Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 44 of 310
Found at i:12964052 original size:22 final size:23
Alignment explanation
Indices: 12964010--12964057 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
12964000 AAATTTTAAA
*
12964010 AAAAAAATCATAAAAGCAAATAT
1 AAAAAAATCATAAAAGAAAATAT
12964033 AAAAAAAT-A-AAAATGAAAATAT
1 AAAAAAATCATAAAA-GAAAATAT
12964055 AAA
1 AAA
12964058 CCTTCATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 11 0.48
23 8 0.35
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (23 bp):
AAAAAAATCATAAAAGAAAATAT
Found at i:12964290 original size:21 final size:23
Alignment explanation
Indices: 12964266--12964308 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
12964256 TCATATATTG
12964266 ATATGTTT-TAT-GTATATTTTA
1 ATATGTTTATATAGTATATTTTA
*
12964287 ATATGTTTATATATTATATTTT
1 ATATGTTTATATAGTATATTTT
12964309 TATTTATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (23 bp):
ATATGTTTATATAGTATATTTTA
Found at i:12964392 original size:13 final size:13
Alignment explanation
Indices: 12964360--12964384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12964350 ATGTAAGTTT
12964360 ATTTATTAATTAA
1 ATTTATTAATTAA
12964373 ATTTATTAATTA
1 ATTTATTAATTA
12964385 TTCTTATTTC
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTATTAATTAA
Found at i:12978827 original size:265 final size:265
Alignment explanation
Indices: 12978354--12978882 Score: 1031
Period size: 265 Copynumber: 2.0 Consensus size: 265
12978344 TAGTGAATTT
12978354 TCAAACTCACATCACTGCTGCTGTCAGCATCTATTTTAAGGTAAATTTCACCTATTTCATAGTTT
1 TCAAACTCACATCACTGCTGCTGTCAGCATCTATTTTAAGGTAAATTTCACCTATTTCATAGTTT
12978419 CCATGATTCAACTAGCCATTTGACATACATAGCACCAAATATGATAGTGATTAACCATTCCAACG
66 CCATGATTCAACTAGCCATTTGACATACATAGCACCAAATATGATAGTGATTAACCATTCCAACG
12978484 GCTAATCATTGCCAAGCATTTCCACACCTCTCAATAACCATATATATATACAAAATGATTTTAAT
131 GCTAATCATTGCCAAGCATTTCCACACCTCTCAATAACCATATATATATACAAAATGATTTTAAT
* *
12978549 ACTATGCTCAAAATATTTAAGCCATTTTCGCTTGGCTATCCAAATATTTACACATTACCAAAGGT
196 ACTATGCTCAAAATATTTAAGCCATTTTCGCATGGCTATCCAAATATATACACATTACCAAAGGT
12978614 ACTTC
261 ACTTC
12978619 TCAAACTCACATCACTGCTGCTGTCAGCATCTATTTTAAGGTAAATTTCACCTATTTCATAGTTT
1 TCAAACTCACATCACTGCTGCTGTCAGCATCTATTTTAAGGTAAATTTCACCTATTTCATAGTTT
12978684 CCATGATTCAACTAGCCATTTGACATACATAGCACCAAATATGATAGTGATTAACCATTCCAACG
66 CCATGATTCAACTAGCCATTTGACATACATAGCACCAAATATGATAGTGATTAACCATTCCAACG
12978749 GCTAATCATTGCCAAGCATTTCCACACCTCTCAATAACCATATATATATACAAAATGATTTTAAT
131 GCTAATCATTGCCAAGCATTTCCACACCTCTCAATAACCATATATATATACAAAATGATTTTAAT
*
12978814 ACTATGCTCAAAATATTTAAGCCATTTTCGCATGGCTATCCAAATATATACACATTATCAAAGGT
196 ACTATGCTCAAAATATTTAAGCCATTTTCGCATGGCTATCCAAATATATACACATTACCAAAGGT
12978879 ACTT
261 ACTT
12978883 GATTAACAAC
Statistics
Matches: 261, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
265 261 1.00
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (265 bp):
TCAAACTCACATCACTGCTGCTGTCAGCATCTATTTTAAGGTAAATTTCACCTATTTCATAGTTT
CCATGATTCAACTAGCCATTTGACATACATAGCACCAAATATGATAGTGATTAACCATTCCAACG
GCTAATCATTGCCAAGCATTTCCACACCTCTCAATAACCATATATATATACAAAATGATTTTAAT
ACTATGCTCAAAATATTTAAGCCATTTTCGCATGGCTATCCAAATATATACACATTACCAAAGGT
ACTTC
Found at i:12980413 original size:248 final size:248
Alignment explanation
Indices: 12979975--12980469 Score: 981
Period size: 248 Copynumber: 2.0 Consensus size: 248
12979965 ATAGCATGGC
12979975 CGGCCACCATCTTCATTTTTTGGTTAATTTGACATGCAAACCCATCATTTTTATAACATGCATCA
1 CGGCCACCATCTTCATTTTTTGGTTAATTTGACATGCAAACCCATCATTTTTATAACATGCATCA
12980040 ATAGGCCACTTTAACATTTTCCTAGCACATTTCTAAATTTTCTCACACAAGTCCTATTTAATAAA
66 ATAGGCCACTTTAACATTTTCCTAGCACATTTCTAAATTTTCTCACACAAGTCCTATTTAATAAA
12980105 ATTCACTTACAATTAACAAAATTCAAACATGAAATTTTCACACATGCATATATACATATAATAAG
131 ATTCACTTACAATTAACAAAATTCAAACATGAAATTTTCACACATGCATATATACATATAATAAG
12980170 CATCAAATATGATGGTTAATTATTTTTATGACTCGATTTTGTGGTCCCGTAAT
196 CATCAAATATGATGGTTAATTATTTTTATGACTCGATTTTGTGGTCCCGTAAT
*
12980223 CGGCCACCATCTTGATTTTTTGGTTAATTTGACATGCAAACCCATCATTTTTATAACATGCATCA
1 CGGCCACCATCTTCATTTTTTGGTTAATTTGACATGCAAACCCATCATTTTTATAACATGCATCA
12980288 ATAGGCCACTTTAACATTTTCCTAGCACATTTCTAAATTTTCTCACACAAGTCCTATTTAATAAA
66 ATAGGCCACTTTAACATTTTCCTAGCACATTTCTAAATTTTCTCACACAAGTCCTATTTAATAAA
12980353 ATTCACTTACAATTAACAAAATTCAAACATGAAATTTTCACACATGCATATATACATATAATAAG
131 ATTCACTTACAATTAACAAAATTCAAACATGAAATTTTCACACATGCATATATACATATAATAAG
12980418 CATCAAATATGATGGTTAATTATTTTTATGACTCGATTTTGTGGTCCCGTAA
196 CATCAAATATGATGGTTAATTATTTTTATGACTCGATTTTGTGGTCCCGTAA
12980470 CCACTTTCCG
Statistics
Matches: 246, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
248 246 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (248 bp):
CGGCCACCATCTTCATTTTTTGGTTAATTTGACATGCAAACCCATCATTTTTATAACATGCATCA
ATAGGCCACTTTAACATTTTCCTAGCACATTTCTAAATTTTCTCACACAAGTCCTATTTAATAAA
ATTCACTTACAATTAACAAAATTCAAACATGAAATTTTCACACATGCATATATACATATAATAAG
CATCAAATATGATGGTTAATTATTTTTATGACTCGATTTTGTGGTCCCGTAAT
Found at i:13000051 original size:27 final size:27
Alignment explanation
Indices: 13000021--13000198 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
13000011 ATATTGAGTC
* * * *
13000021 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
13000048 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
13000075 CGCACACTTAGTGCTACATAGTCAATCT
1 CGCACACTTAGTGCTACATAGTCAA-AT
** * *
13000103 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
13000130 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
13000157 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
13000184 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
13000199 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:13000160 original size:82 final size:81
Alignment explanation
Indices: 13000042--13000197 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
13000032 TGCTATATAA
* * *
13000042 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAATCTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAA-ATCGCA
13000107 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
13000124 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
13000188 CACTTAGTGC
65 CACTTAGTGC
13000198 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:13002985 original size:21 final size:21
Alignment explanation
Indices: 13002959--13003012 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
13002949 TAACAGTGGT
*
13002959 AGTGAGATTAGTTATTGCAGC
1 AGTGAGATTAGATATTGCAGC
* *
13002980 -GATGAGATTGGATATTGTAGC
1 AG-TGAGATTAGATATTGCAGC
13003001 AGTGAGATTAGA
1 AGTGAGATTAGA
13003013 AATAGCAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (21 bp):
AGTGAGATTAGATATTGCAGC
Found at i:13008338 original size:48 final size:48
Alignment explanation
Indices: 13008165--13008388 Score: 185
Period size: 49 Copynumber: 4.7 Consensus size: 48
13008155 TAGGGTATAA
* * * *
13008165 TGCCGATGCTATGTCCCAGACATGGTCTTACACTGACTA--TCGAAATTG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAAC-ACCTCCATA-TG
* * ** * *
13008213 AGGCCAACACCATGTCCCAGACATGGTCTTACACTAGC-TCTCCATATCAG
1 -TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACCTCCATAT--G
* *
13008263 TGTCGATGCCATGTCCCATACATGGTCTTACACTAACACCTCCATATG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACCTCCATATG
* * * *
13008311 TGCCGATGCCATGTCCCAGACACGGTCTTACATTGACACAT-C-TA-G
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACCTCCATATG
*
13008356 TAGCCGATG-CATGTCCCAAACAT-GTCTTACACT
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACT
13008389 GGCTTACATC
Statistics
Matches: 143, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
44 9 0.06
45 14 0.10
46 9 0.06
47 1 0.01
48 37 0.26
49 64 0.45
50 9 0.06
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (48 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACCTCCATATG
Found at i:13008398 original size:46 final size:47
Alignment explanation
Indices: 13008312--13008524 Score: 147
Period size: 46 Copynumber: 4.6 Consensus size: 47
13008302 CTCCATATGT
* * *
13008312 GCCGATGCCATGTCCCAGACACGGTCTTACATTGAC--ACATCTA-GTA
1 GCCGATG-CATGTCCCAGACA-TGTCTTACACTGGCTTACATCTACGTA
*
13008358 GCCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATC-ACG-A
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTACGTA
* * * *
13008403 GGCCGATGCATGTCCCACACATGTCTTACACTAGCTCTA-GTCT-C-AA
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCT-TACATCTACGTA
* * ** * * *
13008449 TGCCGATGCCATGTCCCAGACATGGTTTTACACGGGCTCGCAT-AATGTG
1 -GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTACGTA
* *
13008498 GCCGATGCATGTCCCAGGCTTGTCTTA
1 GCCGATGCATGTCCCAGACATGTCTTA
13008525 TACTAGCACA
Statistics
Matches: 133, Mismatches: 22, Indels: 24
0.74 0.12 0.13
Matches are distributed among these distances:
44 11 0.08
45 14 0.11
46 62 0.47
47 27 0.20
48 19 0.14
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTACGTA
Found at i:13008504 original size:94 final size:92
Alignment explanation
Indices: 13008358--13008531 Score: 222
Period size: 94 Copynumber: 1.9 Consensus size: 92
13008348 ACATCTAGTA
* * *
13008358 GCCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATCACGAGGCCGATGCATGTCCCACAC
1 GCCGATGCATGTCCCAAACATGTCTTACACGGGCTCACATAACGAGGCCGATGCATGTCCCACAC
13008423 ATGTCTTACACTAGCTCTAGTCTCAAT
66 ATGTCTTACACTAGCTCTAGTCTCAAT
* * * * * *
13008450 GCCGATGCCATGTCCCAGACATGGTTTTACACGGGCTCGCATAATGTGGCCGATGCATGTCCCAG
1 GCCGATG-CATGTCCCAAACAT-GTCTTACACGGGCTCACATAACGAGGCCGATGCATGTCCCAC
* * *
13008515 GCTTGTCTTATACTAGC
64 ACATGTCTTACACTAGC
13008532 ACATAAATGT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 7 0.10
93 13 0.19
94 48 0.71
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (92 bp):
GCCGATGCATGTCCCAAACATGTCTTACACGGGCTCACATAACGAGGCCGATGCATGTCCCACAC
ATGTCTTACACTAGCTCTAGTCTCAAT
Found at i:13017113 original size:23 final size:23
Alignment explanation
Indices: 13017083--13017141 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
13017073 ATATGGGTAG
13017083 TCCACACGGGCCAGGCCGTGTGA
1 TCCACACGGGCCAGGCCGTGTGA
