Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003032.1 Hibiscus syriacus cultivar Beakdansim tig00006312_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: 158183
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2104 original size:16 final size:15
Alignment explanation
Indices: 2065--2109 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2055 TTTTAAATTC
2065 TATTTTAATTTTTAT
1 TATTTTAATTTTTAT
2080 TATTGTTAATATTTTAT
1 TATT-TTAAT-TTTTAT
2097 T-TATTTAATTTTT
1 TAT-TTTAATTTTT
2110 TTAGTATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 8 0.30
16 11 0.41
17 8 0.30
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TATTTTAATTTTTAT
Found at i:3933 original size:3 final size:3
Alignment explanation
Indices: 3925--3999 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
3915 TATCTACTCT
* * * * * * *
3925 TGA TGA TGA TGA TGA CGA CGA TAA TGA TAA TGA TGA TGA TGA TGG CGG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
3973 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
4000 GAGTGAGGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.29
Consensus pattern (3 bp):
TGA
Found at i:8629 original size:26 final size:25
Alignment explanation
Indices: 8558--8628 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 25
8548 AACTTATGGT
* * *
8558 ATATTTTATTTATTTGATACTTATTA
1 ATATTTTATTTAATTGTTA-TTTTTA
*
8584 GTATTTTATTTAA---TTA-TTTTA
1 ATATTTTATTTAATTGTTATTTTTA
8605 ATATTTTATTTAATTGTTATTTTT
1 ATATTTTATTTAATTGTTATTTTT
8629 TTGCAGTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
21 16 0.44
23 2 0.06
24 3 0.08
25 4 0.11
26 11 0.31
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (25 bp):
ATATTTTATTTAATTGTTATTTTTA
Found at i:12298 original size:64 final size:66
Alignment explanation
Indices: 12139--12298 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 66
12129 GAATAAATTG
* * * *
12139 AACATCGAATGCATTTCACGCATCGATGGA-CATACTATGCATTGATGCACTCAGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATGA
12203 A
66 A
* * *
12204 AACATCGAATGCATTTGATGCATCGATGCACCA-CCCATGCATCGATGCACTCTG-GCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAG-T-TTTAT
12266 G-A
64 GAA
*
12268 AACATCGAATGCATTTCATGCATCGGTGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
12299 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 31 0.37
65 47 0.57
66 5 0.06
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATGA
A
Found at i:12314 original size:64 final size:63
Alignment explanation
Indices: 12139--12316 Score: 182
Period size: 65 Copynumber: 2.7 Consensus size: 63
12129 GAATAAATTG
* * *
12139 AACATCGAATGCATTTCACGCATCGATGGACATACTATGCATTGATGCACTCAGAGTTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCAC-T-CTATGCATCGATGCACTCAGAGTTTTATGAA
* * * *
12204 AACATCGAATGCATTTGATGCATCGATGCACCACCCATGCATCGATGCACTCTG-GCTATTT-TG
1 AACATCGAATGCATTTCATGCATCGATGCA-C-TCTATGCATCGATGCACTCAGAG-T-TTTATG
12267 -A
62 AA
* *
12268 AACATCGAATGCATTTCATGCATCGGTGCACTCTTAGTGCACCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCACTC-TA-TGCATCGATGCA
12317 AGGGTCCAAC
Statistics
Matches: 96, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 41 0.43
65 47 0.49
66 5 0.05
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTATGCATCGATGCACTCAGAGTTTTATGAA
Found at i:18012 original size:23 final size:22
Alignment explanation
Indices: 17941--18022 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
17931 ACACTTAACA
17941 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * *
17965 GTGTATCGATGCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
17986 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
18009 GTGCATCGATGCAC
1 GTGCATCGATGCAC
18023 AAGGCCATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:20750 original size:65 final size:63
Alignment explanation
Indices: 20633--20840 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
20623 TTTCAAAGTG
* * ** *
20633 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATTCATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATACATT
20696 TC
62 TC
*
20698 ATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATACATT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATACATT
*
20761 TG
62 TC
* * *
20763 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATACATTTC
20827 ATGCATCGATGCAC
1 ATGCATCGATGCAC
20841 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 11, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 48 0.39
65 65 0.53
66 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATACATTTC
Found at i:22952 original size:21 final size:21
Alignment explanation
Indices: 22928--22977 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
22918 CTCATGAAGC
* *
22928 GGTTCTTCTGGTGGAGATGAT
1 GGTTCCTCTGGTAGAGATGAT
22949 GGTTCCTCTGGTAGAGATGAT
1 GGTTCCTCTGGTAGAGATGAT
22970 GGTTCCTC
1 GGTTCCTC
22978 CATGCTCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.14, C:0.16, G:0.34, T:0.36
Consensus pattern (21 bp):
GGTTCCTCTGGTAGAGATGAT
Found at i:25027 original size:2 final size:2
Alignment explanation
Indices: 25020--25090 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
25010 CCTCCTCTTC
25020 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
25062 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 A
25091 AAGAGAGAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25099 original size:4 final size:4
Alignment explanation
Indices: 25092--25253 Score: 75
Period size: 4 Copynumber: 42.0 Consensus size: 4
25082 ATATATATAA
* * * * * * *
25092 AGAG AGAG AGAG AGAG AGAA AAAG AGGG AGGG AGGG GGAG AGGG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * * * * *
25140 AGGG A-AG -GAG AGAG AGGG AGAG AGAA AGAG GGAG GGAG -GGG GGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * * * * * * *
25185 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AG-G AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
25232 AGAG AGAG AG-G AGAG AG-G AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG
25254 GGGGGGGGCC
Statistics
Matches: 131, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
3 14 0.11
4 117 0.89
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:25103 original size:8 final size:8
Alignment explanation
Indices: 25095--25253 Score: 116
Period size: 8 Copynumber: 20.6 Consensus size: 8
25085 TATATAAAGA
*
25095 GAGAGAGA
1 GAGAGAGG
*
25103 GAGAGAGA
1 GAGAGAGG
* *
25111 AAAAGAGG
1 GAGAGAGG
*
25119 GAGGGAGG
1 GAGAGAGG
*
25127 GGGAGAGG
1 GAGAGAGG
25135 GAGAGAGG
1 GAGAGAGG
*
25143 GA-AG-GA
1 GAGAGAGG
25149 GAGAGAGG
1 GAGAGAGG
25157 GAGAGA--
1 GAGAGAGG
*
25163 GAAAGAGG
1 GAGAGAGG
*
25171 GAGGGAGGG
1 GAGAGA-GG
*
25180 GGGAGAGG
1 GAGAGAGG
*
25188 GAGGGAGG
1 GAGAGAGG
*
25196 GAGGGAGG
1 GAGAGAGG
*
25204 GAGGGAGG
1 GAGAGAGG
*
25212 GAGGGAGG
1 GAGAGAGG
*
25220 GAG-GAGA
1 GAGAGAGG
*
25227 GAGAGAGA
1 GAGAGAGG
25235 GAGAGA-G
1 GAGAGAGG
25242 GAGAGA-G
1 GAGAGAGG
25249 GAGAG
1 GAGAG
25254 GGGGGGGGCC
Statistics
Matches: 125, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
6 8 0.06
7 22 0.18
8 89 0.71
9 6 0.05
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:25107 original size:12 final size:12
Alignment explanation
Indices: 25092--25255 Score: 102
Period size: 12 Copynumber: 13.7 Consensus size: 12
25082 ATATATATAA
*
25092 AGAGAGAGAGAG
1 AGAGAGGGAGAG
** *
25104 AGAGAGAAAAAG
1 AGAGAGGGAGAG
* *
25116 AGGGAGGGAGGG
1 AGAGAGGGAGAG
*
25128 GGAGAGGGAGAG
1 AGAGAGGGAGAG
* *
25140 AGGGAAGGAGAG
1 AGAGAGGGAGAG
25152 AGAG-GGAGAGAG
1 AGAGAGG-GAGAG
*
25164 AAAGAGGGAG-G
1 AGAGAGGGAGAG
*
25175 -GAG-GGGGGAG
1 AGAGAGGGAGAG
* *
25185 AGGGAGGGAGGG
1 AGAGAGGGAGAG
* *
25197 AGGGAGGGAGGG
1 AGAGAGGGAGAG
* *
25209 AGGGAGGGAGGG
1 AGAGAGGGAGAG
*
25221 AGGAGAGAGAGAG
1 A-GAGAGGGAGAG
25234 AGAGAGAGGAGAG
1 AGAGAG-GGAGAG
25247 AGGAGAGGG
1 A-GAGAGGG
