Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007844.1 Hibiscus syriacus cultivar Beakdansim tig00110198_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: 2094103
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:250651 original size:23 final size:23
Alignment explanation
Indices: 250594--250652 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
250584 AAATCATAAG
* *
250594 AAATGTGCCACAATAGCAGAGAA
1 AAATGTGCCACAATAGCAAAAAA
* *
250617 AAACGTGTCACAATAGCAAAAAA
1 AAATGTGCCACAATAGCAAAAAA
*
250640 AAATATGCCACAA
1 AAATGTGCCACAA
250653 GGGCATCGAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.14
Consensus pattern (23 bp):
AAATGTGCCACAATAGCAAAAAA
Found at i:262648 original size:2 final size:2
Alignment explanation
Indices: 262643--262672 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
262633 TAGATATCAG
262643 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
262673 ACATTTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:265294 original size:2 final size:2
Alignment explanation
Indices: 265289--265331 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
265279 ACATAACTAC
265289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
265331 T
1 T
265332 TGAATTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:270755 original size:13 final size:13
Alignment explanation
Indices: 270737--270764 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
270727 AATGTGTTTG
270737 AAATATAAATATT
1 AAATATAAATATT
270750 AAATATAAATATT
1 AAATATAAATATT
270763 AA
1 AA
270765 TAGAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATATAAATATT
Found at i:274842 original size:165 final size:165
Alignment explanation
Indices: 274570--274900 Score: 662
Period size: 165 Copynumber: 2.0 Consensus size: 165
274560 TTATATTATT
274570 TATGATTAATGAATTCGTAATATCTTAATTTTTATCTACCAATAGCAGTTGAGATACTGTAAGAA
1 TATGATTAATGAATTCGTAATATCTTAATTTTTATCTACCAATAGCAGTTGAGATACTGTAAGAA
274635 TGCAAAATACTAAAGGACATAAACATTGGATAAATAAAATCTAGTATTAGTTTAAATACATAGAA
66 TGCAAAATACTAAAGGACATAAACATTGGATAAATAAAATCTAGTATTAGTTTAAATACATAGAA
274700 ATAAAAATTATGATACACACCACGTATCATCCTCC
131 ATAAAAATTATGATACACACCACGTATCATCCTCC
274735 TATGATTAATGAATTCGTAATATCTTAATTTTTATCTACCAATAGCAGTTGAGATACTGTAAGAA
1 TATGATTAATGAATTCGTAATATCTTAATTTTTATCTACCAATAGCAGTTGAGATACTGTAAGAA
274800 TGCAAAATACTAAAGGACATAAACATTGGATAAATAAAATCTAGTATTAGTTTAAATACATAGAA
66 TGCAAAATACTAAAGGACATAAACATTGGATAAATAAAATCTAGTATTAGTTTAAATACATAGAA
274865 ATAAAAATTATGATACACACCACGTATCATCCTCC
131 ATAAAAATTATGATACACACCACGTATCATCCTCC
274900 T
1 T
274901 CGGTCATGCA
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 166 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (165 bp):
TATGATTAATGAATTCGTAATATCTTAATTTTTATCTACCAATAGCAGTTGAGATACTGTAAGAA
TGCAAAATACTAAAGGACATAAACATTGGATAAATAAAATCTAGTATTAGTTTAAATACATAGAA
ATAAAAATTATGATACACACCACGTATCATCCTCC
Found at i:277966 original size:111 final size:109
Alignment explanation
Indices: 277791--278088 Score: 401
Period size: 111 Copynumber: 2.7 Consensus size: 109
277781 AAGCGTTGGA
277791 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTT-TC-C-T-TTGGATGAGTTCTTCTCATTATGAAC
*
277856 TCTTCACTGAAAATGTTGATCCA-CTCCTTCTGTGAT-GA-TCGAACCAAGG
62 TCTTCACTGAAAATGTTGACCCATCTCCTTCTGTGATGGATTCG-A--AA-G
277905 TTGAACAAGTTCTTCTCATTATGAACTTCTTTCCTCTTGGATGAGTTCTTCTCATTATGAACTCT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTTCCT-TTGGATGAGTTCTTCTCATTATGAACTCT
* *
277970 TCACTGAAAATGTTGACCCATCTCTTTCTGTGATGGATTTGAAAG
65 TCACTGAAAATGTTGACCCATCTCCTTCTGTGATGGATTCGAAAG
* * * *
278015 --GAACAAGTTCTTCTCATTATGAACTT-TATCCTTTAGATGAGTTCTTCTCATTATGAGCTCTC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTTCCTTTGGATGAGTTCTTCTCATTATGAACTCTT
*
278077 CATTGAAAATGT
66 CACTGAAAATGT
278089 GATGCGAAGT
Statistics
Matches: 172, Mismatches: 9, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
106 38 0.22
107 5 0.03
108 26 0.15
110 1 0.01
111 51 0.30
112 13 0.08
113 5 0.03
114 33 0.19
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (109 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTTCCTTTGGATGAGTTCTTCTCATTATGAACTCTT
CACTGAAAATGTTGACCCATCTCCTTCTGTGATGGATTCGAAAG
Found at i:278174 original size:87 final size:85
Alignment explanation
Indices: 278015--278175 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 85
278005 GATTTGAAAG
* * *
278015 GAACAAGTTCTTCTCATTATGAACTTTATCCTTTAGATGAGTTCTTCTCATTATGAGCTCTCCAT
1 GAACAAGTTCTTCTCATTATGAACTTTATCCTTCAGATGAGTTCTTCTCATTATGAACTCTCCAC
278080 TGAAAATGTGATGCGAAGTT
66 TGAAAATGTGATGCGAAGTT
* *
278100 GAACAAGTTCTTCTCATTATGAACTTCT-TCTTCTTCGGATGAGTTCTTCTCATTATGAACTCTT
1 GAACAAGTTCTTCTCATTATGAACTT-TATC--CTTCAGATGAGTTCTTCTCATTATGAACTCTC
*
278164 CACTGGAAATGT
63 CACTGAAAATGT
278176 TGATCCCTCA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
85 28 0.42
86 1 0.01
87 38 0.57
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (85 bp):
GAACAAGTTCTTCTCATTATGAACTTTATCCTTCAGATGAGTTCTTCTCATTATGAACTCTCCAC
TGAAAATGTGATGCGAAGTT
Found at i:278329 original size:135 final size:136
Alignment explanation
Indices: 278100--278444 Score: 547
Period size: 135 Copynumber: 2.6 Consensus size: 136
278090 ATGCGAAGTT
*
278100 GAACAAGTTCTTCTCATTATGAACTTCTTCT---TCT-TCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * ** * * *
278161 CTTCACTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTTATGAATCGAGTGA
66 CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
278226 TAGGTC
131 TAGGTC
278232 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTC-TCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * *
278296 ATCCATTGGAAATACTGATCCTTCAAGCAAGGTGTCACTGATTCAAAATGTCGTGAATCTAGTGA
66 CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
278361 TAGGTC
131 TAGGTC
278367 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
278432 CTCCATTGGAAAT
66 CTCCATTGGAAAT
278445 GTTGGTTCAC
Statistics
Matches: 195, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
132 30 0.15
135 127 0.65