13017106 TCCACACGGGCCAGGCCGTGTGA
1 TCCACACGGGCCAGGCCGTGTGA
13017129 TCCACACGGGCCA
1 TCCACACGGGCCA
13017142 AAGCCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.37, G:0.32, T:0.12
Consensus pattern (23 bp):
TCCACACGGGCCAGGCCGTGTGA
Found at i:13020162 original size:18 final size:18
Alignment explanation
Indices: 13020141--13020181 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
13020131 ATTTTCTTAA
*
13020141 AATTTAACATTTTTATAT
1 AATTTAACAATTTTATAT
* *
13020159 AATTTTATAATTTTATAT
1 AATTTAACAATTTTATAT
13020177 AATTT
1 AATTT
13020182 TATTTTATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTAACAATTTTATAT
Found at i:13020166 original size:10 final size:10
Alignment explanation
Indices: 13020151--13020184 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
13020141 AATTTAACAT
13020151 TTTTATATAA
1 TTTTATATAA
13020161 -TTT-TATAA
1 TTTTATATAA
13020169 TTTTATATAA
1 TTTTATATAA
13020179 TTTTAT
1 TTTTAT
13020185 TTTATGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.23
9 6 0.27
10 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATATAA
Found at i:13020229 original size:21 final size:21
Alignment explanation
Indices: 13020183--13020223 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
13020173 ATATAATTTT
*
13020183 ATTTTATGAATTTTTTATAAA
1 ATTTTATGAATTTTTAATAAA
13020204 ATTTTAT-AATTTTTAATAAA
1 ATTTTATGAATTTTTAATAAA
13020224 CGTTTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTATGAATTTTTAATAAA
Found at i:13021433 original size:17 final size:17
Alignment explanation
Indices: 13021413--13021456 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
13021403 AATATTTATG
*
13021413 TGAAAGTAATTTTCAAA
1 TGAAAGTAAATTTCAAA
*
13021430 TGAAAATTAAATTTCAAA
1 TG-AAAGTAAATTTCAAA
13021448 -GAAAGTAAA
1 TGAAAGTAAA
13021457 AAATTTTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 7 0.30
17 3 0.13
18 13 0.57
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (17 bp):
TGAAAGTAAATTTCAAA
Found at i:13022717 original size:24 final size:25
Alignment explanation
Indices: 13022670--13022717 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
13022660 CCAAAACATA
13022670 GTTAAGATTGAAAAATAAAAAAAGG
1 GTTAAGATTGAAAAATAAAAAAAGG
13022695 GTTAAGATTGAAAAA-AAAAAAAG
1 GTTAAGATTGAAAAATAAAAAAAG
13022718 AAAGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (25 bp):
GTTAAGATTGAAAAATAAAAAAAGG
Found at i:13029740 original size:42 final size:42
Alignment explanation
Indices: 13029651--13029806 Score: 145
Period size: 42 Copynumber: 3.7 Consensus size: 42
13029641 CCGAGGCTAT
* * * *
13029651 ATGTAAGACCATATCTGGGATATGGCATTATTATAAGACTTT-
1 ATGTAAGACCATATCTAGGATATGACATTAATATGAGA-TTTC
* * *
13029693 GTGTAAGACCATATCTAGGATATGAAATCAATATGAGATTTC
1 ATGTAAGACCATATCTAGGATATGACATTAATATGAGATTTC
* * * * * **
13029735 ATGTAAGACCATAGT-TGGGCTATTGGCATTGATACGAGATCCC
1 ATGTAAGACCATA-TCTAGGATA-TGACATTAATATGAGATTTC
13029778 ATGTAAGACCATATCTAGGATATGACATT
1 ATGTAAGACCATATCTAGGATATGACATT
13029807 GGTGTAGTAC
Statistics
Matches: 90, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
41 3 0.03
42 55 0.61
43 32 0.36
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (42 bp):
ATGTAAGACCATATCTAGGATATGACATTAATATGAGATTTC
Found at i:13041421 original size:21 final size:20
Alignment explanation
Indices: 13041397--13041436 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13041387 ACTTGTTTAA
13041397 CTATCAACAACCATTCAAAAT
1 CTATCAACAACCA-TCAAAAT
* *
13041418 CTATCATCAATCATCAAAA
1 CTATCAACAACCATCAAAA
13041437 ATCATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (20 bp):
CTATCAACAACCATCAAAAT
Found at i:13041839 original size:17 final size:16
Alignment explanation
Indices: 13041817--13041848 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
13041807 TAAGGTTCTA
13041817 TAGCTAATAGATACTTT
1 TAGCTAATAGA-ACTTT
13041834 TAGCTAATAGAACTT
1 TAGCTAATAGAACTT
13041849 CACTTTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
TAGCTAATAGAACTTT
Found at i:13046504 original size:6 final size:6
Alignment explanation
Indices: 13046493--13046530 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
13046483 ATTTTAAATT
13046493 TTCAAA TTCAAA TTCAAA TTCAAA TTCAAA TTCAAA TT
1 TTCAAA TTCAAA TTCAAA TTCAAA TTCAAA TTCAAA TT
13046531 TTTGACTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (6 bp):
TTCAAA
Found at i:13048613 original size:33 final size:33
Alignment explanation
Indices: 13048550--13048613 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
13048540 ATTTTTTAAG
* *
13048550 AAAATAAAATATTCATTTTCAATATGATATTGT
1 AAAATAAAATATTAATTTTCAATATAATATTGT
13048583 AAAATAAAATATTAAGTATTT-AA-ATAATATT
1 AAAATAAAATATTAA-T-TTTCAATATAATATT
13048614 TACATATACC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 21 0.78
34 3 0.11
35 3 0.11
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (33 bp):
AAAATAAAATATTAATTTTCAATATAATATTGT
Found at i:13048648 original size:27 final size:27
Alignment explanation
Indices: 13048617--13048676 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
13048607 TAATATTTAC
*
13048617 ATATACCAACTTAATTTTTAATAAAAA
1 ATATAACAACTTAATTTTTAATAAAAA
13048644 ATATAACAACTTAATTTTTAATAAAAA
1 ATATAACAACTTAATTTTTAATAAAAA
13048671 ATATAA
1 ATATAA
13048677 GAACACTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATAACAACTTAATTTTTAATAAAAA
Found at i:13059642 original size:18 final size:18
Alignment explanation
Indices: 13059619--13059655 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13059609 ATAGACTAAT
13059619 TAGAATTCATTCTAATAA
1 TAGAATTCATTCTAATAA
13059637 TAGAATTCATTCTAATAA
1 TAGAATTCATTCTAATAA
13059655 T
1 T
13059656 GATATAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (18 bp):
TAGAATTCATTCTAATAA
Found at i:13062667 original size:59 final size:59
Alignment explanation
Indices: 13062601--13062735 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 59
13062591 AACTATGTTA
*
13062601 ATATGGGCAAGGCCCAATATA-TCTCGACTTGTATA-GGGCTACGGCCCAGATTGATACTG
1 ATATGGGCAAGGCCCAATATACTCTCGA-TTGTA-AGGGGCTACGGCCCAGATTAATACTG
* * ** *
13062660 ATATGGGCTAGGCCCAGTATACTCTTTATTGTAAGGGGCTACGGCCCAGATTAATATTG
1 ATATGGGCAAGGCCCAATATACTCTCGATTGTAAGGGGCTACGGCCCAGATTAATACTG
13062719 ATATGGGCTAAGGCCCA
1 ATATGGGC-AAGGCCCA
13062736 GTTAACACTG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.02
59 54 0.82
60 11 0.17
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (59 bp):
ATATGGGCAAGGCCCAATATACTCTCGATTGTAAGGGGCTACGGCCCAGATTAATACTG
Found at i:13062726 original size:28 final size:28
Alignment explanation
Indices: 13062636--13062740 Score: 90
Period size: 28 Copynumber: 3.7 Consensus size: 28
13062626 GACTTGTATA
* *
13062636 GGGCTACGGCCCAGATTGATACTGATAT
1 GGGCTACGGCCCAGATTAATATTGATAT
** *
13062664 GGGCTA-GGCCCAGTATACTCTTTATTG-TAAG
1 GGGCTACGGCCCAG-AT--T-AATATTGAT-AT
13062695 GGGCTACGGCCCAGATTAATATTGATAT
1 GGGCTACGGCCCAGATTAATATTGATAT
*
13062723 GGGCTAAGGCCCAG-TTAA
1 GGGCTACGGCCCAGATTAA
13062741 CACTGATTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
27 11 0.18
28 27 0.44
29 2 0.03
30 2 0.03
31 13 0.21
32 7 0.11
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (28 bp):
GGGCTACGGCCCAGATTAATATTGATAT
Found at i:13063446 original size:14 final size:14
Alignment explanation
Indices: 13063427--13063453 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13063417 AACATGGATT
13063427 TTAAATAAAAATTG
1 TTAAATAAAAATTG
13063441 TTAAATAAAAATT
1 TTAAATAAAAATT
13063454 ATAAAACCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
TTAAATAAAAATTG
Found at i:13067319 original size:13 final size:13
Alignment explanation
Indices: 13067301--13067334 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
13067291 GGGACACACG
13067301 CCCGTGTGACCTT
1 CCCGTGTGACCTT
13067314 CCCGTGTGACCTT
1 CCCGTGTGACCTT
*
13067327 CCCATGTG
1 CCCGTGTG
13067335 CTTCACATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.38, G:0.24, T:0.29
Consensus pattern (13 bp):
CCCGTGTGACCTT
Found at i:13077550 original size:51 final size:50
Alignment explanation
Indices: 13077381--13077908 Score: 396
Period size: 50 Copynumber: 10.6 Consensus size: 50
13077371 ATCTGATACG
* * * **
13077381 CATAGTAGCCTGCACTTAGTACTACCCATGCGATCGACA--ATCCAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATC-ACATGATTGAGTACA
* * * * *
13077430 CGTAGTAGCCTGCACTGAGTACTACACACGTGACCTCATCATCTGA-TACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATCACATGAT-TGAGTACA
* * * * * **
13077480 CATAGTAGTCTGCAATTAGTACTACACCCGTGATCAAAGTGATTGAGGATG
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATCACA-TGATTGAGTACA
* * * **
13077531 CATAGTAGCCTGCACTTAGTACTACCCATGCGATCGACA--ATCCAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATC-ACATGATTGAGTACA
* * * * *
13077580 CGTAGTAGCCTGCACTGAGTACTACACACGTGACCTCATCATCTGA-TACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATCACATGAT-TGAGTACA
* * * * * **
13077630 CATAGTAGTCTGCAATTAGTACTACACCCGTGATCAAAGTGATTGAGGATG
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATCACA-TGATTGAGTACA
* * **
13077681 CATAGTAGCCTGCACTTAGTACTACACATGCGATCGACA--ATCCAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATC-ACATGATTGAGTACA
* * * *
13077730 CGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCATCATCTGA-TACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATCACATGAT-TGAGTACA
* * * **
13077780 CATAGTAGTCTGCAATTAGTACTACACACGTGATCAAAGTGATTGAGTATG
1 CATAGTAGCCTGCACTTAGTACTACACACGTGATCACA-TGATTGAGTACA
* * *
13077831 CATAGTAGCCTGCACTTAGTACTACACATGCGACTTAACA-G-TATGA-TACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGA--TCACATGAT-TGAGTACA
* *
13077881 CGTAGTAGCCTACACTTAGTACTACACA
1 CATAGTAGCCTGCACTTAGTACTACACA
13077909 TGTGTATTCA
Statistics
Matches: 368, Mismatches: 91, Indels: 39
0.74 0.18 0.08
Matches are distributed among these distances:
48 6 0.02
49 99 0.27
50 148 0.40
51 108 0.29
52 4 0.01
53 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACACGTGATCACATGATTGAGTACA
Found at i:13077651 original size:150 final size:150
Alignment explanation
