATATTATTAAATCAGTAAAGATTGTTAATGGTG
Found at i:402784 original size:2 final size:2
Alignment explanation
Indices: 402779--402807 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
402769 AAATATTACT
402779 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
402808 TAAAGTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:403036 original size:2 final size:2
Alignment explanation
Indices: 403029--403053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
403019 GATCTCATCC
403029 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
403054 ATGAAAGTAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:404237 original size:20 final size:20
Alignment explanation
Indices: 404212--404261 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
404202 TTTTAGTTAA
404212 TTAAAATATATTTAAAGAGT
1 TTAAAATATATTTAAAGAGT
* * *
404232 TTAAAAATGTGTTTAAAGATT
1 TT-AAAATATATTTAAAGAGT
404253 TTAAAATAT
1 TTAAAATAT
404262 GAAAAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (20 bp):
TTAAAATATATTTAAAGAGT
Found at i:406296 original size:20 final size:18
Alignment explanation
Indices: 406258--406296 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
406248 TGAAAATGAT
*
406258 TTGGTTTTGAAAGCAAAA
1 TTGGTTTTGAAAACAAAA
406276 TTGGATTTTGAAAAACAAAA
1 TTGG-TTTTG-AAAACAAAA
406296 T
1 T
406297 GAAATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (18 bp):
TTGGTTTTGAAAACAAAA
Found at i:417328 original size:19 final size:19
Alignment explanation
Indices: 417304--417343 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
417294 ATTGTACAAA
417304 TTTCCTATCTCTATACTCC
1 TTTCCTATCTCTATACTCC
*
417323 TTTCCTATCTTTATACTCC
1 TTTCCTATCTCTATACTCC
417342 TT
1 TT
417344 ACTCTCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTCCTATCTCTATACTCC
Found at i:419487 original size:20 final size:20
Alignment explanation
Indices: 419462--419505 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
419452 GGTGCTCATA
419462 TTTACATTAGACTCGTATTT
1 TTTACATTAGACTCGTATTT
419482 TTTACATTAGACTCGTATTT
1 TTTACATTAGACTCGTATTT
419502 TTTA
1 TTTA
419506 TTAGGGTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (20 bp):
TTTACATTAGACTCGTATTT
Found at i:421644 original size:18 final size:16
Alignment explanation
Indices: 421621--421665 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
421611 TGTTTATGAG
421621 GGAATTAGAATATGTGAA
1 GGAATTAGAATATGT--A
* *
421639 GGAATTTGAATCTGTA
1 GGAATTAGAATATGTA
421655 GGAATTAGAAT
1 GGAATTAGAAT
421666 CCAATTCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
18 13 0.54
ACGTcount: A:0.40, C:0.02, G:0.27, T:0.31
Consensus pattern (16 bp):
GGAATTAGAATATGTA
Found at i:422644 original size:216 final size:216
Alignment explanation
Indices: 422171--422805 Score: 916
Period size: 216 Copynumber: 2.9 Consensus size: 216
422161 TATAAGATAA
* * *
422171 AATTATATTTTTTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGA-CTCG
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTT-ACCCTAAACCCAAACCCGACCCGATC-CG
*
422235 ACCCGAATACCACACTT-AAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGA
64 ACCCGAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGA
*
422299 ATATATGAATTAGAAATCCGACCCGACCCGACCCGAAATAATAAAAAACTATTTTTATTTAATAA
129 ATATATGAATTAGAAAT-----CCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAA
* * *
422364 AAATAGTGACTTAATCCGACCCGGCCCG
189 AAACAATGACTTAATCCGACCCGACCCG
*
422392 AATTATATATATTTTTGGGTCGGTCCGGTTTTTTTACCCTAAACCCAAACCCGACCCGATCCGAC
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTACCCTAAACCCAAACCCGACCCGATCCGAC
422457 CCGAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAAT
66 CCGAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAAT
* *
422522 ATATGAATTAGAAATCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATGAAAACAAT
131 ATATGAATTAGAAATCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAAT
422587 GACTTAATCCGACCCGACCCG
196 GACTTAATCCGACCCGACCCG
*
422608 AATTATATATATTTTCGGGTCGGTCTGGTTTTTTTACCCTAAACCCAAACCCGACCCGATCCGAC
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTACCCTAAACCCAAACCCGACCCGATCCGAC
* * *
422673 CCGAATATCACACTTAAAAAAACCCGATCCGATCCGACCAAAATAAAGTTTCACCCAACCCATCC
66 CCGAATATCACACTTAAAAAAACCCGA--C---CCGAACAAAATAAAGTTT----CATCCGA-CC
* * *
422738 CGACTCGAATATATGAATTAGAAA-CCCATCCCGACCCGAAATAATAAAAAAAATATTTTTATTC
121 CGACCCGAATATATGAATTAGAAATCCGA-CCCGACCCGAAATAAT-AAAAAAATATTTTTATTT
422802 AATA
184 AATA
422806 TATAAATAAG
Statistics
Matches: 380, Mismatches: 20, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
216 156 0.41
218 1 0.00
220 41 0.11
221 114 0.30
225 8 0.02
226 41 0.11
227 19 0.05
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (216 bp):
AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTACCCTAAACCCAAACCCGACCCGATCCGAC
CCGAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAAT
ATATGAATTAGAAATCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAAT
GACTTAATCCGACCCGACCCG
Found at i:426214 original size:3 final size:3
Alignment explanation
Indices: 426198--426257 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
426188 TACCTATTTT
426198 TTA TTA TTGA -TA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
**
426243 TTA AAA TTA TTA TTA
1 TTA TTA TTA TTA TTA
426258 CAAATAGGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 3 0.06
3 42 0.86
4 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:427853 original size:20 final size:19
Alignment explanation
Indices: 427828--427869 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
427818 CTATTTTATA
427828 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
427848 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
427867 AAT
1 AAT
427870 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:427858 original size:119 final size:118
Alignment explanation
Indices: 427731--427960 Score: 293
Period size: 120 Copynumber: 1.9 Consensus size: 118
427721 GTTTTAATAT
* * * * *
427731 TTATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCCATTTTTT
1 TTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-CATTTTCT
*
427794 GATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAATTGTTTTAA
65 GATATTTTTAAATAAATAAATATCCTA-TTTATAAATT-TATATAAATTGTTTTAA
* * * ** *
427850 TTATTTATTTATTTTTTAATATCGAAGAAAATAGCTGTCTTAAGGCACCTAGAAGTCATTTTCTG
1 TTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTTTCTG
**
427915 ATATTTTTAAATAAATAAATATTTTATTTATAAATTTATATAAATT
66 ATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAATT
427961 AATAAATTTA
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
118 9 0.09
119 31 0.33
120 35 0.37
121 20 0.21
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.47
Consensus pattern (118 bp):
TTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTTTCTG
ATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAATTGTTTTAA
Found at i:430048 original size:8 final size:7
Alignment explanation
Indices: 430024--430065 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
430014 TTTTCATACA
430024 TGCA-TT
1 TGCATTT
430030 TGCATTT
1 TGCATTT
430037 TGCATCTT
1 TGCAT-TT
430045 TGCATTT
1 TGCATTT
* *
430052 TTCATTG
1 TGCATTT
430059 TGCATTT
1 TGCATTT
430066 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:430048 original size:15 final size:14
Alignment explanation
Indices: 430024--430065 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
430014 TTTTCATACA
430024 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
430037 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
430052 TTCATTGTGCATTT
1 TGCATTTTGCATTT
430066 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:430161 original size:27 final size:27
Alignment explanation
Indices: 430125--430184 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