136 38 0.19
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATACTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
TAGGTC
Found at i:279331 original size:7 final size:7
Alignment explanation
Indices: 279321--279404 Score: 58
Period size: 6 Copynumber: 12.7 Consensus size: 7
279311 CCTTTTTCTC
279321 TTTTT-A
1 TTTTTCA
279327 TTTTTCA
1 TTTTTCA
*
279334 --TTTCT
1 TTTTTCA
279339 TTTTTCA
1 TTTTTCA
279346 TTTTTCA
1 TTTTTCA
279353 TTTTTTC-
1 -TTTTTCA
279360 TTTTTCA
1 TTTTTCA
279367 -TTTT--
1 TTTTTCA
279371 TTTTT-A
1 TTTTTCA
279377 TTTTTCA
1 TTTTTCA
*
279384 TCTTTTTA
1 T-TTTTCA
*
279392 TTTGTTCC
1 TTT-TTCA
279400 TTTTT
1 TTTTT
279405 TTTTCTTCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
5 8 0.13
6 20 0.32
7 18 0.29
8 17 0.27
ACGTcount: A:0.10, C:0.12, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:279332 original size:14 final size:14
Alignment explanation
Indices: 279313--279408 Score: 59
Period size: 14 Copynumber: 7.3 Consensus size: 14
279303 CAAACCCTCC
279313 TTTTTCTCTTTTTA
1 TTTTTCTCTTTTTA
* *
279327 TTTTTC-ATTTCT-
1 TTTTTCTCTTTTTA
*
279339 TTTTTCAT-TTTTCA
1 TTTTTC-TCTTTTTA
279353 TTTTT-TCTTTTTCA
1 TTTTTCTCTTTTT-A
279367 --TTT-T-TTTTTA
1 TTTTTCTCTTTTTA
279377 TTTTTCATCTTTTTA
1 TTTTTC-TCTTTTTA
279392 TTTGTTC-CTTTTT-
1 TTT-TTCTCTTTTTA
279405 TTTT
1 TTTT
279409 CTTCAAGCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 24
0.69 0.05 0.25
Matches are distributed among these distances:
10 1 0.02
11 5 0.08
12 15 0.23
13 14 0.21
14 19 0.29
15 9 0.14
16 3 0.05
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTTTCTCTTTTTA
Found at i:279343 original size:19 final size:19
Alignment explanation
Indices: 279315--279371 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
279305 AACCCTCCTT
*
279315 TTTCTCTTTTTATTTTTCA
1 TTTCTTTTTTTATTTTTCA
*
279334 TTTCTTTTTTCATTTTTCA
1 TTTCTTTTTTTATTTTTCA
*
279353 TTTTTTCTTTTTCATTTTT
1 TTTCTT-TTTTT-ATTTTT
279372 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 22 0.69
20 4 0.12
21 6 0.19
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTCTTTTTTTATTTTTCA
Found at i:279351 original size:33 final size:33
Alignment explanation
Indices: 279313--279409 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
279303 CAAACCCTCC
279313 TTTTTC-TCTTTTTATTTTTCATTTCTTTTTTCA
1 TTTTTCATCTTTTTATTTTTCATTT-TTTTTTCA
*
279346 TTTTTCAT-TTTTTCTTTTTCATTTTTTTTT-A
1 TTTTTCATCTTTTTATTTTTCATTTTTTTTTCA
*
279377 TTTTTCATCTTTTTATTTGTTCCTTTTTTTTTC
1 TTTTTCATCTTTTTATTT-TTCATTTTTTTTTC
279410 TTCAAGCATA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
31 9 0.16
32 14 0.25
33 33 0.58
34 1 0.02
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.77
Consensus pattern (33 bp):
TTTTTCATCTTTTTATTTTTCATTTTTTTTTCA
Found at i:294150 original size:2 final size:2
Alignment explanation
Indices: 294145--294178 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
294135 TTTTAAATCG
294145 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
294179 TTGTATTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:294485 original size:21 final size:23
Alignment explanation
Indices: 294461--294504 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
294451 TCCTAAACTC
*
294461 AAAT-CCTTAATTTCAA-ACCCA
1 AAATCCCTTAATTCCAACACCCA
294482 AAATCCCTTAATTCCAACACCCA
1 AAATCCCTTAATTCCAACACCCA
294505 TCCATCTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (23 bp):
AAATCCCTTAATTCCAACACCCA
Found at i:294875 original size:7 final size:7
Alignment explanation
Indices: 294863--294890 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
294853 TGAAATGGAT
294863 GAAGAAG
1 GAAGAAG
294870 GAAGAAG
1 GAAGAAG
294877 GAAGAAG
1 GAAGAAG
294884 GAAGAAG
1 GAAGAAG
294891 AAATGGGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
GAAGAAG
Found at i:306855 original size:4 final size:4
Alignment explanation
Indices: 306848--306887 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
306838 ATATGCACAC
*
306848 GTAT GTAT GTAT GTAT GTAT GTAT GTAT ATAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
306888 ATGTCCATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:314290 original size:95 final size:96
Alignment explanation
Indices: 314110--314293 Score: 219
Period size: 95 Copynumber: 1.9 Consensus size: 96
314100 CTCTAAATGT
* *
314110 AAGTTTCAGATAAAGATAAACGTCTAATAAGAAAGACAAATATTAATATTAGAGAATAGAGCATC
1 AAGTTTCAGATAAAGATAAACGTCTAAAAAGAAAGACAAATATTAATATAAGAGAATAGAGCATC
*
314175 AACTCTCCCAATATAATCTTAGATATACTCG
66 AACTCTCCCAATACAATCTTAGATATACTCG
* ** * * * *
314206 AAGTTTCATATAAAGAT-AGTGTTTAAAAAGAAAGACAAGTATTAATGTAAGAGAGA-AGAGCCT
1 AAGTTTCAGATAAAGATAAACGTCTAAAAAGAAAGACAAATATTAATATAAGAGA-ATAGAGCAT
* * * *
314269 CAGCTTTCCTAATACAGTCTTAGAT
65 CAACTCTCCCAATACAATCTTAGAT
314294 GAAAATCTAT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
95 56 0.77
96 17 0.23
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (96 bp):
AAGTTTCAGATAAAGATAAACGTCTAAAAAGAAAGACAAATATTAATATAAGAGAATAGAGCATC
AACTCTCCCAATACAATCTTAGATATACTCG
Found at i:323060 original size:2 final size:2
Alignment explanation
Indices: 323053--323082 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
323043 TTAACCGCTA
323053 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
323083 TACTGACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332591 original size:13 final size:13
Alignment explanation
Indices: 332559--332584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
332549 AATTATAAAC
332559 ATAACAATAATAA
1 ATAACAATAATAA
332572 ATAACAATAATAA
1 ATAACAATAATAA
332585 TATACAAAGA
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAACAATAATAA
Found at i:332804 original size:61 final size:58
Alignment explanation
Indices: 332706--332840 Score: 180
Period size: 60 Copynumber: 2.3 Consensus size: 58
332696 TTTATATTGA
*
332706 TCTTTAAACTTTTGAATATTTAATTTCATCCCAAAACTATGACTCTCTTTATAAAATAG
1 TCTTTAAACTTTTGAAAATTTAATTTCATCCCAAAACTATGAC-CTCTTTATAAAATAG
* * *