Indices: 13077380--13077908 Score: 927
Period size: 150 Copynumber: 3.5 Consensus size: 150
13077370 TATCTGATAC
*
13077380 GCATAGTAGCCTGCACTTAGTACTACCCATGCGATCGACAATCCAGTACACGTAGTAGCCTGCAC
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGATCGACAATCCAGTACACGTAGTAGCCTGCAC
13077445 TGAGTACTACACACGTGACCTCATCATCTGATACACATAGTAGTCTGCAATTAGTACTACACCCG
66 TGAGTACTACACACGTGACCTCATCATCTGATACACATAGTAGTCTGCAATTAGTACTACACCCG
13077510 TGATCAAAGTGATTGAGGAT
131 TGATCAAAGTGATTGAGGAT
*
13077530 GCATAGTAGCCTGCACTTAGTACTACCCATGCGATCGACAATCCAGTACACGTAGTAGCCTGCAC
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGATCGACAATCCAGTACACGTAGTAGCCTGCAC
13077595 TGAGTACTACACACGTGACCTCATCATCTGATACACATAGTAGTCTGCAATTAGTACTACACCCG
66 TGAGTACTACACACGTGACCTCATCATCTGATACACATAGTAGTCTGCAATTAGTACTACACCCG
13077660 TGATCAAAGTGATTGAGGAT
131 TGATCAAAGTGATTGAGGAT
13077680 GCATAGTAGCCTGCACTTAGTACTACACATGCGATCGACAATCCAGTACACGTAGTAGCCTGCAC
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGATCGACAATCCAGTACACGTAGTAGCCTGCAC
* *
13077745 TTAGTACTACACACGTGACCTCATCATCTGATACACATAGTAGTCTGCAATTAGTACTACACACG
66 TGAGTACTACACACGTGACCTCATCATCTGATACACATAGTAGTCTGCAATTAGTACTACACCCG
*
13077810 TGATCAAAGTGATTGAGTAT
131 TGATCAAAGTGATTGAGGAT
** * *
13077830 GCATAGTAGCCTGCACTTAGTACTACACATGCGACTTAACAGT--ATGATACACGTAGTAGCCTA
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGA-TCGACAATCCA-G-TACACGTAGTAGCCTG
*
13077893 CACTTAGTACTACACA
63 CACTGAGTACTACACA
13077909 TGTGTATTCA
Statistics
Matches: 368, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
149 1 0.00
150 331 0.90
151 36 0.10
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.25
Consensus pattern (150 bp):
GCATAGTAGCCTGCACTTAGTACTACACATGCGATCGACAATCCAGTACACGTAGTAGCCTGCAC
TGAGTACTACACACGTGACCTCATCATCTGATACACATAGTAGTCTGCAATTAGTACTACACCCG
TGATCAAAGTGATTGAGGAT
Found at i:13077858 original size:101 final size:99
Alignment explanation
Indices: 13077371--13077908 Score: 430
Period size: 101 Copynumber: 5.4 Consensus size: 99
13077361 AGCCGAAGCT
* * * * * ** *
13077371 ATCTGATACGCATAGTAGCCTGCACTTAGTACTACCCATGCGATCGACA--ATCCAGTACACGTA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATC-AAATGATTGAGTACACATA
*
13077434 GTAGCCTGCACTGAGTACTACACACGTGACCTCATC
65 GTAGCCTGCACTTAGTACTACACACGTGA-CTCATC
* * * * **
13077470 ATCTGATACACATAGTAGTCTGCAATTAGTACTACACCCGTGATCAAAGTGATTGAGGATGCATA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAA-TGATTGAGTACACATA
* * *
13077535 GTAGCCTGCACTTAGTACTACCCATGCGA-TCGA-C
65 GTAGCCTGCACTTAGTACTACACACGTGACTC-ATC
* * * * ** *
13077569 AATC-CAGTACACGTAGTAGCCTGCACTGAGTACTACACACGTGACCTCATCATCTGA-TACACA
1 -ATCTGA-TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAATGAT-TGAGTACACA
* * * *
13077632 TAGTAGTCTGCAATTAGTACTACACCCGTGA-TCAAAGTG
63 TAGTAGCCTGCACTTAGTACTACACACGTGACTC--A-TC
* ** * * * ** *
13077671 AT-TGAGGATGCATAGTAGCCTGCACTTAGTACTACACATGCGATCGACA--ATCCAGTACACGT
1 ATCTGA-TACACATAGTAGCCTGCACTTAGTACTACACACGTGATC-AAATGATTGAGTACACAT
13077733 AGTAGCCTGCACTTAGTACTACACACGTGACCTCATC
64 AGTAGCCTGCACTTAGTACTACACACGTGA-CTCATC
* * **
13077770 ATCTGATACACATAGTAGTCTGCAATTAGTACTACACACGTGATCAAAGTGATTGAGTATGCATA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAA-TGATTGAGTACACATA
* * * *
13077835 GTAGCCTGCACTTAGTACTACACATGCGACTTAAC
65 GTAGCCTGCACTTAGTACTACACACGTGACTCATC
* * *
13077870 AGTATGATACACGTAGTAGCCTACACTTAGTACTACACA
1 A-TCTGATACACATAGTAGCCTGCACTTAGTACTACACA
13077909 TGTGTATTCA
Statistics
Matches: 341, Mismatches: 78, Indels: 38
0.75 0.17 0.08
Matches are distributed among these distances:
98 4 0.01
99 111 0.33
100 86 0.25
101 136 0.40
102 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (99 bp):
ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAATGATTGAGTACACATAG
TAGCCTGCACTTAGTACTACACACGTGACTCATC
Found at i:13085284 original size:50 final size:50
Alignment explanation
Indices: 13085168--13085447 Score: 264
Period size: 50 Copynumber: 5.6 Consensus size: 50
13085158 CTGATTCGCA
* * * ** *
13085168 TAGTAGCCTGCACTTAGTACTACCCACGTGA-TCGA-AGTCATTGAGTATGCC
1 TAGTAGCCTGCACTTAGTACTACACACGAGACTCAACAGT-A-TGA-TACACG
* * *
13085219 TAGTAGCCCGCACTTAGTACTACACATGAGACTTAACAGTATGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGAGACTCAACAGTATGATACACG
* * * *
13085269 TAGTAGCCTACACTTAGTACTACACACGTGACCTCATCA-TCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGAGA-CTCAACAGTATGATACACG
* * * ** *
13085319 TAGCAGCCTGCACTTAGTACTACACACGTGA-TCGA-AGTCATTGAGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACGAGACTCAACAGT-A-TGA-TACACG
* *
13085370 TAGTAGCCTGCACTTAGTACTACACATGAGACTTAACAGTATGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGAGACTCAACAGTATGATACACG
*
13085420 TAGTAGCCTACACTTAGTACTACACACG
1 TAGTAGCCTGCACTTAGTACTACACACG
13085448 TGTATTCACA
Statistics
Matches: 186, Mismatches: 34, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
47 1 0.01
48 3 0.02
50 101 0.54
51 69 0.37
52 6 0.03
53 6 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGAGACTCAACAGTATGATACACG
Found at i:13085430 original size:151 final size:151
Alignment explanation
Indices: 13085172--13085449 Score: 529
Period size: 151 Copynumber: 1.8 Consensus size: 151
13085162 TTCGCATAGT
* *
13085172 AGCCTGCACTTAGTACTACCCACGTGATCGAAGTCATTGAGTATGCCTAGTAGCCCGCACTTAGT
1 AGCCTGCACTTAGTACTACACACGTGATCGAAGTCATTGAGTATGCATAGTAGCCCGCACTTAGT
13085237 ACTACACATGAGACTTAACAGTATGATACACGTAGTAGCCTACACTTAGTACTACACACGTGACC
66 ACTACACATGAGACTTAACAGTATGATACACGTAGTAGCCTACACTTAGTACTACACACGTGACC
13085302 TCATCATCTGATACACGTAGC
131 TCATCATCTGATACACGTAGC
*
13085323 AGCCTGCACTTAGTACTACACACGTGATCGAAGTCATTGAGTATGCATAGTAGCCTGCACTTAGT
1 AGCCTGCACTTAGTACTACACACGTGATCGAAGTCATTGAGTATGCATAGTAGCCCGCACTTAGT
13085388 ACTACACATGAGACTTAACAGTATGATACACGTAGTAGCCTACACTTAGTACTACACACGTG
66 ACTACACATGAGACTTAACAGTATGATACACGTAGTAGCCTACACTTAGTACTACACACGTG
13085450 TATTCACAAT
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 124 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (151 bp):
AGCCTGCACTTAGTACTACACACGTGATCGAAGTCATTGAGTATGCATAGTAGCCCGCACTTAGT
ACTACACATGAGACTTAACAGTATGATACACGTAGTAGCCTACACTTAGTACTACACACGTGACC
TCATCATCTGATACACGTAGC
Found at i:13088247 original size:11 final size:11
Alignment explanation
Indices: 13088227--13088261 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
13088217 GGAAGATGAC
*
13088227 CACTTTATTTT
1 CACTTAATTTT
*
13088238 CACTTAATTTA
1 CACTTAATTTT
13088249 CACTTAATTTT
1 CACTTAATTTT
13088260 CA
1 CA
13088262 ATCTACCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (11 bp):
CACTTAATTTT
Found at i:13096502 original size:26 final size:26
Alignment explanation
Indices: 13096466--13096516 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
13096456 CAACTTAACA
**
13096466 TATTGAATGAATTCATTCGTCGTTCG
1 TATTGAATGAATGAATTCGTCGTTCG
13096492 TATTGAATGAATGAATTCGTCGTTC
1 TATTGAATGAATGAATTCGTCGTTC
13096517 TAACATGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (26 bp):
TATTGAATGAATGAATTCGTCGTTCG
Found at i:13096696 original size:45 final size:44
Alignment explanation
Indices: 13096595--13096726 Score: 160
Period size: 45 Copynumber: 3.0 Consensus size: 44
13096585 CCCGAATTTA
* *
13096595 TTCACCGGCATT-TTGCCTGCTAGGCTCGAGGCCCGAAA-AATAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCAAGGCCC-AAATAATAT
* * *
13096638 CTCACCGGTATTATAGCCTGCTAGGCTCAAAGGCCCAAATAATGT
1 TTCACCGGCATTATAGCCTGCTAGGCTC-AAGGCCCAAATAATAT
* *
13096683 TTCACCAGCATTATAGCCTGCTAGGCTCCAAGGCCCGAATAATA
1 TTCACCGGCATTATAGCCTGCTAGGCT-CAAGGCCCAAATAATA
13096727 CTGTACAACA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 10 0.13
44 17 0.23
45 47 0.63
46 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (44 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCAAGGCCCAAATAATAT
Found at i:13101575 original size:29 final size:29
Alignment explanation
Indices: 13101533--13101591 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
13101523 TACACCAAAA
*
13101533 TGTCGTCGATAAATGCCACCAGAAATTGG
1 TGTCGTCGATAAATGCCACCAAAAATTGG
13101562 TGTCGTCGATAAATGCCACCAAAAATTGG
1 TGTCGTCGATAAATGCCACCAAAAATTGG
13101591 T
1 T
13101592 CCAGATAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (29 bp):
TGTCGTCGATAAATGCCACCAAAAATTGG
Found at i:13103153 original size:93 final size:93
Alignment explanation
Indices: 13103040--13103397 Score: 680
Period size: 93 Copynumber: 3.8 Consensus size: 93
13103030 CGCCCATAAG
* * * *
13103040 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
13103105 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
13103133 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
13103198 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
13103226 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
13103291 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
13103319 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
13103384 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
13103398 TCAACCATCC
Statistics
Matches: 261, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 261 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:13103155 original size:47 final size:49
Alignment explanation
Indices: 13103033--13103397 Score: 405
Period size: 46 Copynumber: 7.8 Consensus size: 49
13103023 TGTAACCCGC
* *
13103033 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C-GTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTT-ACAT
*
13103079 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACAT
* * *
13103129 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
*
13103172 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACAT
* * *
13103222 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
*
13103265 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACAT
* * *
13103315 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
*
13103358 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
13103398 TCAACCATCC
Statistics
Matches: 269, Mismatches: 25, Indels: 47
0.79 0.07 0.14