25256 GGGGGGCCAT
Statistics
Matches: 119, Mismatches: 25, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
9 4 0.03
10 3 0.03
11 4 0.03
12 84 0.71
13 19 0.16
14 5 0.04
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (12 bp):
AGAGAGGGAGAG
Found at i:26369 original size:17 final size:18
Alignment explanation
Indices: 26347--26393 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
26337 ATATTCTATC
26347 AATTTAATCATAATTT-T
1 AATTTAATCATAATTTAT
*
26364 AATTTAAT-AAAATTTAT
1 AATTTAATCATAATTTAT
**
26381 CCTTTAATCATAA
1 AATTTAATCATAA
26394 AATAATGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 6 0.25
17 15 0.62
18 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTAATCATAATTTAT
Found at i:26407 original size:93 final size:91
Alignment explanation
Indices: 26207--26468 Score: 350
Period size: 93 Copynumber: 2.9 Consensus size: 91
26197 GCAGTTAACC
* *
26207 AAAATGATGTAATTATATATTTGAT-TATCAACACTTACATATTCTATCAATTTAGTCCTAATTT
1 AAAATGATGTAATTACATATTTGATCT-TCAACACTTA-ATATTCTATCAATTTAATCCTAATTT
* *
26271 AATTTAATAAATTTTATTCTTTAATCAT
64 AATTTAATAAAATTTATCCTTTAATCAT
* *
26299 AAAATGATTTAATTACATATTTGATCTTCAACACTTATATATTCTATCAATTTAATCATAATTTT
1 AAAATGATGTAATTACATATTTGATCTTCAACACTTA-ATATTCTATCAATTTAATCCTAA-TTT
26364 AATTTAATAAAATTTATCCTTTAATCAT
64 AATTTAATAAAATTTATCCTTTAATCAT
* * * * * * *
26392 AAAATAATGTAATTACAAACTTGATCCTCAACGCTTAA-GTTCTACCAATTTAATCCTAATTTAA
1 AAAATGATGTAATTACATATTTGATCTTCAACACTTAATATTCTATCAATTTAATCCTAATTTAA
26456 TTTAAT-AAATTTA
66 TTTAATAAAATTTA
26469 ATCATATGAT
Statistics
Matches: 152, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
89 7 0.05
90 11 0.07
91 18 0.12
92 55 0.36
93 61 0.40
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (91 bp):
AAAATGATGTAATTACATATTTGATCTTCAACACTTAATATTCTATCAATTTAATCCTAATTTAA
TTTAATAAAATTTATCCTTTAATCAT
Found at i:28753 original size:22 final size:22
Alignment explanation
Indices: 28728--28769 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
28718 TATAAAAAAT
28728 TATTTTTTA-TTAATATTTTTGA
1 TATTTTTTATTTAAT-TTTTTGA
28750 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTTAATTTTTT
28770 AAATAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
TATTTTTTATTTAATTTTTTGA
Found at i:32096 original size:18 final size:17
Alignment explanation
Indices: 32042--32103 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
32032 TACCAAATTA
*
32042 AAAAGTACTTTTGATCT
1 AAAAGTACTTTCGATCT
*
32059 AAAA-TAC-TTCTAATCT
1 AAAAGTACTTTC-GATCT
32075 AAAAGTACTTTCGATCCT
1 AAAAGTACTTTCGAT-CT
*
32093 AAAAGCACTTT
1 AAAAGTACTTT
32104 GAAAAACATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.05
16 11 0.30
17 9 0.24
18 15 0.41
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (17 bp):
AAAAGTACTTTCGATCT
Found at i:32266 original size:26 final size:28
Alignment explanation
Indices: 32211--32271 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 28
32201 TACTATTTAA
32211 AAATTTTGTAATTAATAATATTTTAATT
1 AAATTTTGTAATTAATAATATTTTAATT
*
32239 AAATTTT-TATTTAA-AAT-TTTATAATT
1 AAATTTTGTAATTAATAATATTT-TAATT
32265 AAATTTT
1 AAATTTT
32272 ATAAATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 3 0.10
26 15 0.48
27 6 0.19
28 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
AAATTTTGTAATTAATAATATTTTAATT
Found at i:32275 original size:13 final size:13
Alignment explanation
Indices: 32210--32271 Score: 65
Period size: 13 Copynumber: 4.6 Consensus size: 13
32200 TTACTATTTA
32210 AAAATTTTGTAATT
1 AAAATTTT-TAATT
32224 AATAATATTTTAATT
1 AA-AAT-TTTTAATT
*
32239 -AAATTTTTATTT
1 AAAATTTTTAATT
32251 AAAATTTTATAATT
1 AAAATTTT-TAATT
32265 -AAATTTT
1 AAAATTTT
32272 ATAAATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
12 7 0.17
13 17 0.40
14 7 0.17
15 8 0.19
16 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
AAAATTTTTAATT
Found at i:36301 original size:20 final size:21
Alignment explanation
Indices: 36272--36316 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
36262 TTTAAATAAA
36272 ATTTAAATATTATT-CTTAAT
1 ATTTAAATATTATTACTTAAT
* * *
36292 ATTTATATATTTTTATTTAAT
1 ATTTAAATATTATTACTTAAT
36313 ATTT
1 ATTT
36317 TCTGTCCAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAAATATTATTACTTAAT
Found at i:40375 original size:84 final size:84
Alignment explanation
Indices: 40284--40470 Score: 216
Period size: 84 Copynumber: 2.2 Consensus size: 84
40274 GACAGTTTTT
* ** * *
40284 GTTGACAGATAGCTTTTCTCGACTTAAGTTATG-TGTAAATTTGACATGCCCTTGAGCTAAATAG
1 GTTGACAGATAACCCTTCTCGACTTAAGTTATGTTGTAAA-TTGACACGCCCTTGAACT-AATAG
*
40348 -AATTGAACTCGAAGGTCTTG
64 TAATCGAACTCGAAGGTCTTG
* * * * * *
40368 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGATACGCCTTTGAACTGATTGTA
1 GTTGACAGATAACCCTTCTCGACTTAAGTTATGTTGTAAATTGACACGCCCTTGAACTAATAGTA
* *
40433 ATCGATCTCGAAGGTCTTT
66 ATCGAACTCGAAGGTCTTG
40452 GTTGACAGATAACCCTTCT
1 GTTGACAGATAACCCTTCT
40471 TGCCTTGAGC
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
83 3 0.03
84 78 0.90
85 6 0.07
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (84 bp):
GTTGACAGATAACCCTTCTCGACTTAAGTTATGTTGTAAATTGACACGCCCTTGAACTAATAGTA
ATCGAACTCGAAGGTCTTG
Found at i:41885 original size:95 final size:95
Alignment explanation
Indices: 41722--41920 Score: 290
Period size: 95 Copynumber: 2.1 Consensus size: 95
41712 GAATATCTCA
* *
41722 ATATTATAAACACCTTTATCATGCTAGCTGAATATTATCCATAAAGTTGGGGCATTTAACCAATT
1 ATATTATAAACACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCATTTAACCAATT
41787 GCTTTAGAGGAACAAATCAAGCTTTATTGT
66 GCTTTAGAGGAACAAATCAAGCTTTATTGT
* * * **
41817 ATATTATAATCATCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGGGGTGTTTAACCAATT
1 ATATTATAAACACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCATTTAACCAATT
* * **
41882 GCTTTAGGGGGACAGCTCAAGCTTTATTGT
66 GCTTTAGAGGAACAAATCAAGCTTTATTGT
41912 ATATATATA
1 ATAT-TATA
41921 TATAATATTA
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
95 88 0.96
96 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (95 bp):
ATATTATAAACACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCATTTAACCAATT
GCTTTAGAGGAACAAATCAAGCTTTATTGT
Found at i:44708 original size:41 final size:45
Alignment explanation
Indices: 44663--44745 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 45
44653 AGGGAAAAAC
44663 AAAAATACAAAAATT-AAAAG-AAAAAAA-TGAATAA-TAAAATA
1 AAAAATACAAAAATTAAAAAGAAAAAAAATTGAATAACTAAAATA
* **
44704 AAAAATGCTTAAATTAAAAAGAAAAAAAATTGAATAACTAAA
1 AAAAATACAAAAATTAAAAAGAAAAAAAATTGAATAACTAAA
44746 CCTTAAAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 12 0.34
42 5 0.14
43 7 0.20
44 7 0.20
45 4 0.11
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (45 bp):
AAAAATACAAAAATTAAAAAGAAAAAAAATTGAATAACTAAAATA
Found at i:46975 original size:13 final size:13
Alignment explanation
Indices: 46957--46981 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46947 TTTATTTTTC
46957 ATAATCATCACTT
1 ATAATCATCACTT
46970 ATAATCATCACT
1 ATAATCATCACT
46982 AACTTTAAAT
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATCATCACTT
Found at i:48316 original size:41 final size:41
Alignment explanation
Indices: 48271--48350 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
48261 ACTTTTAGAC
* *
48271 CAAGCTCTACTAGACTCGATAA-CTCGTGAGCTTAAAATTGT
1 CAAGCTCGACTAGACTCGA-AAGCTCGCGAGCTTAAAATTGT
* *
48312 CAAGCTCGACTTGATTCGAAAGCTCGCGAGCTTAAAATT
1 CAAGCTCGACTAGACTCGAAAGCTCGCGAGCTTAAAATT
48351 TTAAAACTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.06
41 32 0.94
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (41 bp):
CAAGCTCGACTAGACTCGAAAGCTCGCGAGCTTAAAATTGT
Found at i:49178 original size:14 final size:13
Alignment explanation
Indices: 49159--49257 Score: 57
Period size: 13 Copynumber: 7.9 Consensus size: 13
49149 TTCTTCGATA
49159 TTAAAAATAAATAT
1 TTAAAAAT-AATAT
49173 TTAAAAATAATAT