332765 TCTTTAAACTTTTTGAAAATTTTAATTTCATCCCTAAACTATGACCTCTTTCTAAATTAG
1 TCTTTAAAC-TTTTGAAAA-TTTAATTTCATCCCAAAACTATGACCTCTTTATAAAATAG
***
332825 TCCCCAAACTTTTGAA
1 TCTTTAAACTTTTGAA
332841 CATTCCAAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 16 0.24
60 27 0.40
61 24 0.36
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.42
Consensus pattern (58 bp):
TCTTTAAACTTTTGAAAATTTAATTTCATCCCAAAACTATGACCTCTTTATAAAATAG
Found at i:333050 original size:31 final size:31
Alignment explanation
Indices: 333014--333081 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
333004 ATGTTAAAAA
333014 AGTTTGGGGAT-AAATTAAAAATGAA-GGTCAT
1 AGTTTGGGGATGAAATT-AAAAT-AAGGGTCAT
333045 AGTTTGGGGATGAAATTAAAATAAGGGTCAT
1 AGTTTGGGGATGAAATTAAAATAAGGGTCAT
*
333076 ACTTTG
1 AGTTTG
333082 AGGACATGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 2 0.06
31 27 0.79
32 5 0.15
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.31
Consensus pattern (31 bp):
AGTTTGGGGATGAAATTAAAATAAGGGTCAT
Found at i:339305 original size:32 final size:32
Alignment explanation
Indices: 339268--339332 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
339258 TAAAAGAGTT
339268 AATTGGATTTTCATATGATCTTAAATTGCAGC
1 AATTGGATTTTCATATGATCTTAAATTGCAGC
*
339300 AATTGGATTTTCATATGATCTTAAATTTCAGC
1 AATTGGATTTTCATATGATCTTAAATTGCAGC
339332 A
1 A
339333 TATAAAAGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (32 bp):
AATTGGATTTTCATATGATCTTAAATTGCAGC
Found at i:339417 original size:9 final size:9
Alignment explanation
Indices: 339403--339432 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
339393 TTTTTCTATT
339403 TTAACCGAA
1 TTAACCGAA
*
339412 TTAACCGAC
1 TTAACCGAA
339421 TTAACCGAA
1 TTAACCGAA
339430 TTA
1 TTA
339433 GTTCGGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (9 bp):
TTAACCGAA
Found at i:339805 original size:27 final size:28
Alignment explanation
Indices: 339775--339848 Score: 71
Period size: 31 Copynumber: 2.6 Consensus size: 28
339765 TTTTTATATA
*
339775 AATTAGAAAATTTAAATTTTTTTGGTT-
1 AATTAGAAAATTTAAATTTATTTGGTTC
*
339802 AATTCGAAAATTGACTCAAATTTATTTGGTTC
1 AATTAGAAAATT---T-AAATTTATTTGGTTC
*
339834 AATTA-ATAATTTAAA
1 AATTAGAAAATTTAAA
339849 AAAATCAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
27 14 0.37
28 1 0.03
30 1 0.03
31 18 0.47
32 4 0.11
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (28 bp):
AATTAGAAAATTTAAATTTATTTGGTTC
Found at i:340012 original size:25 final size:26
Alignment explanation
Indices: 339971--340020 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
339961 CATGTAAATA
339971 TAAAAAATAGATAATAAACATTTACT
1 TAAAAAATAGATAATAAACATTTACT
339997 TAAAAAA-AGA-ATATAAACATTTAC
1 TAAAAAATAGATA-ATAAACATTTAC
340021 GATATCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 1 0.04
25 15 0.65
26 7 0.30
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (26 bp):
TAAAAAATAGATAATAAACATTTACT
Found at i:341477 original size:32 final size:31
Alignment explanation
Indices: 341404--341488 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
341394 TAATAAGTAT
341404 ACAATTTTGATAAATTTAATGAAAATATTTTA
1 ACAA-TTTGATAAATTTAATGAAAATATTTTA
* **
341436 ACAAGTTGATAAAATTTAATGATTAT-TTTGTA
1 ACAATTTGAT-AAATTTAATGAAAATATTT-TA
* *
341468 ATAATTTGATAACTTTAATGA
1 ACAATTTGATAAATTTAATGA
341489 CCCATTTTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
31 18 0.40
32 27 0.60
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (31 bp):
ACAATTTGATAAATTTAATGAAAATATTTTA
Found at i:347605 original size:15 final size:16
Alignment explanation
Indices: 347584--347633 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
347574 ATTTATACAT
347584 TATATAAAAAGAATAA
1 TATATAAAAAGAATAA
* *
347600 -ATATAACATGAATAA
1 TATATAAAAAGAATAA
* *
347615 TATGTAAAAA-AATTA
1 TATATAAAAAGAATAA
347630 TATA
1 TATA
347634 ATTATATAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (16 bp):
TATATAAAAAGAATAA
Found at i:352387 original size:22 final size:21
Alignment explanation
Indices: 352359--352400 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
352349 AAGTTCAGGG
352359 ATTAAAT-TTTTTGTATCATTTC
1 ATTAAATATTTTT-TAT-ATTTC
352381 ATTAAATATTTTTTATATTT
1 ATTAAATATTTTTTATATTT
352401 ATAATTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTAAATATTTTTTATATTTC
Found at i:352476 original size:37 final size:37
Alignment explanation
Indices: 352402--352477 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
352392 TTTATATTTA
*
352402 TAATTTTGTAAAAAAAATTATATAAATATTATGAATT
1 TAATTTTGTAAAAAAAATTATATAAATATTATCAATT
* * *
352439 TAATTTTTTAAAGAAAA-TATATAAATATTTTACAATT
1 TAATTTTGTAAAAAAAATTATATAAATATTAT-CAATT
352476 TA
1 TA
352478 TAATATTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.38
37 21 0.62
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
TAATTTTGTAAAAAAAATTATATAAATATTATCAATT
Found at i:352497 original size:18 final size:18
Alignment explanation
Indices: 352453--352500 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
352443 TTTTTAAAGA
*
352453 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
352472 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
352489 AAATATATAATA
1 AAATATATAATA
352501 AGGATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:356473 original size:33 final size:35
Alignment explanation
Indices: 356409--356474 Score: 84
Period size: 33 Copynumber: 1.9 Consensus size: 35
356399 AAAATATATA
*
356409 TATATTTTATTTAAAAAAATTAAATTCATAAAATT
1 TATATTTTATTTAAAAAAATTAAAATCATAAAATT
*
356444 TATATTTT-TTT-ACAAAATTGAAAAT-ATAAAA
1 TATATTTTATTTAAAAAAATT-AAAATCATAAAA
356475 AAGTTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 13 0.46
34 7 0.25
35 8 0.29
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (35 bp):
TATATTTTATTTAAAAAAATTAAAATCATAAAATT
Found at i:357061 original size:18 final size:17
Alignment explanation
Indices: 357021--357062 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
357011 TAACTCAAAA
*
357021 ATCTTTCGATTTTCCTT
1 ATCTTTCGATTTTCCTC
357038 ATCTTTCGTATTTTCTCTC