Matches are distributed among these distances:
43 18 0.07
44 6 0.02
45 6 0.02
46 121 0.45
47 87 0.32
48 7 0.03
49 6 0.02
50 15 0.06
51 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
Found at i:13104364 original size:15 final size:16
Alignment explanation
Indices: 13104329--13104365 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
13104319 TTTTTAATTC
*
13104329 ATTTTAATAACTAAAT
1 ATTTTATTAACTAAAT
13104345 A-TTTATTAAC-AAAT
1 ATTTTATTAACTAAAT
13104359 ATTTTAT
1 ATTTTAT
13104366 GCAGTACAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 13 0.68
16 1 0.05
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTATTAACTAAAT
Found at i:13104850 original size:17 final size:17
Alignment explanation
Indices: 13104808--13104855 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
13104798 GAACTTTTTG
* *
13104808 TTTAAGAAAATCGTTCAT
1 TTTAAGAAAA-CTTTAAT
*
13104826 TTTCAGAAAACTTTAAT
1 TTTAAGAAAACTTTAAT
13104843 TTTAAGAAAACTT
1 TTTAAGAAAACTT
13104856 GTAGGGATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (17 bp):
TTTAAGAAAACTTTAAT
Found at i:13114386 original size:11 final size:11
Alignment explanation
Indices: 13114362--13114399 Score: 53
Period size: 9 Copynumber: 3.5 Consensus size: 11
13114352 AATTCAAATG
13114362 ACCAAAATCATA
1 ACCAAAA-CATA
13114374 ACCAAAACATA
1 ACCAAAACATA
13114385 ACC--AACATA
1 ACCAAAACATA
13114394 ACCAAA
1 ACCAAA
13114400 GTCCCTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.38
11 8 0.33
12 7 0.29
ACGTcount: A:0.61, C:0.29, G:0.00, T:0.11
Consensus pattern (11 bp):
ACCAAAACATA
Found at i:13115927 original size:20 final size:20
Alignment explanation
Indices: 13115898--13115938 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
13115888 AGATGTCCAT
13115898 AAATGTCTAA-TACCAATTA
1 AAATGTCTAATTACCAATTA
*
13115917 AAATAGTCTAATTACCACTTA
1 AAAT-GTCTAATTACCAATTA
13115938 A
1 A
13115939 GGACCTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATGTCTAATTACCAATTA
Found at i:13117824 original size:79 final size:81
Alignment explanation
Indices: 13117688--13117872 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
13117678 TTGAATGATG
*
13117688 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
13117752 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
13117767 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
13117829 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
13117847 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
13117873 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:13117886 original size:40 final size:40
Alignment explanation
Indices: 13117689--13117872 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
13117679 TGAATGATGT
* * * *
13117689 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
13117729 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
13117769 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
13117807 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
13117848 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
13117873 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:13117894 original size:79 final size:79
Alignment explanation
Indices: 13117741--13117905 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
13117731 GGACTAAGAT
* **
13117741 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
13117806 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
13117820 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
13117883 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
13117899 CCGAAGG
1 CCGAAGG
13117906 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:13119015 original size:57 final size:57
Alignment explanation
Indices: 13118952--13119066 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
13118942 GAGATATCCA
13118952 AGTCGTAATGCGAAAAGGTCAGTATAGTCGATCCCTGTAACATGGGAGACTTTGACT
1 AGTCGTAATGCGAAAAGGTCAGTATAGTCGATCCCTGTAACATGGGAGACTTTGACT
*
13119009 AGTCGTAATGCGAAAAGGTCAGTGTAGTCGATCCCTGTAACATGGGAGACTTTGACT
1 AGTCGTAATGCGAAAAGGTCAGTATAGTCGATCCCTGTAACATGGGAGACTTTGACT
13119066 A
1 A
13119067 ATAAAATGTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (57 bp):
AGTCGTAATGCGAAAAGGTCAGTATAGTCGATCCCTGTAACATGGGAGACTTTGACT
Found at i:13124754 original size:58 final size:58
Alignment explanation
Indices: 13124664--13124779 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
13124654 TAATGGGGTT
13124664 GAGATTTTTAGGGGTATCACTGGAGTTGCCCCTAATGTGGTTGAATGTTGTATTGAGG
1 GAGATTTTTAGGGGTATCACTGGAGTTGCCCCTAATGTGGTTGAATGTTGTATTGAGG
13124722 GAGATTTTTAGGGGTATCACTGGAGTTGCCCCTAATGTGGTTGAATGTTGTATTGAGG
1 GAGATTTTTAGGGGTATCACTGGAGTTGCCCCTAATGTGGTTGAATGTTGTATTGAGG
13124780 CCATGGAGAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.36
Consensus pattern (58 bp):
GAGATTTTTAGGGGTATCACTGGAGTTGCCCCTAATGTGGTTGAATGTTGTATTGAGG
Found at i:13127990 original size:26 final size:26
Alignment explanation
Indices: 13127961--13128068 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
13127951 TGATACAAAT
13127961 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
13127987 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13128013 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13128039 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
13128065 TGAT
1 TGAT
13128069 GAGAATTTCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:13128323 original size:68 final size:68
Alignment explanation
Indices: 13128214--13128348 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 68
13128204 GGAGAAAGCT
* * *
13128214 CTTGAATGTTCGGTCACTTGGGGAAGAAAATTGAAGGTAAGTTCATGGTAGTTTGCTTTTATTTT
1 CTTGAATGTTCGGTCACTTGGGGAAGAAAATTGAAGGTAAGTTCATGGTAGTTGGCTTCTATCTT
13128279 GAG
66 GAG
*
13128282 CTTGAGTGTTCGGTCACTTGGGGAAGAAAATTGAAGGTAAGTTCATGGTAGTTGGCTTCTATCTT
1 CTTGAATGTTCGGTCACTTGGGGAAGAAAATTGAAGGTAAGTTCATGGTAGTTGGCTTCTATCTT
13128347 GA
66 GA
13128349 TGTTCATGAG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.36
Consensus pattern (68 bp):
CTTGAATGTTCGGTCACTTGGGGAAGAAAATTGAAGGTAAGTTCATGGTAGTTGGCTTCTATCTT
GAG
Found at i:13128820 original size:112 final size:112
Alignment explanation
Indices: 13128679--13128901 Score: 428
Period size: 112 Copynumber: 2.0 Consensus size: 112
13128669 TGAAAGAGTG
13128679 ATTTGGTAATAAATCTGCTTGGGATAGCAGCAGTAACGTGACTTTGGAAAATCACCATAAATTGT
1 ATTTGGTAATAAATCTGCTTGGGATAGCAGCAGTAACGTGACTTTGGAAAATCACCATAAATTGT
*
13128744 GGGAGATGAATTAGAAGCTGAATAAATTATGTAATTAAAGCTTATTA
66 GGGAGATGAATTAGAAGCTGAATAAATTATGTAATTAAAGATTATTA
13128791 ATTTGGTAATAAATCTGCTTGGGATAGCAGCAGTAACGTGACTTTGGAAAATCACCATAAATTGT
1 ATTTGGTAATAAATCTGCTTGGGATAGCAGCAGTAACGTGACTTTGGAAAATCACCATAAATTGT
*
13128856 GGGAGATGAATTAGAAGCTGCATAAATTATGTAATTAAAGATTATT
66 GGGAGATGAATTAGAAGCTGAATAAATTATGTAATTAAAGATTATT
13128902 GAGTCTAGTT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (112 bp):
ATTTGGTAATAAATCTGCTTGGGATAGCAGCAGTAACGTGACTTTGGAAAATCACCATAAATTGT
GGGAGATGAATTAGAAGCTGAATAAATTATGTAATTAAAGATTATTA
Found at i:13129771 original size:26 final size:26
Alignment explanation
Indices: 13129742--13129792 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
13129732 CAGTTTTACT
13129742 CCTAGGAGATAAATT-ACCGAAATACC
1 CCTAGG-GATAAATTGACCGAAATACC
* *
13129768 CCTAGGGTTAAATTGACCTAAATAC
1 CCTAGGGATAAATTGACCGAAATAC
13129793 ATGTTTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (26 bp):
CCTAGGGATAAATTGACCGAAATACC
Found at i:13130262 original size:43 final size:43
Alignment explanation
Indices: 13130214--13130298 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
13130204 GCTGACTTGG
*
13130214 GCTTTAAATGGGTTTTCTTTACACACTGAGTTTCCCTAAACTA
1 GCTTTAAATGGGTTTTCTTTACACACTGAGTTTCCCCAAACTA
13130257 GCTTTAAATGGGTTTTCTTTACACACTGAGTTTCCCCAAACT
1 GCTTTAAATGGGTTTTCTTTACACACTGAGTTTCCCCAAACT
13130299 CACCCCTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (43 bp):
GCTTTAAATGGGTTTTCTTTACACACTGAGTTTCCCCAAACTA
Found at i:13131062 original size:32 final size:33
Alignment explanation
Indices: 13131015--13131079 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
13131005 TACCCAAATG
*
13131015 GTACAACTTGAAAATGTTATGTACAATTTGTGT
1 GTACAACTTGAAAATGTTAGGTACAATTTGTGT
* * *
13131048 GTAC-ACTTGGAAATGTTAGGTATACTTTGTGT
1 GTACAACTTGAAAATGTTAGGTACAATTTGTGT
13131080 ATACTATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (33 bp):
GTACAACTTGAAAATGTTAGGTACAATTTGTGT
Found at i:13131128 original size:33 final size:31
Alignment explanation
Indices: 13131041--13131134 Score: 82
Period size: 33 Copynumber: 2.9 Consensus size: 31
13131031 TTATGTACAA
** *
13131041 TTTGTGTGTA-CACTTGGAAATGTTAGGTATAC
1 TTTGTGTGTACCA-TTGGAAA-GGAATGTATAC
* * *
13131073 TTTGTGTATACTATATGAAAAGGAAATGTATAC
1 TTTGTGTGTACCAT-TGGAAAGG-AATGTATAC
13131106 TTTGTGTGTACCAGTTGGAAAGGAATGTA
1 TTTGTGTGTACCA-TTGGAAAGGAATGTA
13131135 CATCTCAGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
32 17 0.35
33 31 0.63
34 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.37
Consensus pattern (31 bp):
TTTGTGTGTACCATTGGAAAGGAATGTATAC
Found at i:13143131 original size:21 final size:20
Alignment explanation
Indices: 13143094--13143132 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
13143084 GTTTATGGAA
* *
13143094 TTCTTAAATTATTTATAAAT
1 TTCTCAAATTATATATAAAT
13143114 TTCTCAAATTTATATATAA
1 TTCTCAAA-TTATATATAA
13143133 TTGAGTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
TTCTCAAATTATATATAAAT
Found at i:13144004 original size:28 final size:28
Alignment explanation
Indices: 13143964--13144024 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
13143954 AAGTTTCAAA
* *
13143964 AAAAATATAAAAATTATTTTAAAA-TTT
1 AAAAATATAAAAATTATTTAAAAAGTAT
*
13143991 AAAAATCATTAAAATTATTTAAAAAGTAT
1 AAAAAT-ATAAAAATTATTTAAAAAGTAT
13144020 AAAAA
1 AAAAA
13144025 ATTATTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 16 0.55
29 7 0.24
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAAATATAAAAATTATTTAAAAAGTAT
Found at i:13144024 original size:20 final size:21
Alignment explanation