1 TTAAAAATAATAT
**
49186 TT-ATTAT-ATAT
1 TTAAAAATAATAT
49197 TT-AAAA-AATAT
1 TTAAAAATAATAT
* *
49208 TTAACAATAA-AA
1 TTAAAAATAATAT
* * * *
49220 ATACAAATACTAC
1 TTAAAAATAATAT
*
49233 TAAAATAAT-ATAT
1 TTAAA-AATAATAT
49246 TTAAAAATAATA
1 TTAAAAATAATA
49258 AGATAAATGA
Statistics
Matches: 62, Mismatches: 17, Indels: 13
0.67 0.18 0.14
Matches are distributed among these distances:
11 14 0.23
12 16 0.26
13 21 0.34
14 11 0.18
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAATAATAT
Found at i:50658 original size:3 final size:3
Alignment explanation
Indices: 50650--50749 Score: 132
Period size: 3 Copynumber: 34.0 Consensus size: 3
50640 TTAATATATT
*
50650 TAA TAA TAA -AA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
50696 TAA TGA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50744 TAA TAA
1 TAA TAA
50750 AATGGATAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
2 4 0.05
3 80 0.95
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:50757 original size:12 final size:11
Alignment explanation
Indices: 50655--50764 Score: 61
Period size: 12 Copynumber: 9.9 Consensus size: 11
50645 ATATTTAATA
*
50655 ATAA-AAAATA
1 ATAATAAAATG
*
50665 ATAATAATAATA
1 ATAATAA-AATG
*
50677 ATAATAATAATA
1 ATAATAA-AATG
*
50689 AAAATAATAATG
1 ATAATAA-AATG
*
50701 ATAATAATAT-
1 ATAATAAAATG
50711 -TAAT--AATG
1 ATAATAAAATG
50719 ATAATAATAAT-
1 ATAATAA-AATG
50730 ATTAATAATAATG
1 A-TAATAA-AATG
50743 ATAATAAAATGG
1 ATAATAAAAT-G
*
50755 ATAAAAAAAT
1 ATAATAAAAT
50765 AGTATCTTCA
Statistics
Matches: 84, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
7 2 0.02
9 8 0.10
10 4 0.05
11 8 0.10
12 61 0.73
13 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:51225 original size:114 final size:113
Alignment explanation
Indices: 50999--51776 Score: 1240
Period size: 114 Copynumber: 6.8 Consensus size: 113
50989 TCTTGATGAG
50999 TTCTTCTCATTATGAACTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
* * * *
51062 GGTAATGTTGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGAAAAGATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACAAA
*
51111 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
51176 GAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAA
66 GAAAAG-ATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACAAA
51225 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
51290 GAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAG
66 GAAAAGATGATCCATCAA-TTGATGAATTCAAGCAAAAGGTTGAACAAA
*
51339 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
51404 GAAAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAG
66 GAAAAG-ATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACAAA
51453 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
51518 GAAAGGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACAAA
*
51566 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
51631 GAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAG
66 GAAAAGATGATCCATCAA-TTGATGAATTCAAGCAAAAGGTTGAACAAA
*
51680 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
51744 GGAAACA-ATGATCCATCAATTTGATGAATTCAA
65 GGAAA-AGATGATCCATCAA-TTGATGAATTCAA
51777 ATCTTTGCTA
Statistics
Matches: 621, Mismatches: 37, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
112 20 0.03
113 174 0.28
114 415 0.67
115 12 0.02
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:51641 original size:341 final size:340
Alignment explanation
Indices: 50997--51776 Score: 1323
Period size: 341 Copynumber: 2.3 Consensus size: 340
50987 GCTCTTGATG
*
50997 AGTTCTTCTCATTATGAACTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-C
1 AGTTCTTCTCATTATGAACTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT-CTC
* *
51061 TGGTAATG-TTGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
65 TGG-AAAGAATGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
51125 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
129 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
* * *
51190 ATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
194 ACCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
51255 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGATGAATTC
259 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGATGAATTC
51320 AAGCAAAAGGTTGAACA
324 AAGCAAAAGGTTGAACA
51337 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* * *
51402 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
65 TGG-AAAGAATGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
* *
51467 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGGATGATCC
129 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
* *** *
51531 ACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTC
194 ACCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
51596 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGATGAATTC
259 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGATGAATTC
51661 AAGCAAAAGGTTGAACA
324 AAGCAAAAGGTTGAACA
51678 AGTTCTTCTCATTATGAACTTTCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* *
51743 TGGAAACAATGATCCATCAATTTGATGAATTCAA
65 TGGAAAGAATGATCCATCAA-CTGATGAATTCAA
51777 ATCTTTGCTA
Statistics
Matches: 415, Mismatches: 20, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
340 39 0.09
341 273 0.66
342 103 0.25
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (340 bp):
AGTTCTTCTCATTATGAACTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
GGAAAGAATGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCAC
CAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACGATGATCCATCAATTTGATGAATTCAA
GCAAAAGGTTGAACA
Found at i:52468 original size:83 final size:83
Alignment explanation
Indices: 52329--52527 Score: 380
Period size: 83 Copynumber: 2.4 Consensus size: 83
52319 ATGCACTTCT
* *
52329 TCAGATCAAATAACTCAAAGAACGCTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
52394 ATGCTTGATTCTGTCTAA
66 ATGCTTGATTCTGTCTAA
52412 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
52477 ATGCTTGATTCTGTCTAA
66 ATGCTTGATTCTGTCTAA
52495 TCAGATCAGATAACTCAAAGAACACTTCCAGAA
1 TCAGATCAGATAACTCAAAGAACACTTCCAGAA
52528 AATACTATGT
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 114 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
TCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCA
ATGCTTGATTCTGTCTAA
Found at i:52563 original size:52 final size:52
Alignment explanation
Indices: 52477--52899 Score: 699
Period size: 52 Copynumber: 8.1 Consensus size: 52
52467 TCTAAACTCA
* * *
52477 ATGCT-TGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAA
1 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
52529 ATACTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
52581 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
52633 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
52685 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
52737 ATGCTATGTTATGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAA
1 ATGCTATGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
52789 ATGCTATTTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
52841 ATGCTATGTTATGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAA
1 ATGCTATGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
52893 ATGCTAT
1 ATGCTAT
52900 TCTCTTTCAA
Statistics
Matches: 352, Mismatches: 15, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
51 1 0.00
52 347 0.99
53 4 0.01
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (52 bp):
ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:53722 original size:16 final size:16
Alignment explanation
Indices: 53686--53723 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
53676 TGAATTTCCA
53686 AAAATAAATTGAATCT
1 AAAATAAATTGAATCT
*
53702 CAAATAAATTGAA-CTT
1 AAAATAAATTGAATC-T
53718 AAAATA
1 AAAATA