1 ATCTTTCG-ATTTTC-CTC
357057 A-CTTTC
1 ATCTTTC
357063 TCGCAAGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 11 0.50
19 3 0.14
ACGTcount: A:0.12, C:0.26, G:0.05, T:0.57
Consensus pattern (17 bp):
ATCTTTCGATTTTCCTC
Found at i:360562 original size:32 final size:33
Alignment explanation
Indices: 360466--360564 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
360456 AACTCAACAT
* * *
360466 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTAAAATACTTAAAAACTTCCAAGTTCGATA
*
360499 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTAAAATACTTAAAAACTTCCAAGTTCGATA
360532 AATTAAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTAAAATACTTAAAAACTTCCAAGTTCGATA
360564 A
1 A
360565 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 12 0.19
33 50 0.81
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTAAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:360583 original size:21 final size:21
Alignment explanation
Indices: 360559--360600 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
360549 ACTTCAAGTT
360559 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
360580 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
360601 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:368554 original size:32 final size:33
Alignment explanation
Indices: 368518--368592 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 33
368508 AAAATTATCG
**
368518 AATTTAAA-CTTTTAAAAG-TATTTTATTATTTA
1 AATTTAAATCTTAAAAAAGTTATTTTATT-TTTA
368550 AATTTAAATCTTAAAAAAGTTTATTTTATTTTTA
1 AATTTAAATCTTAAAAAAG-TTATTTTATTTTTA
368584 AATTTAAAT
1 AATTTAAAT
368593 ACTAAAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 8 0.21
33 8 0.21
34 13 0.34
35 9 0.24
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (33 bp):
AATTTAAATCTTAAAAAAGTTATTTTATTTTTA
Found at i:369271 original size:27 final size:28
Alignment explanation
Indices: 369228--369286 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
369218 AAAAATATAT
* *
369228 TTAAAAAAACCTTAAAACTTTTCAAATC
1 TTAAAAAAACCTCAAAACTTTTAAAATC
*
369256 TTAAAAAAACC-CAAAACTTTTAAAATT
1 TTAAAAAAACCTCAAAACTTTTAAAATC
369283 TTAA
1 TTAA
369287 TTTTAATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (28 bp):
TTAAAAAAACCTCAAAACTTTTAAAATC
Found at i:382444 original size:8 final size:8
Alignment explanation
Indices: 382426--382454 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
382416 ATGCTGGGTT
382426 TTCTT-CC
1 TTCTTCCC
382433 TTCTTCCC
1 TTCTTCCC
382441 TTCTTCCC
1 TTCTTCCC
382449 TTCTTC
1 TTCTTC
382455 TTGTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (8 bp):
TTCTTCCC
Found at i:384218 original size:60 final size:60
Alignment explanation
Indices: 384083--384218 Score: 138
Period size: 59 Copynumber: 2.3 Consensus size: 60
384073 AATATATGAA
** * * * * *
384083 TAGTCGAATGATTATTTTGTAACTTTTAATAGTTGAAGACTTAACAAAACAACGTCTTAT
1 TAGTCGAATGACCATTTTGTAACTTTTAATAATAGAAGAATTAACAAAACAACGACTCAT
384143 TA-TCG-ATGAACCATTTTGTAACTTTTAATAATCAG-AGAATTCAACAAAACAAC-AC-CAT
1 TAGTCGAATG-ACCATTTTGTAACTTTTAATAAT-AGAAGAATT-AACAAAACAACGACTCAT
384201 GTAGTCGAATGACCATTT
1 -TAGTCGAATGACCATTT
384219 ATGCACTTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
58 5 0.08
59 31 0.49
60 24 0.38
61 3 0.05
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (60 bp):
TAGTCGAATGACCATTTTGTAACTTTTAATAATAGAAGAATTAACAAAACAACGACTCAT
Found at i:388338 original size:22 final size:22
Alignment explanation
Indices: 388313--388385 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
388303 GCCATAAATT
* *
388313 TCAAAGTTCCATGGATATTTAC
1 TCAAAGTTCCATAGATATCTAC
*
388335 TCAAATAGTCTCGTGATAGATATCTAC
1 TC-AA-AGT-TC--CATAGATATCTAC
388362 TCAAAGTTCCATAGATATCTAC
1 TCAAAGTTCCATAGATATCTAC
388384 TC
1 TC
388386 TTTCTTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.38
23 2 0.05
24 5 0.12
25 5 0.12
26 2 0.05
27 12 0.29
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (22 bp):
TCAAAGTTCCATAGATATCTAC
Found at i:397522 original size:63 final size:60
Alignment explanation
Indices: 397418--397605 Score: 187
Period size: 63 Copynumber: 3.0 Consensus size: 60
397408 GAGACATGCT
* * * *
397418 GGAAACAGGAGGAGAATCGAATGCCTGCTTTGTAATATCCTTCTGCTCAGTGTTCTGTTCGTG
1 GGAAGCAGGAGGAGAATCGAATGCC-GCTTT-TAACATCCTTCTGCTCA-AGTTCTGTTCGTA
* *
397481 GGAAGCAGGAGGAGAATCGAATGCTCGCTTTTCAACATCCTTCTGATCCAAGTTCTGTTTGTA
1 GGAAGCAGGAGGAGAATCGAATGC-CGCTTTT-AACATCCTTCTGCT-CAAGTTCTGTTCGTA
* * * * **
397544 GGAGGCAGGAGGAGAGTCAAATGCCCGCTTTGAAACATCCTTCCACTCAACGTTCTGTTCGT
1 GGAAGCAGGAGGAGAATCGAATG-CCGCTTT-TAACATCCTTCTGCTCAA-GTTCTGTTCGT
397606 TTGGCTTCTC
Statistics
Matches: 105, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
62 4 0.04
63 97 0.92
64 4 0.04
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (60 bp):
GGAAGCAGGAGGAGAATCGAATGCCGCTTTTAACATCCTTCTGCTCAAGTTCTGTTCGTA
Found at i:398079 original size:18 final size:18
Alignment explanation
Indices: 398058--398114 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
398048 ATCCCTCATT
398058 CCACCACGCCCACCAAAG
1 CCACCACGCCCACCAAAG
* *
398076 CCACCATC-CCTA--ATA-
1 CCACCA-CGCCCACCAAAG
*
398091 CCGCCACGCCCACCAAAG
1 CCACCACGCCCACCAAAG
398109 CCACCA
1 CCACCA
398115 TCCCTCATTC
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
14 1 0.04
15 8 0.29
16 2 0.07
17 2 0.07
18 14 0.50
19 1 0.04
ACGTcount: A:0.32, C:0.54, G:0.09, T:0.05
Consensus pattern (18 bp):
CCACCACGCCCACCAAAG
Found at i:398080 original size:33 final size:33
Alignment explanation
Indices: 398034--398164 Score: 199
Period size: 33 Copynumber: 4.0 Consensus size: 33
398024 ACCTCCAGGG
* *
398034 CCACCAAAACCACCATCCCTCATTCCACCACGC
1 CCACCAAAGCCACCATCCCTCATACCACCACGC
* *
398067 CCACCAAAGCCACCATCCCTAATACCGCCACGC
1 CCACCAAAGCCACCATCCCTCATACCACCACGC
* *
398100 CCACCAAAGCCACCATCCCTCATTCCACCACGT
1 CCACCAAAGCCACCATCCCTCATACCACCACGC
*
398133 CCACCAAAGCTACCATCCCTCATACCACCACG
1 CCACCAAAGCCACCATCCCTCATACCACCACG
398165 GCTTCCATTG
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.30, C:0.52, G:0.06, T:0.12