Indices: 13143987--13144031 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
13143977 TTATTTTAAA
*
13143987 ATTTAAAAATCAT-TAAAATT
1 ATTTAAAAATCATAAAAAATT
13144007 ATTTAAAAAGT-ATAAAAAATT
1 ATTTAAAAA-TCATAAAAAATT
13144028 ATTT
1 ATTT
13144032 GTAACAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTAAAAATCATAAAAAATT
Found at i:13144806 original size:11 final size:11
Alignment explanation
Indices: 13144792--13144831 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
13144782 CATCTAAATT
*
13144792 AACCCAAATAA
1 AACCCAAATAC
*
13144803 AACCCAAGTAC
1 AACCCAAATAC
13144814 AACCCAAATAC
1 AACCCAAATAC
13144825 AACCCAA
1 AACCCAA
13144832 TACCAACCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.55, C:0.35, G:0.03, T:0.07
Consensus pattern (11 bp):
AACCCAAATAC
Found at i:13144817 original size:22 final size:22
Alignment explanation
Indices: 13144792--13144839 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
13144782 CATCTAAATT
13144792 AACCCAAATAAAACCCAAGTA-C
1 AACCCAAATAAAACCCAA-TACC
*
13144814 AACCCAAATACAACCCAATACC
1 AACCCAAATAAAACCCAATACC
13144836 AACC
1 AACC
13144840 TAACCACTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.52, C:0.38, G:0.02, T:0.08
Consensus pattern (22 bp):
AACCCAAATAAAACCCAATACC
Found at i:13144838 original size:11 final size:10
Alignment explanation
Indices: 13144792--13144839 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 10
13144782 CATCTAAATT
*
13144792 AACCCAAATAA
1 AACCC-AATAC
13144803 AACCCAAGTAC
1 AACCCAA-TAC
13144814 AACCCAAATAC
1 AACCC-AATAC
13144825 AACCCAATACC
1 AACCCAATA-C
13144836 AACC
1 AACC
13144840 TAACCACTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 6 0.18
11 25 0.76
12 2 0.06
ACGTcount: A:0.52, C:0.38, G:0.02, T:0.08
Consensus pattern (10 bp):
AACCCAATAC
Found at i:13145889 original size:3 final size:3
Alignment explanation
Indices: 13145883--13146043 Score: 68
Period size: 3 Copynumber: 53.7 Consensus size: 3
13145873 TTTTTTTACA
* *
13145883 TAT TAT TAA TAT TAT TAC TAT TAT T-T TAT T-T CTAT TAT TAT CT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT
* * * * * *
13145927 TAT TAT TAC TGT TAG TAT TAT T-T TCAT TAC TAT TAT TTT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * * * *
13145972 CA- TAT TAAT TAT T-T TCT AACG TAT TAT TAT TACT AAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT
*
13146018 T-T CTAGT T-T TAT TAT TAT TAA TAT TA
1 TAT -TA-T TAT TAT TAT TAT TAT TAT TA
13146044 ATGTATGTAT
Statistics
Matches: 116, Mismatches: 26, Indels: 32
0.67 0.15 0.18
Matches are distributed among these distances:
2 12 0.10
3 92 0.79
4 11 0.09
5 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:13145911 original size:23 final size:23
Alignment explanation
Indices: 13145885--13145930 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13145875 TTTTTACATA
13145885 TTATTAATATTATTA-CTATTATT
1 TTATTAATATTATTATCT-TTATT
**
13145908 TTATTTCTATTATTATCTTTATT
1 TTATTAATATTATTATCTTTATT
13145931 ATTACTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATTAATATTATTATCTTTATT
Found at i:13146066 original size:17 final size:16
Alignment explanation
Indices: 13146044--13146076 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
13146034 ATTAATATTA
13146044 ATGTATGTATATTATAT
1 ATGTATGTATA-TATAT
13146061 ATGTATGTATATATAT
1 ATGTATGTATATATAT
13146077 TTATATATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (16 bp):
ATGTATGTATATATAT
Found at i:13146305 original size:23 final size:24
Alignment explanation
Indices: 13146278--13146375 Score: 105
Period size: 23 Copynumber: 4.2 Consensus size: 24
13146268 TTTTCAATAT
13146278 TATATTTTTTATA-TATTATTATA
1 TATATTTTTTATACTATTATTATA
* * *
13146301 TATA-TTTTAATATTATTAGT-TA
1 TATATTTTTTATACTATTATTATA
*
13146323 TATATTTTTTATACTATTA-TATG
1 TATATTTTTTATACTATTATTATA
* *
13146346 TATATTTCTAATACTATTATTTATA
1 TATATTTTTTATACTATTA-TTATA
13146371 TATAT
1 TATAT
13146376 ATGTGTGTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
22 14 0.23
23 40 0.65
25 8 0.13
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (24 bp):
TATATTTTTTATACTATTATTATA
Found at i:13146341 original size:43 final size:46
Alignment explanation
Indices: 13146277--13146373 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
13146267 GTTTTCAATA
* *
13146277 TTATAT-TTTTTATATATTATTATA-TATATTT-TAATATTATTAG
1 TTATATATTTTTATATACTATTATAGTATATTTCTAATACTATTAG
*
13146320 TTATATATTTTT-TATACTATTATATGTATATTTCTAATACTATTAT
1 TTATATATTTTTATATACTATTATA-GTATATTTCTAATACTATTAG
13146366 TTATATAT
1 TTATATAT
13146374 ATATGTGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
43 17 0.36
44 5 0.11
45 7 0.15
46 18 0.38
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (46 bp):
TTATATATTTTTATATACTATTATAGTATATTTCTAATACTATTAG
Found at i:13146358 original size:46 final size:45
Alignment explanation
Indices: 13146278--13146373 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 45
13146268 TTTTCAATAT
*
13146278 TATATTTTTTATATATTATTATATATATTTTAATATTATTAGTTA
1 TATATTTTTTATATATTATTATATATATTTTAATACTATTAGTTA
* *
13146323 TATATTTTTTATACTATTA-TATGTATATTTCTAATACTATTATTTA
1 TATATTTTTTATA-TATTATTATATATATTT-TAATACTATTAGTTA
13146369 TATAT
1 TATAT
13146374 ATATGTGTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 23 0.50
46 23 0.50
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (45 bp):
TATATTTTTTATATATTATTATATATATTTTAATACTATTAGTTA
Found at i:13146484 original size:24 final size:23
Alignment explanation
Indices: 13146447--13146554 Score: 67
Period size: 24 Copynumber: 4.4 Consensus size: 23
13146437 GTATATATTG
*
13146447 TATATGTTTTATA-TATGTCATGTA
1 TATAT-TTTTATACCAT-TCATGTA
** * *
13146471 TATATTTTTAATATTATTAATTATA
1 TATATTTTT-ATACCATTCA-TGTA
13146496 TATATTTCTTATA-CATTTCCATGTA
1 TATATTT-TTATACCA-TT-CATGTA
* *
13146521 CATATTTTTATACCATCTTATGTA
1 TATATTTTTATACCAT-TCATGTA
13146545 TATATTTTTA
1 TATATTTTTA
13146555 AATACTATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
23 4 0.06
24 31 0.46
25 30 0.44
26 3 0.04
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (23 bp):
TATATTTTTATACCATTCATGTA
Found at i:13146596 original size:31 final size:30
Alignment explanation
Indices: 13146539--13146598 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
13146529 TATACCATCT
*
13146539 TATGTATATATTTTTAAATACTATATTGTA
1 TATGTATATATTTTTAAATACCATATTGTA
13146569 TATGTATATATATTCTT-AATACCATATTGT
1 TATGTATATAT-TT-TTAAATACCATATTGT
13146599 GTATATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.41
31 14 0.52
32 2 0.07
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52
Consensus pattern (30 bp):
TATGTATATATTTTTAAATACCATATTGTA
Found at i:13157486 original size:99 final size:100
Alignment explanation
Indices: 13157288--13157496 Score: 316
Period size: 99 Copynumber: 2.1 Consensus size: 100
13157278 TATACTCTTT
* * *
13157288 ATTTGGTGTGTTGGTTGGATTAGCTCTTATGAGCATTGGTGTGATGGTTGGTTTAGCTCTTATGA
1 ATTTGGTGTGATGGTTGGATTAGCTCTTATGAACATTGGTGTGATGGTTGGATTAGCTCTTATGA
* *
13157353 ACATTGGTGTGATGGTTGGATTAGCTCTTATGAGC
66 ACATTGGTGTGATGGATGGATTAGCTCTAATGAGC
*
13157388 A-TTGGTGTGATGGTTGGTTTAGCTCTTATGAACATTGGTGTGATGGTTGGATTAGCTCTTATGA
1 ATTTGGTGTGATGGTTGGATTAGCTCTTATGAACATTGGTGTGATGGTTGGATTAGCTCTTATGA
*
13157452 GCATTGGTGTGATGGATGGATT-GACTC-AAGTGAGC
66 ACATTGGTGTGATGGATGGATTAG-CTCTAA-TGAGC
13157487 ATTTGGTGTG
1 ATTTGGTGTG
13157497 TTTGGTTGAA
Statistics
Matches: 99, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
98 2 0.02
99 88 0.89
100 9 0.09
ACGTcount: A:0.18, C:0.09, G:0.33, T:0.40
Consensus pattern (100 bp):
ATTTGGTGTGATGGTTGGATTAGCTCTTATGAACATTGGTGTGATGGTTGGATTAGCTCTTATGA
ACATTGGTGTGATGGATGGATTAGCTCTAATGAGC
Found at i:13157489 original size:33 final size:33
Alignment explanation
Indices: 13157290--13157473 Score: 314
Period size: 33 Copynumber: 5.6 Consensus size: 33
13157280 TACTCTTTAT
*
13157290 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
* *
13157323 TTGGTGTGATGGTTGGTTTAGCTCTTATGAACA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
13157356 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
* *
13157389 TTGGTGTGATGGTTGGTTTAGCTCTTATGAACA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
13157422 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
*
13157455 TTGGTGTGATGGATGGATT
1 TTGGTGTGATGGTTGGATT
13157474 GACTCAAGTG
Statistics
Matches: 141, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 141 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.41
Consensus pattern (33 bp):
TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
Found at i:13158839 original size:94 final size:91
Alignment explanation
Indices: 13158721--13158997 Score: 306
Period size: 94 Copynumber: 3.0 Consensus size: 91
13158711 GTTTGTATTT
**
13158721 ATGTATGATTTGAATGGTTTACTATTATGTTTGTCCAGTAATGCTCTGTAACCCTATTTCAGCGA
1 ATGTATGATTTGAATGGTTTACTATTATGTTTGTCTGGTAATGCTCTGTAACCCT-TTTCAGCGA
*
13158786 TGTATACGGGTTAGAGGTGTTACATTTGG
65 TG-ATAAGGGTTAG-GGTGTTACATTTGG
* *
13158815 ATGTATGATTTGAATGGTTTACTATTCTGTTTGTCTGGTAATGCTACT-TAA-CCTTGTTCCGAC
1 ATGTATGATTTGAATGGTTTACTATTATGTTTGTCTGGTAATGCT-CTGTAACCCTT-TTCAG-C
* * * *
13158878 GACGGATAAAGGTTAGGGATTTTACAATTGG
63 GA-TGATAAGGGTTAGGG-TGTTACATTTGG
* * * * * *
13158909 ATGTATGATTTGAATGGTTTATTATTTTGTTCGTCTGGTAATGCTCTGTAACCCTGGTCCAGCAA
1 ATGTATGATTTGAATGGTTTACTATTATGTTTGTCTGGTAATGCTCTGTAACCCT-TTTCAGCGA
*
13158974 CTGATATGGGTTAGGGTGTTACAT
65 -TGATAAGGGTTAGGGTGTTACAT
13158998 GTTCATTGTT
Statistics
Matches: 154, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
92 1 0.01
93 17 0.11
94 127 0.82
95 9 0.06
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (91 bp):
ATGTATGATTTGAATGGTTTACTATTATGTTTGTCTGGTAATGCTCTGTAACCCTTTTCAGCGAT
GATAAGGGTTAGGGTGTTACATTTGG
Found at i:13159161 original size:55 final size:54
Alignment explanation
Indices: 13159063--13159166 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 54
13159053 AAAAAGACAA
*
13159063 ATTTTTTAAAAGCTTCATGAACTCAACTTTATGTGTACGTTTTTATTAAACTTTC
1 ATTTTTTAAAAGCTTCATGAACTCAACTTTATGTATACGTTTTT-TTAAACTTTC