430115 CATTCACATA
430125 TTTACATTTGCATTTACATTTGCATTT
1 TTTACATTTGCATTTACATTTGCATTT
* * *
430152 TTTACGTTTGTATTTACATTTTCA-TT
1 TTTACATTTGCATTTACATTTGCATTT
430178 TTTACAT
1 TTTACAT
430185 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:430178 original size:12 final size:12
Alignment explanation
Indices: 430124--430151 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
430114 ACATTCACAT
430124 ATTTACATTTGC
1 ATTTACATTTGC
430136 ATTTACATTTGC
1 ATTTACATTTGC
430148 ATTT
1 ATTT
430152 TTTACGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:431805 original size:2 final size:2
Alignment explanation
Indices: 431798--431847 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
431788 ATCCTTTTAA
431798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
431840 AT AT AT AT
1 AT AT AT AT
431848 CATTTGTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:432176 original size:15 final size:16
Alignment explanation
Indices: 432156--432220 Score: 66
Period size: 15 Copynumber: 4.2 Consensus size: 16
432146 AGAAGAAGAA
432156 AAAAAACATAAGAA-G
1 AAAAAACATAAGAAGG
* *
432171 AAAAAAAATAAAAAAGG
1 AAAAAACAT-AAGAAGG
432188 AAAAAACA-AA-AAGG
1 AAAAAACATAAGAAGG
*
432202 AAAAAA-AGAAGAAGG
1 AAAAAACATAAGAAGG
432217 AAAA
1 AAAA
432221 TTGAATCAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
13 1 0.02
14 12 0.28
15 18 0.42
16 4 0.09
17 8 0.19
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAAACATAAGAAGG
Found at i:432191 original size:14 final size:13
Alignment explanation
Indices: 432174--432220 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 13
432164 TAAGAAGAAA
432174 AAAAATAAAAAAGG
1 AAAAA-AAAAAAGG
432188 AAAAAACAAAAAGG
1 AAAAAA-AAAAAGG
432202 AAAAAAAGAAGAAGG
1 AAAAAAA-AA-AAGG
432217 AAAA
1 AAAA
432221 TTGAATCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.07
14 20 0.67
15 8 0.27
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:434686 original size:114 final size:114
Alignment explanation
Indices: 434485--434708 Score: 340
Period size: 114 Copynumber: 2.0 Consensus size: 114
434475 GTGCCACGTT
* *
434485 CTCATAGTAGAAATAAATAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTA
1 CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTA
* * * *
434550 GTTTGGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTG
66 GTTCGGTAGGAACCCCAAAACCAATAATTAGAATTAAAAGATGAATTTG
* *
434599 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTA
* * * *
434664 GTTCGGTAGGAGCCCCAGAACCAATAATTGGAATTGAAAGATGAA
66 GTTCGGTAGGAACCCCAAAACCAATAATTAGAATTAAAAGATGAA
434709 CTGCATGATC
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTA
GTTCGGTAGGAACCCCAAAACCAATAATTAGAATTAAAAGATGAATTTG
Found at i:437390 original size:22 final size:22
Alignment explanation
Indices: 437364--437428 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
437354 TACATCTACA
437364 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
437386 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
437408 CTTTTTAAAGATGATAGATTC
1 CTCTTCAAAGATGATAGATTC
437429 GCTTTTAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:437433 original size:22 final size:22
Alignment explanation
Indices: 437370--437443 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
437360 TACACTCTTC
* *
437370 AAAGATGATAGATTCTCTCTTC
1 AAAGATGATAGATTCTCTTTTT
*
437392 AAAGATGATAAATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
*
437414 AAAGATGATAGATTCGC-TTTT
1 AAAGATGATAGATTCTCTTTTT
437435 AGAAGATGA
1 A-AAGATGA
437444 AAGCTTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.11
22 41 0.89
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTT
Found at i:438237 original size:24 final size:23
Alignment explanation
Indices: 438201--438245 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
438191 GTTCATAATG
438201 AGAAAAACTCAT-ATGAAGAAGGA
1 AGAAAAACTCATAATG-AGAAGGA
*
438224 AGAAGAAATTCATAATGAGAAG