53724 GATAGAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATAAATTGAATCT
Found at i:54050 original size:1 final size:1
Alignment explanation
Indices: 54044--54105 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
54034 TTGACCATTC
* * * * * * *
54044 TTTTTTTTTTTTTCTTTTTCTTTTCTTTTTTTTCTTTTTCTTTTCTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54106 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:54064 original size:20 final size:20
Alignment explanation
Indices: 54041--54103 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
54031 ACCTTGACCA
54041 TTCTTTTTTTTTTTTTCTTT
1 TTCTTTTTTTTTTTTTCTTT
*
54061 TTCTTTTCTTTTTTTTCTTT
1 TTCTTTTTTTTTTTTTCTTT
54081 TTCTTTTCTTTTTTCTTT-TTT
1 TTCTTTT-TTTTTT-TTTCTTT
54102 TT
1 TT
54104 TTCTTCAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
20 26 0.67
21 10 0.26
22 3 0.08
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (20 bp):
TTCTTTTTTTTTTTTTCTTT
Found at i:54067 original size:11 final size:11
Alignment explanation
Indices: 54041--54108 Score: 90
Period size: 11 Copynumber: 6.5 Consensus size: 11
54031 ACCTTGACCA
54041 TTCTTTT-TTT
1 TTCTTTTCTTT
54051 TT-TTTTCTTT
1 TTCTTTTCTTT
54061 TTCTTTTC-TT
1 TTCTTTTCTTT
54071 TT-TTTTCTTT
1 TTCTTTTCTTT
54081 TTCTTTTCTTTT
1 TTCTTTTC-TTT
*
54093 TTCTTTTTTTT
1 TTCTTTTCTTT
54104 TTCTT
1 TTCTT
54109 CAAGCATAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
9 9 0.17
10 15 0.29
11 18 0.35
12 10 0.19
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTCTTTTCTTT
Found at i:57635 original size:8 final size:8
Alignment explanation
Indices: 57622--57646 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
57612 TAAATTTATG
57622 AAATGTAA
1 AAATGTAA
57630 AAATGTAA
1 AAATGTAA
57638 AAATGTAA
1 AAATGTAA
57646 A
1 A
57647 GAAAATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AAATGTAA
Found at i:64687 original size:13 final size:15
Alignment explanation
Indices: 64665--64701 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
64655 CTTGACAGAA
64665 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
64677 AAATAAAATACTTGC
1 AAATAAAATACTTGC
64692 AAATAAAATA
1 AAATAAAATA
64702 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:65407 original size:14 final size:13
Alignment explanation
Indices: 65388--65486 Score: 57
Period size: 13 Copynumber: 7.9 Consensus size: 13
65378 TTCTTCGATA
65388 TTAAAAATAAATAT
1 TTAAAAAT-AATAT
65402 TTAAAAATAATAT
1 TTAAAAATAATAT
**
65415 TT-ATTAT-ATAT
1 TTAAAAATAATAT
65426 TT-AAAA-AATAT
1 TTAAAAATAATAT
* *
65437 TTAACAATAA-AA
1 TTAAAAATAATAT
* * * *
65449 ATACAAATACTAC
1 TTAAAAATAATAT
*
65462 TAAAATAAT-ATAT
1 TTAAA-AATAATAT
65475 TTAAAAATAATA
1 TTAAAAATAATA
65487 AGATAAATGA
Statistics
Matches: 62, Mismatches: 17, Indels: 13
0.67 0.18 0.14
Matches are distributed among these distances:
11 14 0.23
12 16 0.26
13 21 0.34
14 11 0.18
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAATAATAT
Found at i:66881 original size:3 final size:3
Alignment explanation
Indices: 66873--66970 Score: 126
Period size: 3 Copynumber: 33.0 Consensus size: 3
66863 TTAATATATT
* *
66873 TAA TAA TAA -AA AAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
66920 TGA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
66968 TAA
1 TAA
66971 AATGGATAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:66978 original size:12 final size:11
Alignment explanation
Indices: 66875--66985 Score: 61
Period size: 12 Copynumber: 9.9 Consensus size: 11
66865 AATATATTTA
**
66875 ATAATAAAAAA
1 ATAATAAAATG
*
66886 ATAATAATAATA
1 ATAATAA-AATG
*
66898 ATAATAATAATA
1 ATAATAA-AATG
*
66910 AAAATAATAATG
1 ATAATAA-AATG
*
66922 ATAATAATAT-
1 ATAATAAAATG
66932 -TAAT--AATG
1 ATAATAAAATG
66940 ATAATAATAAT-
1 ATAATAA-AATG
66951 ATTAATAATAATG
1 A-TAATAA-AATG
66964 ATAATAAAATGG
1 ATAATAAAAT-G
*
66976 ATAAAAAAAT
1 ATAATAAAAT
66986 AGTATCTTCA
Statistics
Matches: 84, Mismatches: 7, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
7 2 0.02
9 8 0.10
11 13 0.15
12 60 0.71
13 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:68212 original size:17 final size:17
Alignment explanation
Indices: 68190--68225 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
68180 GCAAAATATC
68190 CTTACCATTCAACAACA
1 CTTACCATTCAACAACA
68207 CTTACCATTCAACAACA
1 CTTACCATTCAACAACA
68224 CT
1 CT
68226 GGAGACGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (17 bp):
CTTACCATTCAACAACA
Found at i:81124 original size:25 final size:25
Alignment explanation
Indices: 81096--81150 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
81086 TAGGTAATTT
*
81096 ATTTTTTTTCTATAAAATTCTT-TAA
1 ATTTTTTTTATATAAAATT-TTATAA
* *
81121 ATTTATTTTATCTAAAATTTTATAA
1 ATTTTTTTTATATAAAATTTTATAA
81146 ATTTT
1 ATTTT
81151 AAATTAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTTTTTATATAAAATTTTATAA
Found at i:84954 original size:150 final size:150
Alignment explanation
Indices: 84683--84987 Score: 556
Period size: 150 Copynumber: 2.0 Consensus size: 150
84673 ATGAAGTTGG
84683 GGTTGATCTGTACATCAGAGGTTCCTTCAAGAAGACCTAGCATGGCTGAAGTTGTTCAAGTTCTC
1 GGTTGATCTGTACATCAGAGGTTCCTTCAAGAAGACCTAGCATGGCTGAAGTTGTTCAAGTTCTC
* *
84748 GAGTCCATCCGATCTGTAATCGAACCATAGTTAAAGTTCAAAGAAATGTTAGATGTCATTAATAC
66 GAGTCCATCCGATCTGGAATCGAACCATAGATAAAGTTCAAAGAAATGTTAGATGTCATTAATAC
84813 CGCAAAGAGGACACAGATAA
131 CGCAAAGAGGACACAGATAA
84833 GGTTGATCTGTACATCAGAGGTTCCTTCAAGAAGACCTAGCATGGCTGAAGTTGTTCAAGTTCTC
1 GGTTGATCTGTACATCAGAGGTTCCTTCAAGAAGACCTAGCATGGCTGAAGTTGTTCAAGTTCTC
* *
84898 GAGTCCGTTCGATCTGGAATCGAACCATAGATAAAGTTCAAAGAAATGTTAGATGTCATTAATAC
66 GAGTCCATCCGATCTGGAATCGAACCATAGATAAAGTTCAAAGAAATGTTAGATGTCATTAATAC
*
84963 CGCAAAGAGGACACATATAA
131 CGCAAAGAGGACACAGATAA
*
84983 AGTTG
1 GGTTG
84988 CTGCTAGTTA
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (150 bp):
GGTTGATCTGTACATCAGAGGTTCCTTCAAGAAGACCTAGCATGGCTGAAGTTGTTCAAGTTCTC
GAGTCCATCCGATCTGGAATCGAACCATAGATAAAGTTCAAAGAAATGTTAGATGTCATTAATAC
CGCAAAGAGGACACAGATAA
Found at i:86542 original size:23 final size:23
Alignment explanation
Indices: 86516--86562 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
86506 TCTCTTTTGT
86516 ATTTTTTTTCTTTCTCCAAATGC
1 ATTTTTTTTCTTTCTCCAAATGC
86539 ATTTTTTTTCTTTCTCCAAATGC
1 ATTTTTTTTCTTTCTCCAAATGC
86562 A
1 A
86563 AAGAGGCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTTTTTTTCTTTCTCCAAATGC
Found at i:90873 original size:3 final size:3
Alignment explanation
Indices: 90818--90860 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
90808 TTCATTTAAA
*
90818 TAT TAT T-T ATAT TAT CAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
90861 ATAAATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 31 0.89
4 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:92306 original size:30 final size:31
Alignment explanation
Indices: 92270--92335 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
92260 GTCATATAAA
92270 TATATATATAATAAATAATATTTT-ATATTT-TT
1 TATATATAT-ATAAAT--TATTTTAATATTTATT
92302 TATATATATATAAATTATTTTAATATTTATT
1 TATATATATATAAATTATTTTAATATTTATT
92333 TAT
1 TAT
92336 TTATTTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 6 0.19
30 6 0.19
31 11 0.34
32 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TATATATATATAAATTATTTTAATATTTATT
Found at i:96368 original size:15 final size:15
Alignment explanation
Indices: 96348--96379 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
96338 ATCAATACCT
96348 TTTTGCATACATACA
1 TTTTGCATACATACA
*
96363 TTTTGCATACATTCA
1 TTTTGCATACATACA
96378 TT
1 TT
96380 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:103732 original size:8 final size:8
Alignment explanation
Indices: 103715--103820 Score: 62
Period size: 8 Copynumber: 13.9 Consensus size: 8
103705 ATGCTTGAAT
*
103715 AAAAAAAG
1 AAAAAGAG
103723 AAAAAGAG
1 AAAAAGAG
103731 AAAAA-A-