**
13159118 ATTTTTTTTAAGCTTCATGAACTCAACTCTTAT-TATA-GATTTTTTTAAA
1 ATTTTTTAAAAGCTTCATGAACTCAACT-TTATGTATACG-TTTTTTTAAA
13159167 ATAATATTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
54 6 0.14
55 34 0.77
56 4 0.09
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (54 bp):
ATTTTTTAAAAGCTTCATGAACTCAACTTTATGTATACGTTTTTTTAAACTTTC
Found at i:13160581 original size:27 final size:27
Alignment explanation
Indices: 13160549--13160600 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
13160539 AAAAACATGA
13160549 TTTTAAGTTTTTAGGCATTCTAACAAT
1 TTTTAAGTTTTTAGGCATTCTAACAAT
13160576 TTTTAAGTTTTTAGGCATTCTAACA
1 TTTTAAGTTTTTAGGCATTCTAACA
13160601 CGTATATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (27 bp):
TTTTAAGTTTTTAGGCATTCTAACAAT
Found at i:13163275 original size:18 final size:18
Alignment explanation
Indices: 13163252--13163289 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
13163242 TCACACACAC
*
13163252 ACACACCAAGAACACTTA
1 ACACACAAAGAACACTTA
13163270 ACACACAAAGAACACTTA
1 ACACACAAAGAACACTTA
13163288 AC
1 AC
13163290 CACTGAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.32, G:0.05, T:0.11
Consensus pattern (18 bp):
ACACACAAAGAACACTTA
Found at i:13171035 original size:5 final size:5
Alignment explanation
Indices: 13171025--13171051 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
13171015 GAATTTTGGG
13171025 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
13171052 CAAATGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:13195607 original size:12 final size:12
Alignment explanation
Indices: 13195590--13195616 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13195580 CCGTGTGCTT
13195590 CCACATGGCCTA
1 CCACATGGCCTA
13195602 CCACATGGCCTA
1 CCACATGGCCTA
13195614 CCA
1 CCA
13195617 TACTACCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.44, G:0.15, T:0.15
Consensus pattern (12 bp):
CCACATGGCCTA
Found at i:13226072 original size:15 final size:17
Alignment explanation
Indices: 13226036--13226072 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
13226026 TTCTATCAAT
13226036 TTCATTACCAATATACA
1 TTCATTACCAATATACA
*
13226053 TTCATT-CCAA-ATATA
1 TTCATTACCAATATACA
13226068 TTCAT
1 TTCAT
13226073 CTCAACCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 4 0.21
17 6 0.32
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TTCATTACCAATATACA
Found at i:13226539 original size:20 final size:20
Alignment explanation
Indices: 13226501--13226539 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13226491 TACTGCCAAC
* *
13226501 AGGAGCACGAATGTGCTATT
1 AGGAGCACGAAAGTACTATT
*
13226521 AGGAGTACGAAAGTACTAT
1 AGGAGCACGAAAGTACTAT
13226540 CAAGAGCACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (20 bp):
AGGAGCACGAAAGTACTATT
Found at i:13229094 original size:41 final size:44
Alignment explanation
Indices: 13229040--13229121 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
13229030 AGTTCATGCT
*
13229040 TTTAGGAGCATTA-T-ATT-TTGGATGAACAATTTAAGCTTACA
1 TTTAGAAGCATTATTGATTGTTGGATGAACAATTTAAGCTTACA
* * *
13229081 TTTAGAAGCATTATTGTTTGTTGGATGTATAATTTAAGCTT
1 TTTAGAAGCATTATTGATTGTTGGATGAACAATTTAAGCTT
13229122 GTGCTTAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 12 0.35
42 1 0.03
43 2 0.06
44 19 0.56
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.44
Consensus pattern (44 bp):
TTTAGAAGCATTATTGATTGTTGGATGAACAATTTAAGCTTACA
Found at i:13235797 original size:5 final size:5
Alignment explanation
Indices: 13235789--13235814 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13235779 GAAAGAAATT
13235789 TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA T
13235815 GATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:13237605 original size:41 final size:41
Alignment explanation
Indices: 13237526--13237605 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
13237516 TATAGCCTTA
* * * *
13237526 ATCTGTTCTACTGCAACTTCAGAGAGATTAGGTTTGTTTTG
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTTTTG
*
13237567 ATCTGCTCTACTGCAACTTCAGAGGGATAAGATCTGTTT
1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTTT
13237606 GTCCACAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (41 bp):
ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTTTTG
Found at i:13237815 original size:89 final size:89
Alignment explanation
Indices: 13237691--13237874 Score: 332
Period size: 89 Copynumber: 2.1 Consensus size: 89
13237681 TTTAGAGATA
* *
13237691 CAAGATCTGTAATTTTCAGCCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGGTGGCTTGAATC
1 CAAGATCTGTAATTTCCAGCCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGGTGGCTTAAATC
13237756 TGCTTCACTGCAACTTCAGGAAGG
66 TGCTTCACTGCAACTTCAGGAAGG
*
13237780 CAAGATCTGTAATTTCCAGCCTATTACCCTACTGCTTAGGGGGTTTAGGCTTGGTGGCTTAAATC
1 CAAGATCTGTAATTTCCAGCCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGGTGGCTTAAATC
*
13237845 TGCTTCACTGCAATTTCAGGAAGG
66 TGCTTCACTGCAACTTCAGGAAGG
13237869 CAAGAT
1 CAAGAT
13237875 TCACCGTTGT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (89 bp):
CAAGATCTGTAATTTCCAGCCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGGTGGCTTAAATC
TGCTTCACTGCAACTTCAGGAAGG
Found at i:13256026 original size:131 final size:127
Alignment explanation
Indices: 13255749--13256095 Score: 392
Period size: 131 Copynumber: 2.7 Consensus size: 127
13255739 TTATTTAGTC
* * * *
13255749 CAACGAAAAATCGAAACCCAGCAC-AGTAGGGCACGATTCCCCGGATTTCTAAACATTGAACATT
1 CAACGAAAAATCGAAACCCAGCACGA-TAGGGCACGATTCCCCGAATTGCCAAACATCGAACATT
* * ** * * * *
13255813 GCCTTGTTTT-AGAATTTAGAAAACGTGAGTGAAATTCTAAGGGAATATTCGATTATTTTGAA
65 CCCTCGTTTTAAGAATTTTTAAAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTCGAA
** * * *
13255875 CAAATAGGAAATCGTAACCCAGCACGATAGGGCACGATTCCCCGAACTGCCAAACATCGAACATT
1 CAACGA-AAAATCGAAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATT
*
13255940 ACCCTCGTTTTGAAGAATTTTTAAAGACATGAGTGAAATTCCAAAGGAATATTTGATTATTTCGA
65 -CCCTCGTTTT-AAGAATTTTTAAA-ACATGAGTGAAATTCCAAAGGAATATTCGATTATTTCGA
13256005 A
127 A
* * * *
13256006 CAAGCGAAAAATTGCAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACACCGAATATT
1 CAA-CGAAAAATCGAAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATT
**
13256071 GCATTCGTTTTAAAGAATTTTTAAA
65 -CCCTCGTTTT-AAGAATTTTTAAA
13256096 TGAATTGTTA
Statistics
Matches: 184, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
126 4 0.02
127 49 0.27
128 9 0.05
130 10 0.05
131 111 0.60
132 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (127 bp):
CAACGAAAAATCGAAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTC
CCTCGTTTTAAGAATTTTTAAAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTCGAA
Found at i:13257066 original size:40 final size:40
Alignment explanation
Indices: 13256972--13257051 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
13256962 TATGTAGGAT
13256972 CATATAATAAAATATAAGAATAAATTAAAAAGGAATTATA
1 CATATAATAAAATATAAGAATAAATTAAAAAGGAATTATA
13257012 CATATAATAAAATATAAGAATAAATTAAAAAGGAATTATA
1 CATATAATAAAATATAAGAATAAATTAAAAAGGAATTATA
13257052 TGTATAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (40 bp):
CATATAATAAAATATAAGAATAAATTAAAAAGGAATTATA
Found at i:13258944 original size:89 final size:89
Alignment explanation
Indices: 13258694--13259346 Score: 861
Period size: 89 Copynumber: 7.4 Consensus size: 89
13258684 TTATATTTAG
* * * * * *
13258694 TCTGCTCCTCTGCCACTTCAGGGAGATAAGA-CTCGTAA--TTCAGCCTGTTACCCTACCACTTA
1 TCTGTTCCACTGCAACTTCAGGGAGACAAGATCT-GCAATCTTCAGCCTGTTACCCTACTACTTA
* ** *
13258756 GGGAGTTAAGGCTCACTGTCTTCGA
65 GGGGGTTAAGGCTTGCTTTCTTCGA
*
13258781 TCTGTTCCACTGTAACTTCAGGGAGACAAGATCTGCAA--TTCAGCCTGTTACCCTACTACTTAG
1 TCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAG
** *
13258844 GGGGTTAAGGCTCAAC-GTCTTCGA
66 GGGGTTAAGGCT-TGCTTTCTTCGA
* * * *
13258868 TCTGTTCCACTGAAACTTCAGGGAGACAAAATTTGTAATCTTCAGCCTGTTACCCTACTACTTAG
1 TCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAG
13258933 GGGGTTAAGGCTTGC-TTCTTCGA
66 GGGGTTAAGGCTTGCTTTCTTCGA
* * * * *
13258956 TCTGCTCAACTGTAACTTTAGGGAGACAAGATCTGCAATCTTCAGCCTATTACCCTACTACTTAG
1 TCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAG
13259021 GGGGTTAAGGCTTGCTTTCTTCGA
66 GGGGTTAAGGCTTGCTTTCTTCGA
* * * *
13259045 TCTGCTCCACTGCAACTTCAGGGAGACAAGATCTTCAATCTTCGGCCTGTTACCCTACAACTTAG
1 TCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAG
* ** **
13259110 GGGGTTAAAGCTCACCGTCTTCGA
66 GGGGTTAAGGCTTGCTTTCTTCGA
* * * * * *
13259134 TCTGTTCCACTGCGACTTCAGAGAGACAAGATCTGTAATCTTCGGCTTGTTACCCTGCTACTTAG
1 TCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAG
13259199 GGGGTTAAGGCTTGCTTTCTTCGA
66 GGGGTTAAGGCTTGCTTTCTTCGA
* * * *
13259223 TCTGTTCCACTGCAACTTCAGGGAGACAAGATTTGTAATCTTCGGCCTGTTACCCTGCTACTTAG
1 TCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAG
13259288 GGGGTTAAGGCTTGCTTTCTTCGA
66 GGGGTTAAGGCTTGCTTTCTTCGA
13259312 TCTGTTCCACTGCAACTTCAGGGAGACAAGATCTG
1 TCTGTTCCACTGCAACTTCAGGGAGACAAGATCTG
13259347 TGAATTCACT
Statistics
Matches: 507, Mismatches: 54, Indels: 8
0.89 0.09 0.01
Matches are distributed among these distances:
87 106 0.21
88 84 0.17
89 317 0.63
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (89 bp):
TCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGCAATCTTCAGCCTGTTACCCTACTACTTAG
GGGGTTAAGGCTTGCTTTCTTCGA
Found at i:13259107 original size:45 final size:44
Alignment explanation
Indices: 13258973--13259289 Score: 139
Period size: 44 Copynumber: 7.1 Consensus size: 44
13258963 AACTGTAACT
* * * * *
13258973 TTAGGGAGACAAGATCTGCAATCTTCAGCCTATTACCCTACTAC
1 TTAGGGAGACAAGATCTTCAATCTTCGGCCTGTTACCCTGCAAC
* ** * ** ** *
13259017 TTAGGGGGTTAAG-GCTTGCTTTCTTCGATCTGCT-CCACTGCAAC
1 TTAGGGAGACAAGATCTT-CAATCTTCGGCCTGTTACC-CTGCAAC
*
13259061 TTCAGGGAGACAAGATCTTCAATCTTCGGCCTGTTACCCTACAAC
1 TT-AGGGAGACAAGATCTTCAATCTTCGGCCTGTTACCCTGCAAC
* * * ** ** *
13259106 TTAGGGGGTTA-AAGCTC-ACCGTCTTCGATCTGTT-CCACTGCGAC
1 TTAGGGAG--ACAAGATCTTCAATCTTCGGCCTGTTACC-CTGCAAC
* * *
13259150 TTCAGAGAGACAAGATCTGT-AATCTTCGGCTTGTTACCCTGCTAC