Consensus pattern (33 bp):
CCACCAAAGCCACCATCCCTCATACCACCACGC
Found at i:405801 original size:23 final size:22
Alignment explanation
Indices: 405758--405803 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
405748 AATTAAATTA
405758 TAATAAAAATGTAATAGAATAT
1 TAATAAAAATGTAATAGAATAT
*
405780 TAATATAAAGTGTAAT-GTAATAT
1 TAATA-AAAATGTAATAG-AATAT
405803 T
1 T
405804 TATTCAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (22 bp):
TAATAAAAATGTAATAGAATAT
Found at i:405914 original size:25 final size:24
Alignment explanation
Indices: 405886--405956 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
405876 ATTTAAGATG
405886 AATATAAAAATTAAATTTTATATCT
1 AATA-AAAAATTAAATTTTATATCT
* * * *
405911 AATAATAAATTTATTTTTATATAT
1 AATAAAAAATTAAATTTTATATCT
* *
405935 -TTAAAAAAATAAATGTTTATAT
1 AATAAAAAATTAAAT-TTTATAT
405957 TATGATTATC
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
23 9 0.25
24 23 0.64
25 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
AATAAAAAATTAAATTTTATATCT
Found at i:406238 original size:15 final size:17
Alignment explanation
Indices: 406218--406255 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
406208 GTCTAAATGC
406218 TTTTTTTCT-TC-CTTT
1 TTTTTTTCTCTCTCTTT
406233 TTTTTTTCTCTCTCTTT
1 TTTTTTTCTCTCTCTTT
406250 TCTTTT
1 T-TTTT
406256 GGTTGTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 2 0.10
17 5 0.25
18 4 0.20
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTCTCTCTCTTT
Found at i:424848 original size:22 final size:21
Alignment explanation
Indices: 424820--424891 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
424810 GAATTGCAGA
424820 ATTTGGTTTAGTTTTCATGGTG
1 ATTTGGTTTAGTTTTCA-GGTG
* * *
424842 ATTTGGTTTTA-ATTGCA-G-A
1 ATTTGG-TTTAGTTTTCAGGTG
*
424861 AATTGGTTTAGTTTTCACGGTG
1 ATTTGGTTTAGTTTTCA-GGTG
424883 ATTTGGTTT
1 ATTTGGTTT
424892 CAATTGCAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
18 4 0.11
19 9 0.24
20 1 0.03
21 1 0.03
22 18 0.49
23 4 0.11
ACGTcount: A:0.18, C:0.06, G:0.25, T:0.51
Consensus pattern (21 bp):
ATTTGGTTTAGTTTTCAGGTG
Found at i:424856 original size:41 final size:41
Alignment explanation
Indices: 424811--424905 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
424801 TGTTGTCTTG
* *
424811 AATTGCAGAATTTGGTTTAGTTTTCATGGTGATTTGGTTTT
1 AATTGCAGAATTTGGTTTAGTTTTCACGGTGATTTGGTTTC
*
424852 AATTGCAGAAATTGGTTTAGTTTTCACGGTGATTTGGTTTC
1 AATTGCAGAATTTGGTTTAGTTTTCACGGTGATTTGGTTTC
424893 AATTGCAGAATTT
1 AATTGCAGAATTT
424906 AAGGAATGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.46
Consensus pattern (41 bp):
AATTGCAGAATTTGGTTTAGTTTTCACGGTGATTTGGTTTC
Found at i:426573 original size:36 final size:36
Alignment explanation
Indices: 426533--426615 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
426523 TGTAGGTGGT
*
426533 AAATGAAATTTGTTAATCGAATTAGTTGAGTTATAG
1 AAATGAAATTTGTTAATCGAAATAGTTGAGTTATAG
*
426569 AAATGAAATTTGTTAATCGAAATAGTTGAGTTATCG
1 AAATGAAATTTGTTAATCGAAATAGTTGAGTTATAG
426605 AAATGAAATTT
1 AAATGAAATTT
426616 ATTTATTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (36 bp):
AAATGAAATTTGTTAATCGAAATAGTTGAGTTATAG
Found at i:426606 original size:17 final size:17
Alignment explanation
Indices: 426548--426608 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
426538 AAATTTGTTA
*
426548 ATCGAATTAGTTGAGTT
1 ATCGAAATAGTTGAGTT
* * *
426565 ATAGAAATGAAATT-TGTT
1 ATCGAAAT--AGTTGAGTT
426583 AATCGAAATAGTTGAGTT
1 -ATCGAAATAGTTGAGTT
426601 ATCGAAAT
1 ATCGAAAT
426609 GAAATTTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
17 17 0.52
18 6 0.18
19 10 0.30
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (17 bp):
ATCGAAATAGTTGAGTT
Found at i:426808 original size:36 final size:36
Alignment explanation
Indices: 426733--426816 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
426723 TTTAATATAC
* * * * *
426733 ATTTAATTAAAATCCATTGGAAACTAGAAGATACGT
1 ATTTAATTCAAACCCATTGGAAACTAAAAAATACAT
**
426769 ATTTAATTCAAACCCATTGGAAACTAAAAAATTTAT
1 ATTTAATTCAAACCCATTGGAAACTAAAAAATACAT
426805 ATTTAATTCAAA
1 ATTTAATTCAAA
426817 TCCGTTTGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.33
Consensus pattern (36 bp):
ATTTAATTCAAACCCATTGGAAACTAAAAAATACAT
Found at i:436079 original size:25 final size:25
Alignment explanation
Indices: 436051--436109 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
436041 TTAAGAAACG
436051 AAAATAAATT-ATCAATAAAAAAATT
1 AAAA-AAATTGATCAATAAAAAAATT
*
436076 AAAAAAATTGATCTATAAAAAAATT
1 AAAAAAATTGATCAATAAAAAAATT
436101 AAAAAAATT
1 AAAAAAATT
436110 TAGAAGATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAAAAATTGATCAATAAAAAAATT
Found at i:436123 original size:4 final size:4
Alignment explanation
Indices: 436110--437641 Score: 2720
Period size: 4 Copynumber: 391.0 Consensus size: 4
436100 TAAAAAAATT
436110 TAGA -AGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436157 TAGA TAGA TAGA TAGA TAGA TAGA TAGA GTAGA T--A TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA -TAGA TAGA TAGA TAGA TAGA
436204 -AGA TAG- -AGA TAGA TAGA T--A TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436247 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436295 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA GTAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA -TAGA
436344 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TA-A TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
*
436391 TAGA TAGA TAGA T-GA TAGA TAGA TAGA TAGA TAGA TAGA TAGC TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436438 TAGA TAGA TAGA TAGA TAGA TAGA -AGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436485 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436533 TAGA TAGA TAGA T--A TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436579 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436627 TAGA T--A TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436673 TAGA TAGA -AGA TAGA TAGA TAGA TAGA TAGA T--A TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436718 TAGA TAGA TAGA TAG- TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