1 AAAAAGAG
*
103737 AAGAAAGAA
1 AA-AAAGAG
103746 AAAAAGA-
1 AAAAAGAG
* *
103753 AAAAAAAA
1 AAAAAGAG
*
103761 AAAAAGAA
1 AAAAAGAG
* *
103769 AAAAAAAA
1 AAAAAGAG
*
103777 AAAAAAAG
1 AAAAAGAG
*
103785 AAAAAAAG
1 AAAAAGAG
103793 AAAAA-A-
1 AAAAAGAG
**
103799 AAAGGGA-
1 AAAAAGAG
103806 AAAAAGAG
1 AAAAAGAG
103814 AAAAAGA
1 AAAAAGA
103821 AAGGAAAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
6 5 0.06
7 17 0.20
8 59 0.71
9 2 0.02
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:103736 original size:15 final size:14
Alignment explanation
Indices: 103715--103831 Score: 111
Period size: 13 Copynumber: 8.5 Consensus size: 14
103705 ATGCTTGAAT
103715 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
103729 AGAAAAAA-AAGAAAG
1 A-AAAAAAGAA-AAAG
*
103744 AAAAAAAGAAAAAAA
1 AAAAAAAG-AAAAAG
103759 AAAAAAAGAAAAA-
1 AAAAAAAGAAAAAG
103772 AAAAAAA-AAAAAG
1 AAAAAAAGAAAAAG
103785 AAAAAAAG-AAAA-
1 AAAAAAAGAAAAAG
**
103797 AAAAAGGGAAAAAAG
1 AAAAAAAG-AAAAAG
* *
103812 AGAAAAAG-AAAGG
1 AAAAAAAGAAAAAG
103825 AAAAAAA
1 AAAAAAA
103832 AAGGGGGTCA
Statistics
Matches: 86, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
12 11 0.13
13 28 0.33
14 18 0.21
15 27 0.31
16 2 0.02
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:103776 original size:41 final size:44
Alignment explanation
Indices: 103716--103801 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 44
103706 TGCTTGAATA
*
103716 AAAAAAGAAAAAGAGAAAAAAAAGAAAGAAAAAAAGAAAAAAAA
1 AAAAAAGAAAAAGAGAAAAAAAAAAAAGAAAAAAAGAAAAAAAA
103760 AAAAAAG-AAAA-A-AAAAAAAAAAAAGAAAAAAAGAAAAAAAA
1 AAAAAAGAAAAAGAGAAAAAAAAAAAAGAAAAAAAGAAAAAAAA
103801 A
1 A
103802 GGGAAAAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
41 29 0.71
42 1 0.02
43 4 0.10
44 7 0.17
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (44 bp):
AAAAAAGAAAAAGAGAAAAAAAAAAAAGAAAAAAAGAAAAAAAA
Found at i:103818 original size:1 final size:1
Alignment explanation
Indices: 103715--103801 Score: 93
Period size: 1 Copynumber: 87.0 Consensus size: 1
103705 ATGCTTGAAT
* * * * * * *
103715 AAAAAAAGAAAAAGAGAAAAAAAAGAAAGAAAAAAAGAAAAAAAAAAAAAAGAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
103780 AAAAGAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
103802 GGGAAAAAAG
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:103829 original size:21 final size:19
Alignment explanation
Indices: 103715--103831 Score: 119
Period size: 21 Copynumber: 5.8 Consensus size: 19
103705 ATGCTTGAAT
*
103715 AAAAAAAGAAAAAGAGAAAA
1 AAAAAAAGAAAAAAAG-AAA
103735 AAAAGAAAGAAAAAAAGAAAAAAA
1 AAAA-AAAGAAAAAAAG----AAA
103759 AAAAAAAGAAAAAAA-AAA
1 AAAAAAAGAAAAAAAGAAA
103777 AAAAAAAGAAAAAAAGAAA
1 AAAAAAAGAAAAAAAGAAA
*
103796 AAAAAAGGGAAAAAAGAGAAA
1 AAAAAA-AGAAAAAA-AGAAA
* *
103817 AAGAAAGGAAAAAAA
1 AAAAAAAGAAAAAAA
103832 AAGGGGGTCA
Statistics
Matches: 87, Mismatches: 3, Indels: 15
0.83 0.03 0.14
Matches are distributed among these distances:
18 18 0.21
19 10 0.11
20 19 0.22
21 21 0.24
23 11 0.13
24 8 0.09
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAGAAA
Found at i:103829 original size:53 final size:55
Alignment explanation
Indices: 103715--103833 Score: 154
Period size: 53 Copynumber: 2.2 Consensus size: 55
103705 ATGCTTGAAT
*
103715 AAAAAAAGAAAAAGAGAAAAAAAAGAAAGAAAAAAAGAAAAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAAGAGAAAAAAAAGAAAGAAAAAAAGAAAAAAAAAAAAAAGAAA
* * *
103770 AAAAAAAAAAAAA-AG-AAAAAAAGAAA-AAAAAAGGGAAAAAAGAGAAAAAGAAA
1 AAAAAAAAAAAAAGAGAAAAAAAAGAAAGAAAAAA-AGAAAAAAAAAAAAAAGAAA
**
103823 GGAAAAAAAAA
1 AAAAAAAAAAA
103834 GGGGGTCAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
52 6 0.11
53 37 0.65
54 2 0.04
55 12 0.21
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (55 bp):
AAAAAAAAAAAAAGAGAAAAAAAAGAAAGAAAAAAAGAAAAAAAAAAAAAAGAAA
Found at i:104985 original size:93 final size:93
Alignment explanation
Indices: 104826--105208 Score: 687
Period size: 93 Copynumber: 4.1 Consensus size: 93
104816 ACAAGTGCTG
104826 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
104891 AAACCAATCATTGAATTTGGAAGATGAA
66 AAACCAATCATTGAATTTGGAAGATGAA
104919 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
104984 AAACCAATCATTGAATTTGGAAGATGAA
66 AAACCAATCATTGAATTTGGAAGATGAA
105012 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
*
105077 AAACCAATCATTGAATTTAGAAGATGAA
66 AAACCAATCATTGAATTTGGAAGATGAA
* *
105105 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTTGTATGAA-ACCAC
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA-
* * *
105169 ATAACCAATCATTGGATTTGAAAGATGAA
65 AAAACCAATCATTGAATTTGGAAGATGAA
*
105198 TGTGTTCATAG
1 TGTGCTCATAG
105209 TAAAAATAAG
Statistics
Matches: 281, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
92 3 0.01
93 278 0.99
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (93 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
AAACCAATCATTGAATTTGGAAGATGAA
Found at i:106194 original size:36 final size:34
Alignment explanation
Indices: 106147--106235 Score: 151
Period size: 36 Copynumber: 2.6 Consensus size: 34
106137 TTTCCAGAGA
106147 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTG-A-AAGAAG
106183 AAGTTCATAATGAGAAGAACTCATCTGAAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAAGAAG
*
106217 AAATTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
106236 TTTGTTCAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
34 24 0.46
35 1 0.02
36 27 0.52
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.20
Consensus pattern (34 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAAGAAG
Found at i:106224 original size:34 final size:36
Alignment explanation
Indices: 106144--106235 Score: 152
Period size: 34 Copynumber: 2.6 Consensus size: 36
106134 GCTTTTCCAG
106144 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 AGAAA-TTCATAATGAGAAGAACTCATCTGAAGAAGA
*
106181 AGAAGTTCATAATGAGAAGAACTCATCTG-A-AAGA
1 AGAAATTCATAATGAGAAGAACTCATCTGAAGAAGA
106215 AGAAATTCATAATGAGAAGAA
1 AGAAATTCATAATGAGAAGAA
106236 TTTGTTCAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
34 24 0.45
35 1 0.02
36 24 0.45
37 4 0.08
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.20
Consensus pattern (36 bp):
AGAAATTCATAATGAGAAGAACTCATCTGAAGAAGA
Found at i:106301 original size:143 final size:150
Alignment explanation
Indices: 106034--106348 Score: 466
Period size: 143 Copynumber: 2.1 Consensus size: 150
106024 TTTCCAGAGA
106034 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAACTTGTT
* * *
106099 CAACTTTTTGTTCAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
66 CAACTTTTTGTTCAAAACCATCACTTGATGGATAAACTTTTCCAGAGAAAGTTCATAATGAGAAG
106164 AACTCATCTGAAGAA-GAAG
131 AACTCATCTGAAGAAGGAAG
* *
106183 AAGTTCATAATGAGAAGAACTCATCTG-A-AA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAACTTGTT
* *
106242 CAACTTTTTGTTCAAAACCATCACTTGATGGATCAAAC-TTTCCAGAGGAAGTTCGTAATGAGAA
66 CAACTTTTTGTTCAAAACCATCACTTGATGGAT-AAACTTTTCCAGAGAAAGTTCATAATGAGAA
*
106306 GAATTCATCTGAAGAAGGAAG
130 GAACTCATCTGAAGAAGGAAG
106327 AAGAAATTCATAATGAGAAGAA
1 AAG---TTCATAATGAGAAGAA
106349 TTTGTTCAAC
Statistics
Matches: 153, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
143 91 0.59
144 11 0.07
145 1 0.01
146 4 0.03
147 18 0.12
148 1 0.01
149 27 0.18
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.27
Consensus pattern (150 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATAAGAAGAACTTGTT
CAACTTTTTGTTCAAAACCATCACTTGATGGATAAACTTTTCCAGAGAAAGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAG
Found at i:106345 original size:24 final size:23
Alignment explanation
Indices: 106302--106346 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
106292 GTTCGTAATG
*
106302 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
106325 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