1 TT-AGGGAGACAAGATCT-TCAATCTTCGGCCTGTTACCCTGCAAC
* ** * ** **
13259195 TTAGGGGGTTAAG-GCTTGCTTTCTTCGATCTGTT-CCACTGCAAC
1 TTAGGGAGACAAGATCTT-CAATCTTCGGCCTGTTACC-CTGCAAC
* *
13259239 TTCAGGGAGACAAGAT-TTGTAATCTTCGGCCTGTTACCCTGCTAC
1 TT-AGGGAGACAAGATCTT-CAATCTTCGGCCTGTTACCCTGCAAC
13259284 TTAGGG
1 TTAGGG
13259290 GGTTAAGGCT
Statistics
Matches: 190, Mismatches: 64, Indels: 38
0.65 0.22 0.13
Matches are distributed among these distances:
42 1 0.01
43 11 0.06
44 84 0.44
45 84 0.44
46 10 0.05
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (44 bp):
TTAGGGAGACAAGATCTTCAATCTTCGGCCTGTTACCCTGCAAC
Found at i:13259221 original size:44 final size:44
Alignment explanation
Indices: 13259172--13259310 Score: 140
Period size: 44 Copynumber: 3.1 Consensus size: 44
13259162 AGATCTGTAA
13259172 TCTTCGGCTTGTTACCCTGCTACTTAGGGGGTTAAGGCTTGCTT
1 TCTTCGGCTTGTTACCCTGCTACTTAGGGGGTTAAGGCTTGCTT
* * * ** ** *
13259216 TCTTC-GATCTGTT-CCACTGCAACTTCAGGGAGACAAGATTTG-TAA
1 TCTTCGGCT-TGTTACC-CTGCTACTT-AGGGGGTTAAGGCTTGCT-T
*
13259261 TCTTCGGCCTGTTACCCTGCTACTTAGGGGGTTAAGGCTTGCTT
1 TCTTCGGCTTGTTACCCTGCTACTTAGGGGGTTAAGGCTTGCTT
13259305 TCTTCG
1 TCTTCG
13259311 ATCTGTTCCA
Statistics
Matches: 71, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
43 4 0.06
44 35 0.49
45 29 0.41
46 3 0.04
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (44 bp):
TCTTCGGCTTGTTACCCTGCTACTTAGGGGGTTAAGGCTTGCTT
Found at i:13271111 original size:131 final size:128
Alignment explanation
Indices: 13270840--13271179 Score: 443
Period size: 131 Copynumber: 2.6 Consensus size: 128
13270830 GTCCAAAGAA
* * * * * * *
13270840 AAATCGAAACCCAGCACGGTAGGGCACGATTCCCCGGATTTCCAAACATTGAACATTGCCTTGTT
1 AAATCGCAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTCCCTCGTT
** * * *
13270905 TT-AGAATTTAGAAAACGTGAGTGAAATTCTAAGAGAATATTCGATTATTTTGAACAAACAGG
66 TTAAGAATTTTTAAAACATGAGTGAAATTCAAAGAGAATATTCGATTATTTCGAACAAACAGG
13270967 AAATCGCAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCCTCGT
1 AAATCGCAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATT-CCCTCGT
*
13271032 TTTGAAGAATTTTTAAAGACATGAGTGAAATTCCAAAG-GAATATTCGATTATTTCGAACAAGC-
65 TTT-AAGAATTTTTAAA-ACATGAGTGAAATT-CAAAGAGAATATTCGATTATTTCGAACAAACA
13271095 GG
127 GG
* * * *
13271097 CAAATTGCAACCCAGCACGATAGGACACGATTCCCCGAATTGCCAAACACCGAACATTGCCTTCG
1 -AAATCGCAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATT-CCCTCG
13271162 TTTTAAAGAATTTTTAAA
64 TTTT-AAGAATTTTTAAA
13271180 TAAATAGTTA
Statistics
Matches: 188, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
127 52 0.28
128 8 0.04
130 12 0.06
131 112 0.60
132 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (128 bp):
AAATCGCAACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTCCCTCGTT
TTAAGAATTTTTAAAACATGAGTGAAATTCAAAGAGAATATTCGATTATTTCGAACAAACAGG
Found at i:13278670 original size:22 final size:22
Alignment explanation
Indices: 13278634--13278678 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
13278624 GTTGCACGGG
*
13278634 TTGTTCTGATAGACTGTGGGCC
1 TTGTTCCGATAGACTGTGGGCC
*
13278656 TTGTTCCGATCGACTGTGGGCC
1 TTGTTCCGATAGACTGTGGGCC
13278678 T
1 T
13278679 ACCATTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.22, G:0.31, T:0.36
Consensus pattern (22 bp):
TTGTTCCGATAGACTGTGGGCC
Found at i:13283193 original size:24 final size:25
Alignment explanation
Indices: 13283149--13283195 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
13283139 CAAGTGTGTG
13283149 ATAAAATAAATGACATGTGTAATTA
1 ATAAAATAAATGACATGTGTAATTA
* *
13283174 ATAAAATACAT-ACATTTGTAAT
1 ATAAAATAAATGACATGTGTAAT
13283196 ACATGTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (25 bp):
ATAAAATAAATGACATGTGTAATTA
Found at i:13284568 original size:6 final size:6
Alignment explanation
Indices: 13284550--13284583 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
13284540 TTTGTGTACC
*
13284550 GTTACT GTGACT GTTACT GTTACT GTTACT -TTAC
1 GTTACT GTTACT GTTACT GTTACT GTTACT GTTAC
13284584 CATTGCGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (6 bp):
GTTACT
Found at i:13284777 original size:18 final size:18
Alignment explanation
Indices: 13284725--13284777 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
13284715 GTTTGCTACG
* *
13284725 GAATAATTGACTGTTACT
1 GAATAAATGACTGTTATT
13284743 GAATAAATGACTGTTATT
1 GAATAAATGACTGTTATT
* *
13284761 GTATAACTGACTGTTAT
1 GAATAAATGACTGTTAT
13284778 AGAGTAACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (18 bp):
GAATAAATGACTGTTATT
Found at i:13284785 original size:18 final size:16
Alignment explanation
Indices: 13284727--13284788 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 16
13284717 TTGCTACGGA
*
13284727 ATAATTGACTGTTACTG
1 ATAACTGACTGTTA-TG
*
13284744 AATAAATGACTGTTATTG
1 -ATAACTGACTGTTA-TG
13284762 TATAACTGACTGTTATAG
1 -ATAACTGACTGTTAT-G
13284780 AGTAACTGA
1 A-TAACTGA
13284789 ATGCTACTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 2 0.05
18 36 0.95
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (16 bp):
ATAACTGACTGTTATG
Found at i:13285974 original size:13 final size:13
Alignment explanation
Indices: 13285956--13285981 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13285946 TACAAAATGA
13285956 CTTAATTTTAATT
1 CTTAATTTTAATT
13285969 CTTAATTTTAATT
1 CTTAATTTTAATT
13285982 TATGTATCAT
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:0.00, T:0.62
Consensus pattern (13 bp):
CTTAATTTTAATT
Found at i:13290435 original size:35 final size:35
Alignment explanation
Indices: 13290317--13290446 Score: 109
Period size: 35 Copynumber: 3.6 Consensus size: 35
13290307 CTCATTGAAG
* * * *
13290317 TACCATACCTACATTTTACAACTCGGTATGGGA-AA
1 TACCATACCTACGTTTCACAACTCAGTAT-GGATGA
** * **
13290352 TGTCATATCTACGTTTCTTAACTCAGTATGGATTTGATAA
1 TACCATACCTACGTTTCACAACTCAGTATGGA--TG---A
13290392 TACCATACCTACGTTTCACAACTCAGTATGGATGA
1 TACCATACCTACGTTTCACAACTCAGTATGGATGA
*
13290427 TACCATACCTGCGTTTCACA
1 TACCATACCTACGTTTCACA
13290447 CTTTTCCATA
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
34 3 0.04
35 41 0.55
38 2 0.03
40 28 0.38
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (35 bp):
TACCATACCTACGTTTCACAACTCAGTATGGATGA
Found at i:13295409 original size:32 final size:32
Alignment explanation
Indices: 13295339--13295411 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
13295329 GGCTATTGAT
13295339 TTTTTAAGG-TCTATTTAGATTTCCTAATTTTG
1 TTTTT-AGGATCTATTTAGATTTCCTAATTTTG
* * *
13295371 TTTTTAGGATCTGTTTAGGTTTCCTGATTTTG
1 TTTTTAGGATCTATTTAGATTTCCTAATTTTG
13295403 TTTTTAGGA
1 TTTTTAGGA
13295412 GCTTTATTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 3 0.08
32 34 0.92
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (32 bp):
TTTTTAGGATCTATTTAGATTTCCTAATTTTG
Found at i:13297090 original size:21 final size:22
Alignment explanation
Indices: 13297052--13297093 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
13297042 TCTTAATCTT
*
13297052 AAAAATATACATATAAATTTTC
1 AAAAATATACATAAAAATTTTC
13297074 AAAAATATA-ATAAAAATTTT
1 AAAAATATACATAAAAATTTT
13297094 AAATTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATATACATAAAAATTTTC
Found at i:13297112 original size:6 final size:6
Alignment explanation
Indices: 13297101--13297156 Score: 69
Period size: 6 Copynumber: 9.2 Consensus size: 6
13297091 TTTAAATTTT
* *
13297101 ATATTA ATATTA ATATTA ATATTA ATATTA A-ATAA ATATAATT ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATAT--TA ATATTA
13297150 ATATTA A
1 ATATTA A
13297157 ATAAAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
5 4 0.09
6 35 0.81
8 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATATTA
Found at i:13297147 original size:25 final size:24
Alignment explanation
Indices: 13297119--13297165 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
13297109 ATTAATATTA
13297119 ATATTAATATTAAATAAATATAATT
1 ATATTAATATTAAATAAA-ATAATT
13297144 ATATTAATATTAAATAAAATAA
1 ATATTAATATTAAATAAAATAA
13297166 AAATCTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATTAATATTAAATAAAATAATT
Found at i:13297966 original size:22 final size:22
Alignment explanation
Indices: 13297941--13297997 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
13297931 TTTGTTGTTG
13297941 TTTCGTTGTTATTTTGCTACAA
1 TTTCGTTGTTATTTTGCTACAA
* * *
13297963 TTTCGTTATTATATTGCTACTA
1 TTTCGTTGTTATTTTGCTACAA
**
13297985 TTTTATTGTTATT
1 TTTCGTTGTTATT
13297998 GTTTGGATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.60
Consensus pattern (22 bp):
TTTCGTTGTTATTTTGCTACAA
Found at i:13298197 original size:23 final size:24
Alignment explanation
Indices: 13298137--13298197 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
13298127 ATTGAGAAGC
*
13298137 ATTTA-TTTTA-ATATTTTTAGTAT
1 ATTTATTTTTATATATTTTTAG-AA
*
13298160 ATTTGATTTAT-TATATTTTTA-AA
1 ATTT-ATTTTTATATATTTTTAGAA
13298183 ATTTATTTTTATATA
1 ATTTATTTTTATATA
13298198 AAAATAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 5 0.16
23 13 0.42
24 1 0.03
25 12 0.39
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (24 bp):
ATTTATTTTTATATATTTTTAGAA
Found at i:13299404 original size:22 final size:20
Alignment explanation
Indices: 13299365--13299407 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
13299355 TCAGTCCATC
*
13299365 ATTTATAAAATAATTTAATNA
1 ATTTATAAAATAAATTAAT-A
*
13299386 ATTTATATGAATAAATTAATA
1 ATTTATA-AAATAAATTAATA
13299407 A
1 A
13299408 CTATATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTATAAAATAAATTAATA
Found at i:13307625 original size:16 final size:17
Alignment explanation
Indices: 13307604--13307643 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
13307594 TTCTATATAG
*
13307604 ATTTTACT-TTTATTTT
1 ATTTTACTATATATTTT
13307620 ATTTTACTACTATATTTT
1 ATTTTACTA-TATATTTT
13307638 ATTTTA
1 ATTTTA
13307644 ACAAGGATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
18 13 0.62
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTACTATATATTTT
Found at i:13312490 original size:35 final size:35
Alignment explanation