1 AGAA-AAACTCATAATGAGAAG
438246 AGCTTGCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 12 0.63
25 3 0.16
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (23 bp):
AGAAAAACTCATAATGAGAAGGA
Found at i:439069 original size:113 final size:113
Alignment explanation
Indices: 438191--439056 Score: 1207
Period size: 113 Copynumber: 7.7 Consensus size: 113
438181 TTCCAGAAGG
* * * *
438191 GTTCATAATGAGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAGCTTGCTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
*
438256 ACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
* **
438304 GTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAAGAAGAATTTGTTC
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG-AGAAGAGCTTGTTC
* ** * * ** * * *
438369 AACCTTTTGTTTGAATTCATCATTTAATGGATCAACATTGCCAG-GTAGA
65 AACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAG-AAA
*
438418 GTTCATAATGAGAAGAACTCTTCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
**
438483 ACCTTTTGCTCAAATCCATCACTCGATGGATCAGTTTTTCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
438531 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* *
438596 ACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
438644 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * *
438709 ACCTTTTGCTCAAATCCATAACTCGATAGATCAACTTTTCCAGAGATA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
**
438757 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * ** * * * * * *
438822 ACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAG-AAA
* * **
438870 GTTCATAATGAGAAGAACTCGTCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* ** * *
438935 A-CTTTTAGTTTGAATTCATCACTCGATGTATCAACTTTTCCAGAGAAA
66 ACCTTTT-GCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
* * * * *
438983 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAATTTCATAATAAAAAGAGCTTGTTCG
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
439048 ACCTTTTGC
66 ACCTTTTGC
439057 ATGACTCTAT
Statistics
Matches: 672, Mismatches: 74, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
112 5 0.01
113 565 0.84
114 102 0.15
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
Found at i:440797 original size:3 final size:3
Alignment explanation
Indices: 440789--440821 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
440779 TTTACTTTTA
*
440789 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
440822 TAGCCATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:441030 original size:20 final size:19
Alignment explanation
Indices: 441005--441046 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
440995 CTATTTTATA
441005 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
441025 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
441044 AAT
1 AAT
441047 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:441048 original size:119 final size:117
Alignment explanation
Indices: 440901--441137 Score: 282
Period size: 120 Copynumber: 2.0 Consensus size: 117
440891 ATTTTAATCC
* * *
440901 TGTTTTAATATTGATTTATTTTTCAATAT-TAAGAAAGA-ACA-GTCTTAAAACAACTGGATGTC
1 TGTTTTAATATTGATTTATTTTTCAATATCGAAGAAA-ATACATGTCTTAAAACAACTAGAAGTC
*
440963 CATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
65 C-TTTTCTGATATTTTTAAATAAATAAATATCCTA-TTTATAAATT-TATATAAAT
* * * * ** *
441019 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAATAGATTTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTGATTTATTTTTCAATATCGAAGAAAATACATGTCTTAAAACAACTAGAAGTC
* **
441084 CTTTTTTGATATTTTTAAATAAATAAATATTTTATTTATAAATTTATATAAAT
65 CTTTTCTGATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAAT
441137 T
1 T
441138 AATAAATTTA
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
118 17 0.17
119 30 0.30
120 38 0.38
121 16 0.16
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (117 bp):
TGTTTTAATATTGATTTATTTTTCAATATCGAAGAAAATACATGTCTTAAAACAACTAGAAGTCC
TTTTCTGATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAAT
Found at i:441135 original size:10 final size:10
Alignment explanation
Indices: 441120--441165 Score: 64
Period size: 9 Copynumber: 5.0 Consensus size: 10
441110 ATATTTTATT
441120 TATAAATTTA
1 TATAAATTTA
441130 TATAAA-TTA
1 TATAAATTTA
441139 -ATAAATTTA
1 TATAAATTTA
441148 TATAAA-TTA
1 TATAAATTTA
441157 -ATAAATTTA
1 TATAAATTTA
441166 CTTAAAATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 10 0.30
9 12 0.36
10 11 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TATAAATTTA
Found at i:441178 original size:18 final size:18
Alignment explanation
Indices: 441121--441165 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
441111 TATTTTATTT
441121 ATAAATTTATATAAATTA
1 ATAAATTTATATAAATTA
441139 ATAAATTTATATAAATTA
1 ATAAATTTATATAAATTA
441157 ATAAATTTA
1 ATAAATTTA
441166 CTTAAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATTTATATAAATTA
Found at i:448395 original size:6 final size:6
Alignment explanation
Indices: 448377--448411 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
448367 TTAATTGCGA
448377 AAATTT GAAATTT AAATTT AAATTT AAATTT AAAT
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAAT
448412 CATTCGATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:448584 original size:29 final size:31
Alignment explanation
Indices: 448551--448611 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
448541 AAAAATATAT
* *
448551 ATATATAATAAT-GAAAATT-AATAAATAAA
1 ATATATAATAATAAAAAATTAAATAAAGAAA
448580 ATATATAATAATAAAAAATTAAATAAAGAAA
1 ATATATAATAATAAAAAATTAAATAAAGAAA
448611 A
1 A
448612 AAACAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.43
30 6 0.21
31 10 0.36
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (31 bp):
ATATATAATAATAAAAAATTAAATAAAGAAA
Found at i:448588 original size:16 final size:15
Alignment explanation
Indices: 448551--448595 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
448541 AAAAATATAT
*
448551 ATATATAATAATGAA
1 ATATATAATAATAAA
448566 A-AT-TAATAAATAAA
1 ATATATAAT-AATAAA
448580 ATATATAATAATAAA
1 ATATATAATAATAAA
448595 A
1 A
448596 AATTAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 4 0.15
14 8 0.31
15 10 0.38
16 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
ATATATAATAATAAA
Found at i:448666 original size:15 final size:15
Alignment explanation
Indices: 448648--448729 Score: 53
Period size: 16 Copynumber: 5.3 Consensus size: 15
448638 AGTCAAAGGA
448648 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
** *
448663 AAAAAGGAAATCAA-
1 AAAAATAAAATAAAT
*
448677 AGAAATCGAAAA-AAAT
1 AAAAAT--AAAATAAAT
*
448693 AAAAAAATAAATAAA-
1 AAAAATA-AAATAAAT
448708 ATAAAATAAAATAAAAT
1 A-AAAATAAAAT-AAAT
448725 AAAAA
1 AAAAA
448730 ATAATTAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 15
0.66 0.14 0.20
Matches are distributed among these distances:
14 5 0.10
15 21 0.43
16 22 0.45
17 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:448709 original size:5 final size:5
Alignment explanation
Indices: 448688--448741 Score: 62
Period size: 5 Copynumber: 11.4 Consensus size: 5
448678 GAAATCGAAA
448688 AAAAT -AAA- AAAAT -AAAT AAAAT AAAAT AAAAT AAAAT AAAA- AATAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT
*
448735 TAAAT AA
1 AAAAT AA
448742 TATTAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 12 0.29
5 29 0.69
6 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:448768 original size:19 final size:20
Alignment explanation
Indices: 448686--448751 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
448676 AAGAAATCGA
**
448686 AAAAAATAAAAAAATAA-AT
1 AAAAAATAATTAAATAATAT
* *
448705 AAAATAA-AATAAAATAAAAT
1 AAAA-AATAATTAAATAATAT
448725 AAAAAATAATTAAATAATAT
1 AAAAAATAATTAAATAATAT
*
448745 TAAAAAT
1 AAAAAAT
448752 GTTAAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 15 0.38