*
436765 TCGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAG- -AGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
*
436811 TAGA TAGA TAGA TAGA TAGA TAGA -ATA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436858 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAG-
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
436905 -AGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
*
436952 TAGA GAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437000 TAGA TAG- TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437047 TAGA TAGA TAGA TAGA TTAGA TAGA TAGA TAGA TAGA T-GA TAGA TAGA
1 TAGA TAGA TAGA TAGA -TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
*
437095 TAGA TAGA TAGA TAGA GAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437143 TAGA -AGA TAGA TAGA TAGA TAG- -AGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437188 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
*
437236 TAGA TAGA TAGA TAGA GAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
*
437284 TAGA TCGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437332 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437380 T--A TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437426 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAG- -AGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437472 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437520 TAGA TAGA TAGA T-GA TA-A TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
*
437566 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA GAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437614 TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA
437642 ATGGTATTTA
Statistics
Matches: 1474, Mismatches: 16, Indels: 76
0.94 0.01 0.05
Matches are distributed among these distances:
2 22 0.01
3 38 0.03
4 1402 0.95
5 12 0.01
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
TAGA
Found at i:437750 original size:51 final size:49
Alignment explanation
Indices: 437674--437771 Score: 153
Period size: 51 Copynumber: 2.0 Consensus size: 49
437664 TTATACAAAA
*
437674 CGCGGTACTTGCCACGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
1 CGCGGTACATGCCACGCGCTATATAAAATTAT-T-AGGAGTAAAGGTATGT
437725 CGCGGTACATGTCC-CGCGCTATATAAAATTATTAGGAGTAAAGGTAT
1 CGCGGTACATG-CCACGCGCTATATAAAATTATTAGGAGTAAAGGTAT
437772 AACGAGATAC
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
49 14 0.31
50 1 0.02
51 28 0.62
52 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (49 bp):
CGCGGTACATGCCACGCGCTATATAAAATTATTAGGAGTAAAGGTATGT
Found at i:437791 original size:49 final size:51
Alignment explanation
Indices: 437688--437795 Score: 132
Period size: 49 Copynumber: 2.2 Consensus size: 51
437678 GTACTTGCCA
** * * *
437688 CGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCGCGGTACATGTCC
1 CGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAACGAGATACATATCC
*
437739 CGCGCTATATAAAATTAT-T-AGGAGTAAAGGTATAACGAGATACCTAAT-C
1 CGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAACGAGATACAT-ATCC
437788 CGCGCTAT
1 CGCGCTAT
437796 TCCCTTACAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
49 30 0.60
50 2 0.04
51 18 0.36
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (51 bp):
CGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAACGAGATACATATCC
Found at i:440049 original size:17 final size:17
Alignment explanation
Indices: 440029--440066 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
440019 TTATTTTACG
440029 ATTATTGTACTTT-TATT
1 ATTATTGT-CTTTGTATT
*
440046 ATTATTGTGTTTGTATT
1 ATTATTGTCTTTGTATT
440063 ATTA
1 ATTA
440067 CATGGCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.63
Consensus pattern (17 bp):
ATTATTGTCTTTGTATT
Found at i:445763 original size:6 final size:6
Alignment explanation
Indices: 445752--445788 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
445742 TTAACTAAAA
* *
445752 AGAGAG AGAGAG AGAGGG AGAGGG AGAGGG AGAGGG A
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG A
445789 AAGAGAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:446103 original size:2 final size:2
Alignment explanation
Indices: 446096--446143 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
446086 CGAGATTTTA
446096 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
446138 AT AT AT
1 AT AT AT
446144 TTTTGGTGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:457315 original size:29 final size:29
Alignment explanation
Indices: 457281--457376 Score: 192
Period size: 29 Copynumber: 3.3 Consensus size: 29
457271 TGAGTCACTT
457281 GACTATTAAAAGTTACAAAATGTTAACTC
1 GACTATTAAAAGTTACAAAATGTTAACTC
457310 GACTATTAAAAGTTACAAAATGTTAACTC
1 GACTATTAAAAGTTACAAAATGTTAACTC
457339 GACTATTAAAAGTTACAAAATGTTAACTC
1 GACTATTAAAAGTTACAAAATGTTAACTC
457368 GACTATTAA
1 GACTATTAA
457377 TTATATTCTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (29 bp):
GACTATTAAAAGTTACAAAATGTTAACTC
Found at i:457767 original size:179 final size:179
Alignment explanation
Indices: 457461--457824 Score: 570
Period size: 179 Copynumber: 2.0 Consensus size: 179
457451 GATATGATAG
* * *
457461 TCATTTGTTATGCAATTAGATTTTATCATATCTCAGTCAACATGTTAATGTCCAGCTCATATTGT
1 TCATTTGTTATGCAATTAGATTTTATCATATCTCAGTCAACACGTTAATGTACAGCTCAGATTGT
*
457526 TTTCAAATTTTTAACGAAAAATAATGAGTTTTGAACATAATAAATAGTTGGGTGACCATTTTGTA
66 TTTCAAATTTTTAACGAAAAATAATGAGTTTTGAACATAATAAATAGTTGAGTGACCATTTTGTA
* * *
457591 ACTTCTTATAATCGATGGACTCAATAAAGCAACTTCCTATGATCGAAGA
131 ACTTCTTATAATCGATGGACTCAACAAAACAACTTCCTATGATCGAAAA
* *
457640 TCATTTGTTATG-AGATTAGATTTTATCATATCTCAGTCAACACGTTAATGTACAGTTTAGATT-
1 TCATTTGTTATGCA-ATTAGATTTTATCATATCTCAGTCAACACGTTAATGTACAGCTCAGATTG
* * * *
457703 TTTTTAATTTTTTTAACGAAAAATAATGAGTTTTGAACCTAATAAATAGTTGAGTGATCATTTTG
65 TTTTCAA-ATTTTTAACGAAAAATAATGAGTTTTGAACATAATAAATAGTTGAGTGACCATTTTG
*