Indices: 13312449--13312613 Score: 197
Period size: 35 Copynumber: 4.7 Consensus size: 35
13312439 TCCATGGCAA
* *
13312449 AGTTGTGAAACGTAGGTATGGTATCATCCATACTA
1 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
* *
13312484 AATTGTGAAACGTAGGTATGGTATTAACCATACTG
1 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
*
13312519 AGTTGTGAAGCGTAGGTATGGTATTATCCATACTG
1 AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
** ** *
13312554 AGTTAAGAAACGTAGGTATGACATT-TCCCATACCG
1 AGTTGTGAAACGTAGGTATGGTATTAT-CCATACTG
* * *
13312589 AGTTGTAAAATGTAGGCATGGTATT
1 AGTTGTGAAACGTAGGTATGGTATT
13312614 TCAATAAGGA
Statistics
Matches: 109, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
34 1 0.01
35 108 0.99
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (35 bp):
AGTTGTGAAACGTAGGTATGGTATTATCCATACTG
Found at i:13316664 original size:13 final size:13
Alignment explanation
Indices: 13316646--13316679 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
13316636 TTAATTAAGA
*
13316646 AATTAATTTAGTT
1 AATTAATTTAATT
*
13316659 AATTAAATTAATT
1 AATTAATTTAATT
13316672 AATTAATT
1 AATTAATT
13316680 AGTATTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
AATTAATTTAATT
Found at i:13320362 original size:2 final size:2
Alignment explanation
Indices: 13320355--13320379 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13320345 TTTTTGATGG
13320355 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 T
13320380 TTACTATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13323630 original size:6 final size:6
Alignment explanation
Indices: 13323616--13323676 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
13323606 ATTTGAAAAC
* * *
13323616 TTAAAT TTAATT TTAGATA TTAGTT TTAAATT TTAATT TTAGA-T TTAATT
1 TTAATT TTAATT TTA-ATT TTAATT TT-AATT TTAATT TTA-ATT TTAATT
*
13323666 TTAAGT TTAAT
1 TTAATT TTAAT
13323677 AGTATAAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
5 1 0.02
6 32 0.73
7 11 0.25
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (6 bp):
TTAATT
Found at i:13323643 original size:19 final size:18
Alignment explanation
Indices: 13323620--13323669 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
13323610 GAAAACTTAA
13323620 ATTTAATTTTAGATATTAG
1 ATTTAATTTTA-ATATTAG
* *
13323639 TTTTAAATTTTAATTTTAG
1 ATTT-AATTTTAATATTAG
13323658 ATTTAATTTTAA
1 ATTTAATTTTAA
13323670 GTTTAATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.30
19 12 0.44
20 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
ATTTAATTTTAATATTAG
Found at i:13323667 original size:25 final size:25
Alignment explanation
Indices: 13323616--13323676 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
13323606 ATTTGAAAAC
*
13323616 TTAAATTTAATTTTAGATATTAGTT
1 TTAAATTTAATTTTAGATATTAATT
13323641 TTAAATTTTAATTTTAGAT-TTAATT
1 TTAAA-TTTAATTTTAGATATTAATT
*
13323666 TTAAGTTTAAT
1 TTAAATTTAAT
13323677 AGTATAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 6 0.18
25 14 0.42
26 13 0.39
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (25 bp):
TTAAATTTAATTTTAGATATTAATT
Found at i:13323952 original size:20 final size:21
Alignment explanation
Indices: 13323927--13323976 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
13323917 CATTTTAAAC
* *
13323927 TATAAAAAATT-ATTAAAAAT
1 TATAAAAAATTCATAAAAAAA
*
13323947 TATAAAAATTTCATAAAAAAA
1 TATAAAAAATTCATAAAAAAA
13323968 TATAAAAAA
1 TATAAAAAA
13323977 AGGTCATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
TATAAAAAATTCATAAAAAAA
Found at i:13323977 original size:10 final size:10
Alignment explanation
Indices: 13323927--13323976 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
13323917 CATTTTAAAC
13323927 TATAAAAAAT
1 TATAAAAAAT
*
13323937 TATTAAAAAT
1 TATAAAAAAT
*
13323947 TATAAAAATT
1 TATAAAAAAT
*
13323957 TCATAAAAAAA
1 T-ATAAAAAAT
13323968 TATAAAAAA
1 TATAAAAAA
13323977 AGGTCATTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
TATAAAAAAT
Found at i:13325147 original size:53 final size:53
Alignment explanation
Indices: 13325084--13325194 Score: 213
Period size: 53 Copynumber: 2.1 Consensus size: 53
13325074 ATTTTGGGCC
13325084 TAGTAGGAACAGTGGTTTCAGAACCACTAACTCGAGGTCGAAGAAATTATTCT
1 TAGTAGGAACAGTGGTTTCAGAACCACTAACTCGAGGTCGAAGAAATTATTCT
*
13325137 TAGTAGGAACAGTGGTTTCAGAACCACTAACTCGAGGTCGGAGAAATTATTCT
1 TAGTAGGAACAGTGGTTTCAGAACCACTAACTCGAGGTCGAAGAAATTATTCT
13325190 TAGTA
1 TAGTA
13325195 TTATTTTATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (53 bp):
TAGTAGGAACAGTGGTTTCAGAACCACTAACTCGAGGTCGAAGAAATTATTCT
Found at i:13325915 original size:48 final size:48
Alignment explanation
Indices: 13325851--13325970 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 48
13325841 TGTGTGCTAG
* * * *
13325851 TGTAAGACTATATTTGGAATATGGCATCAGCCACGATA-TGAGAGCCAA
1 TGTAAGACCATGTTTGGAACATGGCATCAGCAACG-TAGTGAGAGCCAA
* * *
13325899 TGTAAGACCATGTTTGGAACATGGCATCGGCAATGTAGTGAGAGCCAG
1 TGTAAGACCATGTTTGGAACATGGCATCAGCAACGTAGTGAGAGCCAA
* * *
13325947 TGTAGGACCATGTCTGGGACATGG
1 TGTAAGACCATGTTTGGAACATGG
13325971 TATCGGCATT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
47 2 0.03
48 59 0.97
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (48 bp):
TGTAAGACCATGTTTGGAACATGGCATCAGCAACGTAGTGAGAGCCAA
Found at i:13326020 original size:144 final size:144
Alignment explanation
Indices: 13325836--13326121 Score: 328
Period size: 144 Copynumber: 2.0 Consensus size: 144
13325826 GACATTTGGG
* * * * *
13325836 TGATATGTGTGCTAGTGTAAGACTATATTTGGAATATGGCATCAGCCACGATATGAGAGCCAAT-
1 TGATATGTGCGCTAGAGTAAGACTATATCTGGAACATGGCATCAGCCACCATATGAGAGCC-ATC
* * *
13325900 GTAAGACCATGTT-T-GGAACATGGCATCGGCAATGTAG-TGAGAGCCAGTGTAGGACCATGTCT
65 GTAAGACCAT-TTCTAGG-ACATGGCATCGACAATG-AGACGAGAGCCAGTGTAAGACCATGTCT
*
13325962 GGGACATGGTATCGGCAT
127 GGGACATGGCATCGGCAT
* ** * * *
13325980 TGATATGTGCGCTAGAGTAAGACTATGTCTGGGGCATGGCATCGGCCACCTTATGAGAGCCGTCG
1 TGATATGTGCGCTAGAGTAAGACTATATCTGGAACATGGCATCAGCCACCATATGAGAGCCATCG
* * * *
13326045 TAAGACCATTTCTAGGACATGGCATTGATATTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGA
66 TAAGACCATTTCTAGGACATGGCATCGACAATGAGACGAGAGCCAGTGTAAGACCATGTCTGGGA
*
13326110 CATTGCATCGGC
131 CATGGCATCGGC
13326122 CTCGAAATGT
Statistics
Matches: 118, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
143 5 0.04
144 111 0.94
145 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (144 bp):
TGATATGTGCGCTAGAGTAAGACTATATCTGGAACATGGCATCAGCCACCATATGAGAGCCATCG
TAAGACCATTTCTAGGACATGGCATCGACAATGAGACGAGAGCCAGTGTAAGACCATGTCTGGGA
CATGGCATCGGCAT
Found at i:13326141 original size:48 final size:48
Alignment explanation
Indices: 13325871--13326151 Score: 230
Period size: 48 Copynumber: 5.9 Consensus size: 48
13325861 TATTTGGAAT
* * * *
13325871 ATGGCATCAGCCA-CGATATGAGAGCCAATGTAAGACCATGTTTGGAAC
1 ATGGCATC-GGCATCGATATGAGAGCCAGTGTAAGACCATGTCTGGGAC
*
13325919 ATGGCATCGGCAAT-G-TAGTGAGAGCCAGTGTAGGACCATGTCTGGGAC
1 ATGGCATCGGC-ATCGATA-TGAGAGCCAGTGTAAGACCATGTCTGGGAC
* * * * * * * *
13325967 ATGGTATCGGCATTGATATGTGCGCTAGAGTAAGACTATGTCTGGGGC
1 ATGGCATCGGCATCGATATGAGAGCCAGTGTAAGACCATGTCTGGGAC
** * *
13326015 ATGGCATCGGCCA-CCTTATGAGAGCC-GTCGTAAGACCATTTCTAGGAC
1 ATGGCATCGG-CATCGATATGAGAGCCAGT-GTAAGACCATGTCTGGGAC
* ** * * * *
13326063 ATGGCATTGATATTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGAC
1 ATGGCATCGGCATCGATATGAGAGCCAGTGTAAGACCATGTCTGGGAC
* * * *
13326111 ATTGCATCGGCCTCGAAATGTGAGCCAGTGTAAGACCATGT
1 ATGGCATCGGCATCGATATGAGAGCCAGTGTAAGACCATGT
13326152 TTAGAACATA
Statistics
Matches: 178, Mismatches: 46, Indels: 18
0.74 0.19 0.07
Matches are distributed among these distances:
47 8 0.04
48 164 0.92
49 6 0.03
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (48 bp):
ATGGCATCGGCATCGATATGAGAGCCAGTGTAAGACCATGTCTGGGAC
Found at i:13332597 original size:10 final size:10
Alignment explanation
Indices: 13332580--13332644 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
13332570 ACTTTTCTTA
13332580 ATTT-TTATT
1 ATTTATTATT
13332589 ATTTATTA-T
1 ATTTATTATT
*
13332598 -TTTATT-TC
1 ATTTATTATT
*
13332606 ATTTTATTAGT
1 A-TTTATTATT
13332617 ATTTATTATT
1 ATTTATTATT
*
13332627 -TTATTTTATT
1 ATT-TATTATT
13332637 ATTTATTA
1 ATTTATTA
13332645 CTTTATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
8 6 0.14
9 7 0.16
10 27 0.63
11 3 0.07
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (10 bp):
ATTTATTATT
Found at i:13332600 original size:35 final size:35
Alignment explanation
Indices: 13332559--13332636 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
13332549 AACCCAACAT
* * *
13332559 TTATTTT-TTTTACTTTTCTTAATTTTTATTATTTA
1 TTATTTTATTTCA-TTTTATTAATATTTATTATTTA
*
13332594 TTATTTTATTTCATTTTATTAGTATTTATTA-TT-
1 TTATTTTATTTCATTTTATTAATATTTATTATTTA
13332627 TTATTTTATT
1 TTATTTTATT
13332637 ATTTATTACT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 10 0.26
34 2 0.05
35 22 0.58
36 4 0.11
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (35 bp):
TTATTTTATTTCATTTTATTAATATTTATTATTTA
Found at i:13332634 original size:13 final size:13
Alignment explanation
Indices: 13332590--13332640 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
13332580 ATTTTTATTA
13332590 TTTATTATTTTAT
1 TTTATTATTTTAT
*
13332603 TTCATT-TTATTAGT
1 TTTATTATT-TTA-T
13332617 ATTTATTATTTTAT
1 -TTTATTATTTTAT
13332631 TTTATTATTT
1 TTTATTATTT
13332641 ATTACTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 2 0.06
13 18 0.56
14 2 0.06
15 8 0.25
16 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:13332639 original size:20 final size:20
Alignment explanation
Indices: 13332590--13332653 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
13332580 ATTTTTATTA
13332590 TTTATTATTTTATTTCATTTTA-
1 TTTATTA-TTTA-TT-ATTTTAT
*
13332612 -TTAGTATTTATTATTTTAT
1 TTTATTATTTATTATTTTAT
*
13332631 TTTATTATTTATTACTTTAT
1 TTTATTATTTATTATTTTAT
13332651 TTT
1 TTT
13332654 TGGATATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.16
19 2 0.05
20 24 0.65
21 5 0.14
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATTATTTATTATTTTAT
Done.