20 25 0.62
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAAATAATTAAATAATAT
Found at i:454627 original size:18 final size:18
Alignment explanation
Indices: 454579--454628 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
454569 TTATATATAT
454579 AATAATT-TT-TAAAATA
1 AATAATTATTATAAAATA
*
454595 AAT-ATAATTAGTAAAATA
1 AATAATTATTA-TAAAATA
454613 AATAATTATTATAAAA
1 AATAATTATTATAAAA
454629 ATTAAATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 2 0.07
16 5 0.18
18 15 0.54
19 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AATAATTATTATAAAATA
Found at i:457244 original size:21 final size:21
Alignment explanation
Indices: 457220--457261 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
457210 GAAGAATTTG
457220 AGGCCTTGGATTTGTCCTTTT
1 AGGCCTTGGATTTGTCCTTTT
457241 AGGCCTTGGATTTGTCCTTTT
1 AGGCCTTGGATTTGTCCTTTT
457262 GATTATTTTT
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:0.10, C:0.19, G:0.24, T:0.48
Consensus pattern (21 bp):
AGGCCTTGGATTTGTCCTTTT
Found at i:461059 original size:20 final size:20
Alignment explanation
Indices: 461012--461052 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
461002 TTCACAAGAG
461012 ATTTTAATTTATTGTAATAT
1 ATTTTAATTTATTGTAATAT
461032 ATTTTAATTTATT-TAA-AT
1 ATTTTAATTTATTGTAATAT
461050 ATT
1 ATT
461053 AATTAATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTAATTTATTGTAATAT
Found at i:463301 original size:32 final size:32
Alignment explanation
Indices: 463260--463323 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
463250 TCCCTTTCAC
*
463260 TTATGAATATCACAACTGTTCTTCAAGGTATT
1 TTATGAATATCACAACTATTCTTCAAGGTATT
463292 TTATGAATATCACAACTATTCTTCAAGGTATT
1 TTATGAATATCACAACTATTCTTCAAGGTATT
463324 GAAGCGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (32 bp):
TTATGAATATCACAACTATTCTTCAAGGTATT
Found at i:467741 original size:18 final size:18
Alignment explanation
Indices: 467715--467749 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
467705 AAATACTATA
*
467715 ATTATCATATAAAAATAT
1 ATTAACATATAAAAATAT
467733 ATTAACATATAAAAATA
1 ATTAACATATAAAAATA
467750 ACTAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTAACATATAAAAATAT
Found at i:469335 original size:32 final size:30
Alignment explanation
Indices: 469290--469348 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
469280 TCTAAACCTT
*
469290 ATTTCTATGCATCTTCAACCAATTCCATATCA
1 ATTTCAATGCATCTTCAACC--TTCCATATCA
* *
469322 ATTTCAATTCATCTTTAACCTTCCATA
1 ATTTCAATGCATCTTCAACCTTCCATA
469349 AAAACCCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.29
32 17 0.71
ACGTcount: A:0.31, C:0.27, G:0.02, T:0.41
Consensus pattern (30 bp):
ATTTCAATGCATCTTCAACCTTCCATATCA
Found at i:476416 original size:20 final size:21
Alignment explanation
Indices: 476357--476415 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
476347 ATTATAGGAA
*
476357 TTCATGGCCTCGACAAAAGAT
1 TTCATGGCCTCAACAAAAGAT
476378 TTCATGGCCTCAACAAAAGA-
1 TTCATGGCCTCAACAAAAGAT
*
476398 TTCAATGGCTTCAACAAA
1 TTC-ATGGCCTCAACAAA
476416 GTTCCTGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 3 0.09
21 32 0.91
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (21 bp):
TTCATGGCCTCAACAAAAGAT
Found at i:480880 original size:18 final size:16
Alignment explanation
Indices: 480859--480901 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
480849 ATGTTATGCA
480859 TTATTTACTTGTTTTACT
1 TTATTTA-TTGTTTT-CT
480877 TTA-TT-TTGTTTTCT
1 TTATTTATTGTTTTCT
480891 TTATTTATTGT
1 TTATTTATTGT
480902 AGGCATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 4 0.17
17 2 0.09
18 3 0.13
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (16 bp):
TTATTTATTGTTTTCT
Found at i:480892 original size:14 final size:15
Alignment explanation
Indices: 480867--480896 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
480857 CATTATTTAC
480867 TTGTTTTACTTTATT
1 TTGTTTTACTTTATT