106347 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:106351 original size:113 final size:112
Alignment explanation
Indices: 106182--106817 Score: 671
Period size: 113 Copynumber: 5.7 Consensus size: 112
106172 TGAAGAAGAA
106182 GAAGTTCATAATGAGAAGAACTCATCT---G-A-AAGAAGAAATTCATAATGAGAAGAATTTGTT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * *
106242 CAACTTTTTGTTCAAAACCATCACTTGATGGATCAAAC-TTTCCAGAG
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATC-AACTTTTCCAGAG
* *
106289 GAAGTTCGTAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGT
* *
106354 TCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAG
65 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAG
* *
106402 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGT
* * * * * * * *
106467 TAAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAG-G
65 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAG
*
106514 TAGAGTTCATAATGAGAAGAACACGTCATCT---GAAGAAGAAGAAATTCATAATGAGAAGAATT
1 GA-AGTTCATAATGAGAAG-A-AC-TCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATT
*
106576 TGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGA-
62 TGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAG
* **
106626 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG---TTCACAATGAGAAGAGCTTGTT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * * * *
106688 CAACCTTTTACAT-AATTTTATCACAAAAGCAAATAGATTAGCATCAAAC-TTTCCAGAG
66 CAACCTTTTGC-TCAA----ATC-C---ATC-ACTTGA-T-GGATC-AACTTTTCCAGAG
* * ** *
106746 AAAGTTCATAATGAGAAGAACTCATCTGAAGAATAAGAAG---TTCATAATGAGAAGAGCTTATT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
106808 CAACCTTTTG
66 CAACCTTTTG
106818 AATGACTCTA
Statistics
Matches: 455, Mismatches: 45, Indels: 45
0.83 0.08 0.08
Matches are distributed among these distances:
107 25 0.05
108 37 0.08
109 3 0.01
110 2 0.00
111 27 0.06
112 75 0.16
113 189 0.42
114 1 0.00
115 2 0.00
116 8 0.02
117 4 0.01
118 1 0.00
119 12 0.03
120 69 0.15
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (112 bp):
GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
CAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGAG
Found at i:106610 original size:225 final size:221
Alignment explanation
Indices: 106181--106696 Score: 737
Period size: 225 Copynumber: 2.3 Consensus size: 221
106171 CTGAAGAAGA
106181 AGAAGTTCATAATGAGAAGAACTCATCTGA-AAGAAG-A-AA-TTCATAATGAGAAGAATTTGTT
1 AGAAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * *
106242 CAACTTTTTGTTCAAAACCATCACTTGATGGATCAAACTTTCCAGAGGAAGTTCGTAATGAGAAG
66 CAACCTTTTGTTCAAAACCATCACTTGATGGATCAAACTTGCCAGAGGAAGTTCATAATGAGAAG
*
106307 AATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
131 AAGTCATCT--AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAAT
*
106372 CCATCATTTGATGGATCAGCTTTTCCAG
194 CCATCACTTGATGGATCAGCTTTTCCAG
106400 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
1 AG-AAGTTCATAATGAGAAGAACTCATCTG-AGAA-GAAGAAGAAGTTCATAATGAGAAGAATTT
* * ** * * *
106465 GTTAAACCTTTTGTTTAAATTCATCATTTGATGGAT-TAACATTGCCAG-GTAGAGTTCATAATG
63 GTTCAACCTTTTGTTCAAAACCATCACTTGATGGATCAAAC-TTGCCAGAGGA-AGTTCATAATG
106528 AGAAGAACACGTCATCT-GAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
126 AGAAG-A-A-GTCATCTAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
106591 TCAAATCCATCACTTGATGGATCAGCTTTTCCAG
188 TCAAATCCATCACTTGATGGATCAGCTTTTCCAG
* **
106625 AGAAGTTCATAATGAGAAGAACTCATCT--GAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTT
1 AGAAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
106688 CAACCTTTT
66 CAACCTTTT
106697 ACATAATTTT
Statistics
Matches: 269, Mismatches: 16, Indels: 23
0.87 0.05 0.07
Matches are distributed among these distances:
219 2 0.01
220 64 0.24
221 4 0.01
222 2 0.01
223 4 0.01
224 27 0.10
225 85 0.32
226 73 0.27
227 1 0.00
228 1 0.00
229 6 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (221 bp):
AGAAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTGTTCAAAACCATCACTTGATGGATCAAACTTGCCAGAGGAAGTTCATAATGAGAAG
AAGTCATCTAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCC
ATCACTTGATGGATCAGCTTTTCCAG
Found at i:106768 original size:120 final size:117
Alignment explanation
Indices: 106618--106903 Score: 380
Period size: 120 Copynumber: 2.4 Consensus size: 117
106608 TGGATCAGCT
*
106618 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAG
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGTTCACAATGAGAAGAG
* * * * *
106682 CTTGTTCAACCTTTT-ACATAATTTTATCACAAAAGCAAATAGATTAGCATCAA-A
66 CTTATTCAACCTTTTGA-ATAACTCTATCACAAAAGCAAATAG-GT--CAACAACA
* *
106736 CTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATAAGAAGTTCATAATGAGAAGA
1 -TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGTTCACAATGAGAAGA
* * *
106801 GCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACAACA
65 GCTTATTCAACCTTTTGAATAACTCTATCACAAAAGCAAATAGGTCAACAACA
* *
106854 TTCCCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAG
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAG
106904 AATTTATTCA
Statistics
Matches: 150, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
117 11 0.07
118 41 0.27
119 10 0.07
120 87 0.58
121 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (117 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAGAAGTTCACAATGAGAAGAG
CTTATTCAACCTTTTGAATAACTCTATCACAAAAGCAAATAGGTCAACAACA
Found at i:107103 original size:3 final size:3
Alignment explanation
Indices: 107042--107090 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
107032 TTCATTTAAA
107042 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
107086 TAT TA
1 TAT TA
107091 ATAAATATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 3 0.07
3 39 0.91
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:108438 original size:28 final size:28
Alignment explanation
Indices: 108370--108440 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
108360 ATTTTAATTT
* *
108370 TATTATAATTTA-GTCACTAATTTTAAA
1 TATTATAATTTATTTTACTAATTTTAAA
* * *
108397 TATTTTTATTTATTTTACTACTTTTAAA
1 TATTATAATTTATTTTACTAATTTTAAA
108425 TA-TATAATTGTATTTT
1 TATTATAATT-TATTTT
108441 TATTGTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.58
Consensus pattern (28 bp):
TATTATAATTTATTTTACTAATTTTAAA
Found at i:112457 original size:28 final size:28
Alignment explanation
Indices: 112417--112473 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
112407 TCGTCTAACC
112417 GTCCTCAATTCAGCGGTGAAGGAATGCT
1 GTCCTCAATTCAGCGGTGAAGGAATGCT
112445 GTCCTCAATTCAGCGGTGAAGGAATGCT
1 GTCCTCAATTCAGCGGTGAAGGAATGCT
112473 G
1 G
112474 ACTACGACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (28 bp):
GTCCTCAATTCAGCGGTGAAGGAATGCT
Found at i:125583 original size:14 final size:14
Alignment explanation
Indices: 125552--125604 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
125542 TAAAAATATT
* *
125552 TAATGATTTGATAC
1 TAATGATTTAATAA
125566 TAATGATTTAATAA
1 TAATGATTTAATAA
125580 T-A--A-TTAATAA
1 TAATGATTTAATAA
125590 TAATGATTTAATAA
1 TAATGATTTAATAA
125604 T
1 T
125605 TATTATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 8 0.24
11 2 0.06
13 2 0.06
14 21 0.64
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:125596 original size:24 final size:24
Alignment explanation
Indices: 125566--125614 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
125556 GATTTGATAC
125566 TAATGATTTAATAATAATTAATAA
1 TAATGATTTAATAATAATTAATAA
* *
125590 TAATGATTTAATAATTATTATTAA
1 TAATGATTTAATAATAATTAATAA
125614 T
1 T
125615 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
TAATGATTTAATAATAATTAATAA
Found at i:125621 original size:75 final size:74
Alignment explanation
Indices: 125536--125673 Score: 213
Period size: 75 Copynumber: 1.9 Consensus size: 74
125526 GTTGAATTTT
***
125536 TTAATTTAAAAATATTTAATGATTTGATACTAATGATTTAATAATAATTAATAATAATGATTTAA