457768 TAACTTCTTATAATCGATTGACTCAACAAAACAACTTCCTATGATCGAAAA
129 TAACTTCTTATAATCGATGGACTCAACAAAACAACTTCCTATGATCGAAAA
457819 TCATTT
1 TCATTT
457825 TATGATTTTT
Statistics
Matches: 169, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
178 7 0.04
179 162 0.96
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (179 bp):
TCATTTGTTATGCAATTAGATTTTATCATATCTCAGTCAACACGTTAATGTACAGCTCAGATTGT
TTTCAAATTTTTAACGAAAAATAATGAGTTTTGAACATAATAAATAGTTGAGTGACCATTTTGTA
ACTTCTTATAATCGATGGACTCAACAAAACAACTTCCTATGATCGAAAA
Found at i:462790 original size:24 final size:24
Alignment explanation
Indices: 462770--462824 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
462760 GAACGTTCGA
*
462770 TTATGTTCGTTTATATGCGTTTAG
1 TTATGTTCGTTTATATGCGTTCAG
* *
462794 TTATGTTCGTTTATGTGCGTTCAT
1 TTATGTTCGTTTATATGCGTTCAG
462818 TTATGTT
1 TTATGTT
462825 TAACATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.09, G:0.20, T:0.56
Consensus pattern (24 bp):
TTATGTTCGTTTATATGCGTTCAG
Found at i:464350 original size:10 final size:10
Alignment explanation
Indices: 464335--464409 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
464325 GGGTCTCCAA
464335 CGTTTATGTT
1 CGTTTATGTT
464345 CGTTTATGTT
1 CGTTTATGTT
464355 CG----TGTT
1 CGTTTATGTT
*
464361 CATTTATGTT
1 CGTTTATGTT
*
464371 CGTGTT-CGTTT
1 CGT-TTATG-TT
* *
464382 ATGTTTGTGTT
1 -CGTTTATGTT
464393 CGTTTATGTT
1 CGTTTATGTT
464403 CGTTTAT
1 CGTTTAT
464410 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:464366 original size:16 final size:16
Alignment explanation
Indices: 464341--464405 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
464331 CCAACGTTTA
464341 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
464357 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
464373 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
464389 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
464405 T
1 T
464406 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:467101 original size:26 final size:26
Alignment explanation
Indices: 467072--467126 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
467062 GCCTATTGTG
467072 TAGGCCAGGGTCTATCTAGGGGTATA
1 TAGGCCAGGGTCTATCTAGGGGTATA
467098 TAGGCCAGGGTCTATCTAGGGGTATA
1 TAGGCCAGGGTCTATCTAGGGGTATA
467124 TAG
1 TAG
467127 ACCAAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.27
Consensus pattern (26 bp):
TAGGCCAGGGTCTATCTAGGGGTATA
Found at i:469167 original size:14 final size:14
Alignment explanation
Indices: 469148--469175 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
469138 TCTCAGTCTT
469148 GGTTGAGATATTTA
1 GGTTGAGATATTTA
469162 GGTTGAGATATTTA
1 GGTTGAGATATTTA
469176 TAGTTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
GGTTGAGATATTTA
Found at i:470491 original size:2 final size:2
Alignment explanation
Indices: 470484--470516 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
470474 GAAATGCAGA
470484 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
470517 AAAGAGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:470868 original size:31 final size:31
Alignment explanation
Indices: 470825--470885 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
470815 AACAAGTTTT
* * *
470825 ATGTATCTAAAATGATTATATGATATATGTA
1 ATGTATCTAAAATGATGACATGACATATGTA
*
470856 ATGTGTCTAAAATGATGACATGACATATGT
1 ATGTATCTAAAATGATGACATGACATATGT
470886 CTCATGTCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (31 bp):
ATGTATCTAAAATGATGACATGACATATGTA
Found at i:472073 original size:29 final size:29
Alignment explanation
Indices: 472036--472103 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
472026 GAAACATATG
* * * *
472036 AATACTCGAATGACCATTTTGTAATTTTT
1 AATACTCGAAGGACCATTTTATAACTTTC
* *
472065 AATAGTCGAAGGATCATTTTATAACTTTC
1 AATACTCGAAGGACCATTTTATAACTTTC
472094 AATACTCGAA
1 AATACTCGAA
472104 AGACTCAACA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (29 bp):
AATACTCGAAGGACCATTTTATAACTTTC
Found at i:477967 original size:38 final size:38
Alignment explanation
Indices: 477912--477989 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
477902 TCGGGTTAGA
477912 TTTTTTAAGTGCGATATTCAGGTC-GAGTCAG-GTCGGGT
1 TTTTTTAAGTGCGATATTCAGGTCAG-GTC-GTGTCGGGT
** *
477950 TTTTTTAAGTGTTATATTCGGGTCAGGTCGTGTCGGGT
1 TTTTTTAAGTGCGATATTCAGGTCAGGTCGTGTCGGGT
477988 TT
1 TT
477990 AGGGTGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 1 0.03
38 33 0.94
39 1 0.03
ACGTcount: A:0.15, C:0.12, G:0.31, T:0.42
Consensus pattern (38 bp):
TTTTTTAAGTGCGATATTCAGGTCAGGTCGTGTCGGGT
Found at i:489330 original size:25 final size:23
Alignment explanation
Indices: 489298--489365 Score: 118
Period size: 25 Copynumber: 2.9 Consensus size: 23
489288 TCATAACATC
489298 TCATGCCTACATACCTACATGCA
1 TCATGCCTACATACCTACATGCA
489321 TCATGCGCCTACATACCTACATGCA
1 TCAT--GCCTACATACCTACATGCA
489346 TCATGCCTACATACCTACAT
1 TCATGCCTACATACCTACAT
489366 ACATACTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
23 20 0.47
25 23 0.53
ACGTcount: A:0.29, C:0.35, G:0.09, T:0.26
Consensus pattern (23 bp):
TCATGCCTACATACCTACATGCA
Found at i:504806 original size:20 final size:20
Alignment explanation
Indices: 504774--504812 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
504764 ATGTAACTCC
504774 AATTTCTATTTTTAACAATA
1 AATTTCTATTTTTAACAATA
504794 AATTTACTATTTTT-ACAAT
1 AATTT-CTATTTTTAACAAT
504813 TTAATCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTCTATTTTTAACAATA
Found at i:509166 original size:171 final size:171
Alignment explanation
Indices: 508881--509222 Score: 684
Period size: 171 Copynumber: 2.0 Consensus size: 171
508871 CGCCGCGACA
508881 CTGCACATGAACAAGATGGAGAGAGAGGAAAACATACTTGCCGCTTTCACCTATTTCGACAAAGA
1 CTGCACATGAACAAGATGGAGAGAGAGGAAAACATACTTGCCGCTTTCACCTATTTCGACAAAGA
508946 CGGTAGTGGCTACATCACCATAGATGAACTCCAACAAGCTTGCAAAGAGTACGGCCTAGGGGACG
66 CGGTAGTGGCTACATCACCATAGATGAACTCCAACAAGCTTGCAAAGAGTACGGCCTAGGGGACG
509011 TTCCGCTTGAGGACATGATCCGAGAAATCGACCAAGATAAC
131 TTCCGCTTGAGGACATGATCCGAGAAATCGACCAAGATAAC