480882 TTGTTTT-CTTTATT
1 TTGTTTTACTTTATT
480896 T
1 T
480897 ATTGTAGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.77
Consensus pattern (15 bp):
TTGTTTTACTTTATT
Found at i:486862 original size:17 final size:17
Alignment explanation
Indices: 486840--486877 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
486830 TCTAAAGGAA
486840 GAAGGGAATGGGCCCAT
1 GAAGGGAATGGGCCCAT
486857 GAAGGGAATGGGCCCAT
1 GAAGGGAATGGGCCCAT
486874 GAAG
1 GAAG
486878 TCAATGCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.42, T:0.11
Consensus pattern (17 bp):
GAAGGGAATGGGCCCAT
Found at i:486883 original size:17 final size:17
Alignment explanation
Indices: 486840--486883 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
486830 TCTAAAGGAA
*
486840 GAAGGGAATGGGCCCAT
1 GAAGGCAATGGGCCCAT
*
486857 GAAGGGAATGGGCCCAT
1 GAAGGCAATGGGCCCAT
*
486874 GAAGTCAATG
1 GAAGGCAATG
486884 CCCCATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.39, T:0.14
Consensus pattern (17 bp):
GAAGGCAATGGGCCCAT
Found at i:496371 original size:2 final size:2
Alignment explanation
Indices: 496364--496418 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
496354 AAGGTAAAAT
496364 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
496406 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
496419 TGGAAGAAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:498253 original size:32 final size:30
Alignment explanation
Indices: 498206--498295 Score: 99
Period size: 32 Copynumber: 2.9 Consensus size: 30
498196 TATAAGATAT
*
498206 AATTATTTTTAATATTTACTATTAGGGGTTC
1 AATT-TTTTTAATATTTATTATTAGGGGTTC
* * *
498237 AATATTTTTCTAATATTTATTATTATGAGTTT
1 AAT-TTTTT-TAATATTTATTATTAGGGGTTC
*
498269 AGTTTTTTTTAATATTTATTATTAGGG
1 A-ATTTTTTTAATATTTATTATTAGGG
498296 ATATACTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
31 23 0.47
32 25 0.51
33 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
AATTTTTTTAATATTTATTATTAGGGGTTC
Found at i:500176 original size:13 final size:13
Alignment explanation
Indices: 500157--500207 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
500147 TTTCATTGAA
500157 AAACCGAAAAACC
1 AAACCGAAAAACC
*
500170 GAACCGAAAAACC
1 AAACCGAAAAACC
500183 AAACCGTTTAAAAAACC
1 AAACCG----AAAAACC
500200 AAACCGAA
1 AAACCGAA
500208 CCGAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 19 0.59
17 13 0.41
ACGTcount: A:0.57, C:0.27, G:0.10, T:0.06
Consensus pattern (13 bp):
AAACCGAAAAACC
Found at i:522164 original size:21 final size:21
Alignment explanation
Indices: 522138--522194 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
522128 GATTTCTATG
522138 TGGTCCTTCGGGACATATATA
1 TGGTCCTTCGGGACATATATA
*
522159 TGGTCCTTCGGGACATATATG
1 TGGTCCTTCGGGACATATATA
* *
522180 TGATTCTTCGGGACA
1 TGGTCCTTCGGGACA
522195 AATTTTATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
TGGTCCTTCGGGACATATATA
Found at i:523808 original size:34 final size:34
Alignment explanation
Indices: 523765--523849 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
523755 TAGGAGATTG
* * * *
523765 CTTAATGTTCGAGAGAATGACTACGTAGCATCTC
1 CTTAGTGTTCGAGAGAATGAATAAGTAGCATATC
523799 CTTAGTGTTCGAGAGAATGAATAAGTAGCATATC
1 CTTAGTGTTCGAGAGAATGAATAAGTAGCATATC
523833 CTTAGTGTTCGAGAGAA
1 CTTAGTGTTCGAGAGAA
523850 ACTAGGGAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (34 bp):
CTTAGTGTTCGAGAGAATGAATAAGTAGCATATC
Found at i:526777 original size:46 final size:46
Alignment explanation
Indices: 526705--526821 Score: 189
Period size: 46 Copynumber: 2.5 Consensus size: 46
526695 AACCGAATAT
* * *
526705 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
1 ATAAATAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCA
*
526751 ATAAATAAAATTCATGAAAGGATGCATTAAGGAATGAAAGGATGCA
1 ATAAATAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCA
*
526797 ATAAATAAAGTGCATGAAAGGATGC
1 ATAAATAAAATGCATGAAAGGATGC