1 TTAATTTAAAAATAAGAAATGATTTGATACTAATGATTTAATAATAATTAATAATAATGATTTAA
125601 TAATTATTA
66 TAATTATTA
* * *
125610 TTAATTTTAAAAATAAGAAATGATTTGATACTAATGATTTAGTAATGATTATTAATAATGATTT
1 TTAA-TTTAAAAATAAGAAATGATTTGATACTAATGATTTAATAATAATTAATAATAATGATTT
125674 CGTTGTTGTC
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
74 4 0.07
75 53 0.93
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.45
Consensus pattern (74 bp):
TTAATTTAAAAATAAGAAATGATTTGATACTAATGATTTAATAATAATTAATAATAATGATTTAA
TAATTATTA
Found at i:126779 original size:13 final size:14
Alignment explanation
Indices: 126756--126785 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
126746 TTTAATAAAT
126756 TTAAGATAAAAAAA
1 TTAAGATAAAAAAA
126770 TTAA-ATAAAAAAA
1 TTAAGATAAAAAAA
126783 TTA
1 TTA
126786 CCTTCCGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
TTAAGATAAAAAAA
Found at i:127208 original size:50 final size:50
Alignment explanation
Indices: 127118--127217 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
127108 TCATTATTGG
* * ***
127118 TAATCATTATTAAATCATTAGTATCAAATTATTTCTTATTTTTAAATTAA
1 TAATAATTATTAAATCATTAGTATCAAATCATTAAATATTTTTAAATTAA
127168 TAATAATTATTAAATCATTAGTATCAAATCATTAAATATTTTTAAATTAA
1 TAATAATTATTAAATCATTAGTATCAAATCATTAAATATTTTTAAATTAA
127218 AAAATTCAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (50 bp):
TAATAATTATTAAATCATTAGTATCAAATCATTAAATATTTTTAAATTAA
Found at i:127534 original size:19 final size:19
Alignment explanation
Indices: 127510--127546 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
127500 ATGACCAACA
*
127510 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
127529 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
127547 CAGTATCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:127680 original size:20 final size:20
Alignment explanation
Indices: 127657--127783 Score: 157
Period size: 20 Copynumber: 6.3 Consensus size: 20
127647 ATGTAAATCA
127657 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
**
127677 CAACGCGATAAT-ACATAATCG
1 CAACGCGATTCTGAC-T-ATCG
***
127698 CAATTTGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
*
127718 CAACGTGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
*
127738 CAACGCAATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
*
127758 CAACGCGATTCTGACTTTCG
1 CAACGCGATTCTGACTATCG
127778 CAACGC
1 CAACGC
127784 TGAATTTCAA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 75 0.82
21 12 0.13
22 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (20 bp):
CAACGCGATTCTGACTATCG
Found at i:128357 original size:20 final size:20
Alignment explanation
Indices: 128332--128384 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
128322 ATAATACATA
128332 ATCGCAACGCGATTCTAACT
1 ATCGCAACGCGATTCTAACT
128352 ATCGCAACGCGATTCTAACT
1 ATCGCAACGCGATTCTAACT
*
128372 ATCGTAACGCGAT
1 ATCGCAACGCGAT
128385 AATACATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTAACT
Found at i:128600 original size:11 final size:11
Alignment explanation
Indices: 128586--128650 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
128576 AAAATTCAAG
128586 AGCTCGATTGA
1 AGCTCGATTGA
*
128597 AGCTCGAGACTCG-
1 AGCTC--GA-TTGA
128610 AGCTCGATTGA
1 AGCTCGATTGA
128621 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
128633 AGCTCGATTCA
1 AGCTCGATTGA
128644 AGCTCGA
1 AGCTCGA
128651 ACTTGATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 4 0.09
11 21 0.48
12 7 0.16
13 10 0.23
14 2 0.05
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:128656 original size:23 final size:23
Alignment explanation
Indices: 128585--128656 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
128575 AAAAATTCAA
*
128585 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGA-ACTT
**
128609 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGAACTT
*
128632 GAGCTCGATTCAAGCTCGAACTT
1 GAGCTCGATTGAAGCTCGAACTT
128655 GA
1 GA
128657 TTAAAGCTCG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 23 0.55
24 19 0.45
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGAACTT
Found at i:128663 original size:17 final size:17
Alignment explanation
Indices: 128638--128670 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
128628 TTTTGAGCTC
*
128638 GATTCAAGCTCGAACTT
1 GATTAAAGCTCGAACTT
128655 GATTAAAGCTCGAACT
1 GATTAAAGCTCGAACT
128671 CAAACTCGAA
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:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (17 bp):
GATTAAAGCTCGAACTT
Found at i:128975 original size:21 final size:21
Alignment explanation
Indices: 128950--129043 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
128940 TGGCATAACT
128950 TAAACCCTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
*
128971 TAAACCTTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
* * * *
128992 TAAACTCTAA-ACTTTAAATCT
1 TAAACCCTAACAC-ATAAACCC
* * *
129013 TAAATCCTATCACATAAACTC
1 TAAACCCTAACACATAAACCC
*
129034 TAAATCCTAA
1 TAAACCCTAA
129044 ACCCTAAACC
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACCCTAACACATAAACCC
Found at i:129345 original size:15 final size:14
Alignment explanation
Indices: 129319--129348 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
129309 TTTATTCATC
129319 AATAATGTATTTTT
1 AATAATGTATTTTT
*
129333 AATAATGTAATTTT
1 AATAATGTATTTTT
129347 AA
1 AA
129349 AAAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:129577 original size:20 final size:20
Alignment explanation
Indices: 129552--129703 Score: 164
Period size: 20 Copynumber: 7.5 Consensus size: 20
129542 TACAGCCCTA
129552 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
129572 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
*
129592 AATCGCAACACGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
129613 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * **
129633 ACCGCAATGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
*
129653 AATCGCAACTCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
129674 ATTGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
129694 GTCGCAACGC
1 ATCGCAACGC
129704 TGAATTTCAA
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
19 4 0.04
20 73 0.68
21 26 0.24
22 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:129647 original size:61 final size:61
Alignment explanation
Indices: 129552--129703 Score: 250
Period size: 61 Copynumber: 2.5 Consensus size: 61
129542 TACAGCCCTA
*
129552 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATAATCGCAACACGATTCTGACT
1 ATCGCAACGCGATTCTGACTACCGCAACGCGATAATACATAATCGCAACACGATTCTGACT
* *
129613 ATCGCAACGCGATTCTGACTACCGCAATGCGATAATACATAATCGCAACTCGATTCTGACT
1 ATCGCAACGCGATTCTGACTACCGCAACGCGATAATACATAATCGCAACACGATTCTGACT
* **
129674 ATTGCAACGCGATTCTGACTGTCGCAACGC
1 ATCGCAACGCGATTCTGACTACCGCAACGC
129704 TGAATTTCAA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 84 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (61 bp):
ATCGCAACGCGATTCTGACTACCGCAACGCGATAATACATAATCGCAACACGATTCTGACT
Found at i:131522 original size:20 final size:20
Alignment explanation
Indices: 131497--131542 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
131487 GCGATTATCT
*
131497 CGTTGCGGTAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
131517 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
131537 CGTTGC
1 CGTTGC
131543 AATTTTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.28, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:133490 original size:20 final size:20
Alignment explanation
Indices: 133442--133531 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
133432 TCTGAAACTT
*
133442 AAAAGCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
133462 AAAACCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** ** **
133482 ACTATCGCAACGTGAATTTG
1 AAAATCGCAACACGAAAATG
** *
133502 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
133521 AAAATCGCAAC
1 AAAATCGCAAC
133532 GAGAAAATCG
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
19 12 0.21
20 45 0.79
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:133539 original size:14 final size:14
Alignment explanation
Indices: 133520--133551 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
133510 AACGCGAAAT
133520 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
133534 GAAAATCGCAACGT
1 GAAAATCGCAACGA
133548 GAAA
1 GAAA
133552 CTAAAATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.22, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:133793 original size:3 final size:3
Alignment explanation
Indices: 133778--133818 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
133768 ATTACCAATA
* *
133778 AAC AAC AAT AAC AAC AAC AAT AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
133819 TACCCTATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.27, G:0.00, T:0.05
Consensus pattern (3 bp):
AAC
Found at i:133795 original size:12 final size:12
Alignment explanation
Indices: 133778--133818 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
133768 ATTACCAATA
133778 AACAACAATAAC
1 AACAACAATAAC
133790 AACAACAATAAC
1 AACAACAATAAC
*
133802 AACAACAACAAC
1 AACAACAATAAC
133814 AACAA
1 AACAA
133819 TACCCTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.68, C:0.27, G:0.00, T:0.05
Consensus pattern (12 bp):
AACAACAATAAC
Found at i:135423 original size:20 final size:19
Alignment explanation
Indices: 135400--135445 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
135390 GGAAACTGAT
* *
135400 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
135420 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
135439 TTGCGAT
1 TTGCGAT
135446 TTTGTTTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:135435 original size:19 final size:19
Alignment explanation
Indices: 135411--135447 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
135401 TGCGATACTG
*
135411 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
135430 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
135448 TGTTTGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:135555 original size:11 final size:11
Alignment explanation
Indices: 135541--135609 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
135531 ATCAAAAATG
135541 TTATAAAATCA
1 TTATAAAATCA
*
135552 TTAT--TATCA
1 TTATAAAATCA
135561 TTATAAAATCA
1 TTATAAAATCA
*
135572 TTAT--TATCA
1 TTATAAAATCA
*
135581 TTATTAAATCA
1 TTATAAAATCA
135592 TTATTATCAAATCA
1 TTA-TA--AAATCA
135606 TTAT
1 TTAT
135610 TATCAAATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
9 16 0.35
11 19 0.41
12 1 0.02
13 1 0.02
14 9 0.20
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.46
Consensus pattern (11 bp):
TTATAAAATCA
Found at i:135566 original size:20 final size:20
Alignment explanation
Indices: 135541--135600 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
135531 ATCAAAAATG
135541 TTATAAAATCATTATTATCA
1 TTATAAAATCATTATTATCA
135561 TTATAAAATCATTATTATCA
1 TTATAAAATCATTATTATCA
*
135581 TTATTAAATCATTATTATCA
1 TTATAAAATCATTATTATCA
135601 AATCATTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATAAAATCATTATTATCA
Found at i:135577 original size:14 final size:14
Alignment explanation
Indices: 135560--135625 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 14
135550 CATTATTATC
135560 ATTATAAAATCATT
1 ATTATAAAATCATT
135574 ATTATCATTATTAAATCATT
1 ATTAT-A--A--A-ATCATT
*
135594 ATTATCAAATCATT
1 ATTATAAAATCATT
* *
135608 ATTATCAAATTATT
1 ATTATAAAATCATT
135622 ATTA
1 ATTA
135626 AATATTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
14 28 0.64
15 2 0.05
17 2 0.05
19 1 0.02
20 11 0.25
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATAAAATCATT
Found at i:135614 original size:9 final size:9
Alignment explanation
Indices: 135548--135600 Score: 61
Period size: 9 Copynumber: 5.4 Consensus size: 9
135538 ATGTTATAAA
135548 ATCATTATT
1 ATCATTATT
*
135557 ATCATTATAAA
1 ATCATTAT--T
135568 ATCATTATT
1 ATCATTATT
135577 ATCATTATT
1 ATCATTATT
135586 AAATCATTATT
1 --ATCATTATT
135597 ATCA
1 ATCA
135601 AATCATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 21 0.55
11 17 0.45
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (9 bp):
ATCATTATT
Found at i:136632 original size:24 final size:24
Alignment explanation
Indices: 136576--136634 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
136566 TCATTTATTA
*
136576 TGTTCGTTTATGTTTGTTTACATC
1 TGTTCGTTTATGTTTGTTCACATC
* * * * *
136600 CGTTTGTTTGTGTTTGTTCATATG
1 TGTTCGTTTATGTTTGTTCACATC
136624 TGTTCGTTTAT
1 TGTTCGTTTAT
136635 CATTTAAATG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.59
Consensus pattern (24 bp):
TGTTCGTTTATGTTTGTTCACATC
Found at i:136960 original size:18 final size:19
Alignment explanation
Indices: 136925--136961 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
136915 CACGGAATGT
136925 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
136945 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
136962 GGATTACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:137677 original size:90 final size:89
Alignment explanation
Indices: 137516--137692 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 89
137506 AATGTGGATT
*
137516 ACATTCTCATGTGAATCTCACATTCCCCCATCCAAACACCCTCTAAGTCTCCATCTTCTCCAAAG
1 ACATTCTCATGTGAATCTCACATTCCCCCATCCAAACACCCTCTAAATCTCCATCTTCTCCAAAG
137581 AAGGGGGAAGGTCGTAATTTCGTCC
66 AAGGGGG-AGGTCGTAATTTCGTCC
* **
137606 ACATTTTCATGTGAATCTCACATTCTTCCATCCAAACACCC-CTAAATCTCCATCTTCTCCAAAG
1 ACATTCTCATGTGAATCTCACATTCCCCCATCCAAACACCCTCTAAATCTCCATCTTCTCCAAAG
137670 AAGGGGGGAGGTCGTAATTTCGT
66 AA-GGGGGAGGTCGTAATTTCGT
137693 GACTCTACTT
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
89 39 0.48
90 43 0.52
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (89 bp):
ACATTCTCATGTGAATCTCACATTCCCCCATCCAAACACCCTCTAAATCTCCATCTTCTCCAAAG
AAGGGGGAGGTCGTAATTTCGTCC
Found at i:151408 original size:238 final size:238
Alignment explanation
Indices: 150977--151465 Score: 735
Period size: 238 Copynumber: 2.1 Consensus size: 238
150967 AAGAATATTT
* ** *
150977 TTCAATTCTGCCAGCCGATTTTCATGAAGAAACAAACTGCTATTTTGTGAAGAGGTTCTCCACCA
1 TTCAAATCTGCCAGCCGATTTTCATGAAGAAACAAACAACTATTTTGTAAAGAGGTTCTCCACCA
* * * *
151042 CCGACTGACTCATCTTCCACAACCAATTTCCCACTGACGGCCTCATTTCCCATTCTTTTCTTCCG
66 CCGACTAACACATCTTCCACAACCAATTTCCCACTGACGCCCTCATTTCCCATTCTTCTCTTCCG
* * *
151107 CCGTTGATCACCGGATCTTCTAGATTTGCTTGCCTGGACACCAACATCAAGGATATGCTTCGTTT
131 CCGTTGATCACCGGATCTTCCAGATTTGCTTGCCTCGACACCAACATCAAGGATATACTTCGTTT
*
151172 CTTGAGGGAGATCCTCATCTTAATGAACCTAAGCCAAGTGTTC
196 CTTGAGGGAGATCCTCATCTCAATGAACCTAAGCCAAGTGTTC
* * * *
151215 TTCAAATCTGCCAGTCGATTTTCATGAAGAAACAAGCAATTGTTTTGTAAAGAGGTTCTCCACCA
1 TTCAAATCTGCCAGCCGATTTTCATGAAGAAACAAACAACTATTTTGTAAAGAGGTTCTCCACCA
* * * * * *
151280 CCGACTAACACATCTTCCATAGCCGATTTCTCACTGACGCCCTCTTTTCCCGTTCTTCTCTTCCG
66 CCGACTAACACATCTTCCACAACCAATTTCCCACTGACGCCCTCATTTCCCATTCTTCTCTTCCG
* *
151345 TCGTTGATCACCGGATCTTCCAGATTTGCTTGCCTCGACACCAGCATCAAGGATATACTTCGTTT
131 CCGTTGATCACCGGATCTTCCAGATTTGCTTGCCTCGACACCAACATCAAGGATATACTTCGTTT
* * *
151410 CTTGAGGGAGATCCTCATCTCAGTGGACCTAAGCCGAGTGTTC
196 CTTGAGGGAGATCCTCATCTCAATGAACCTAAGCCAAGTGTTC
151453 TTCAAATCTGCCA
1 TTCAAATCTGCCA
151466 CCGTCGCCGA
Statistics
Matches: 224, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
238 224 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (238 bp):
TTCAAATCTGCCAGCCGATTTTCATGAAGAAACAAACAACTATTTTGTAAAGAGGTTCTCCACCA
CCGACTAACACATCTTCCACAACCAATTTCCCACTGACGCCCTCATTTCCCATTCTTCTCTTCCG
CCGTTGATCACCGGATCTTCCAGATTTGCTTGCCTCGACACCAACATCAAGGATATACTTCGTTT
CTTGAGGGAGATCCTCATCTCAATGAACCTAAGCCAAGTGTTC
Done.