526822 CATAAATAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.21
Consensus pattern (46 bp):
ATAAATAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCA
Found at i:526821 original size:72 final size:72
Alignment explanation
Indices: 526736--526893 Score: 262
Period size: 72 Copynumber: 2.2 Consensus size: 72
526726 ATGCATTAAG
* *
526736 GCATGAAAGGATGCCATAAATAAAATTCATGAAAGGATGCATTAAGGAATGAAAGGATGCAATAA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGAATTAAGGAATGAAAGGATGCAATAA
*
526801 ATAAAGT
66 ATAAAAT
* *
526808 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGAATTAAGGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGAATTAAGGAATGAAAGGATGCAATAA
526873 ATAAAAT
66 ATAAAAT
*
526880 GCATGAAATGATGC
1 GCATGAAAGGATGC
526894 ATTAAGGCAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 80 1.00
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.20
Consensus pattern (72 bp):
GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGAATTAAGGAATGAAAGGATGCAATAA
ATAAAAT
Found at i:526858 original size:46 final size:46
Alignment explanation
Indices: 526808--526926 Score: 220
Period size: 46 Copynumber: 2.6 Consensus size: 46
526798 TAAATAAAGT
526808 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGAATTAAG
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGAATTAAG
* *
526854 GCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGAATTAAG
526900 GCATGAAAGGATGCCATAAATAAAATG
1 GCATGAAAGGATGCCATAAATAAAATG
526927 AAATTTAAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGAATTAAG
Found at i:526919 original size:118 final size:118
Alignment explanation
Indices: 526705--526923 Score: 384
Period size: 118 Copynumber: 1.9 Consensus size: 118
526695 AACCGAATAT
* * *
526705 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATTCATGAAA
1 ATAAATAAAATGCATGAAAGGATGAATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAA
526770 GGATGCATTAAGGAATGAAAGGATGCAATAAATAAAGTGCATGAAAGGATGCC
66 GGATGCATTAAGGAATGAAAGGATGCAATAAATAAAGTGCATGAAAGGATGCC
526823 ATAAATAAAATGCATGAAAGGATGAATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAA
1 ATAAATAAAATGCATGAAAGGATGAATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAA
* * *
526888 TGATGCATTAAGGCATGAAAGGATGCCATAAATAAA
66 GGATGCATTAAGGAATGAAAGGATGCAATAAATAAA
526924 ATGAAATTTA
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 95 1.00
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.21
Consensus pattern (118 bp):
ATAAATAAAATGCATGAAAGGATGAATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAA
GGATGCATTAAGGAATGAAAGGATGCAATAAATAAAGTGCATGAAAGGATGCC
Found at i:527407 original size:2 final size:2
Alignment explanation
Indices: 527400--527438 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
527390 TGAAAGGATG
527400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
527439 ATGTACATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:535555 original size:41 final size:39
Alignment explanation
Indices: 535490--535566 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
535480 TCACTTCACC
* * *
535490 GAAAGTGGGGGGCTTTAGTCAGAAATAAGACAAAAAGAG
1 GAAAGTGGGGGACTTTAGTCAGAAAAAAAACAAAAAGAG
*
535529 GAAAGTGGGAGAGACTTTAGTTAGAAAAAAAACAAAAA
1 GAAAGTGGG-G-GACTTTAGTCAGAAAAAAAACAAAAA
535567 AATGGGTCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 9 0.28
40 1 0.03
41 22 0.69
ACGTcount: A:0.49, C:0.06, G:0.29, T:0.16
Consensus pattern (39 bp):
GAAAGTGGGGGACTTTAGTCAGAAAAAAAACAAAAAGAG
Found at i:535682 original size:24 final size:23
Alignment explanation
Indices: 535636--535683 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
535626 ACAAGGTTTT
* **
535636 AAAAAATAATATAATAATGAATA
1 AAAAAATAAAATAATAAAAAATA
535659 AAAAAATGAAAATAATAAAAAATA
1 AAAAAAT-AAAATAATAAAAAATA
535683 A
1 A
535684 TATATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (23 bp):
AAAAAATAAAATAATAAAAAATA
Done.