509052 CTGCACATGAACAAGATGGAGAGAGAGGAAAACATACTTGCCGCTTTCACCTATTTCGACAAAGA
1 CTGCACATGAACAAGATGGAGAGAGAGGAAAACATACTTGCCGCTTTCACCTATTTCGACAAAGA
509117 CGGTAGTGGCTACATCACCATAGATGAACTCCAACAAGCTTGCAAAGAGTACGGCCTAGGGGACG
66 CGGTAGTGGCTACATCACCATAGATGAACTCCAACAAGCTTGCAAAGAGTACGGCCTAGGGGACG
509182 TTCCGCTTGAGGACATGATCCGAGAAATCGACCAAGATAAC
131 TTCCGCTTGAGGACATGATCCGAGAAATCGACCAAGATAAC
509223 GTAAGTGCAT
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 171 1.00
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (171 bp):
CTGCACATGAACAAGATGGAGAGAGAGGAAAACATACTTGCCGCTTTCACCTATTTCGACAAAGA
CGGTAGTGGCTACATCACCATAGATGAACTCCAACAAGCTTGCAAAGAGTACGGCCTAGGGGACG
TTCCGCTTGAGGACATGATCCGAGAAATCGACCAAGATAAC
Found at i:513201 original size:28 final size:28
Alignment explanation
Indices: 513147--513202 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
513137 GAAAAATGTC
* **
513147 AAATATTTATATTTTATTTATTTAAATA
1 AAATATTTATATTTTATGTATCAAAATA
513175 AAATAGTTTATATTTTATGT-TCAAAATA
1 AAATA-TTTATATTTTATGTATCAAAATA
513203 TATATTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (28 bp):
AAATATTTATATTTTATGTATCAAAATA
Found at i:522011 original size:31 final size:31
Alignment explanation
Indices: 521973--522037 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
521963 TAAAAATTAT
* * *
521973 AAATAATTATTAAATTTATTCCGTTATTGTA
1 AAATAATTATTAAACTTATTCAGTTATTGCA
522004 AAATAATTATTAAACTTATTCAGTTATTGCA
1 AAATAATTATTAAACTTATTCAGTTATTGCA
522035 AAA
1 AAA
522038 AAAAAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (31 bp):
AAATAATTATTAAACTTATTCAGTTATTGCA
Found at i:526866 original size:23 final size:23
Alignment explanation
Indices: 526836--526882 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
526826 CATGGTTTCA
526836 TTCATACATGTATTATCGCACTG
1 TTCATACATGTATTATCGCACTG
526859 TTCATACATGTATTATCGCACTG
1 TTCATACATGTATTATCGCACTG
526882 T
1 T
526883 CATTCTTAAA
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:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (23 bp):
TTCATACATGTATTATCGCACTG
Found at i:534652 original size:2 final size:2
Alignment explanation
Indices: 534645--534671 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
534635 TTATGTGAAA
534645 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 A
534672 ATTTTAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:542879 original size:17 final size:18
Alignment explanation
Indices: 542857--542890 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
542847 ATCATAATCA
542857 TGCAAA-TAAATTAGAAT
1 TGCAAAGTAAATTAGAAT
*
542874 TGCAAAGTATATTAGAA
1 TGCAAAGTAAATTAGAA
542891 ATCAATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (18 bp):
TGCAAAGTAAATTAGAAT
Found at i:545716 original size:26 final size:28
Alignment explanation
Indices: 545687--545742 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
545677 GTACGCTTTC
*
545687 ATCCTTGAGAC-A-TTTTTTTCTAATTA
1 ATCCTTGACACAATTTTTTTTCTAATTA
545713 ATCCTTGACACAATTTTTTTTCTAATTA
1 ATCCTTGACACAATTTTTTTTCTAATTA
545741 AT
1 AT
545743 TTGAGATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 10 0.37
27 1 0.04
28 16 0.59
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (28 bp):
ATCCTTGACACAATTTTTTTTCTAATTA
Found at i:552997 original size:15 final size:16
Alignment explanation
Indices: 552958--553001 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
552948 TAAAAATATC
*
552958 TAAATTTTATAAGAATT
1 TAAATTTT-TTAGAATT
552975 TAAATTTTTTAGAATT
1 TAAATTTTTTAGAATT
*
552991 TAATTTTTTTA
1 TAAATTTTTTA
553002 AGGGTGACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
TAAATTTTTTAGAATT
Found at i:553844 original size:6 final size:6
Alignment explanation
Indices: 553826--554681 Score: 1596
Period size: 6 Copynumber: 145.0 Consensus size: 6
553816 ATTGAATCAG
* *
553826 TGTATA TGGATA TGCATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
553874 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
553922 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
553970 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554018 TG--TA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554064 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554112 TGTATA TGTATA TGTATA TGTATA TGTATA TG--TA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554158 TGTATA TGTATA TG--TA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554204 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554252 TGTATA TGTATA TGTATA TG--TA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554298 TGTATA TG--TA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554344 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554392 TGTATA TGTATA TGTATA --TATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554438 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554486 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554534 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TG--TA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554580 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554628 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
554676 TGTATA
1 TGTATA
554682 ATCACAAAAT
Statistics
Matches: 833, Mismatches: 3, Indels: 28
0.96 0.00 0.03
Matches are distributed among these distances:
4 28 0.03
6 805 0.97
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:557054 original size:18 final size:18
Alignment explanation
Indices: 557031--557065 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
557021 CAAGCTGAAA
557031 AATA-TTAAAAACAATAAT
1 AATATTTAAAAA-AATAAT
557049 AATATTTAAAAAAATAA
1 AATATTTAAAAAAATAA
557066 ACATAAGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATTTAAAAAAATAAT
Found at i:557389 original size:23 final size:21
Alignment explanation
Indices: 557346--557409 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
557336 TTTTAGGGTG
*
557346 AATTACTT-ATATATTCA-TTT
1 AATTACTTAAT-TATTTATTTT
557366 AATTA-TTATATTAATTTTATTTT
1 AATTACTTA-ATT-A-TTTATTTT
557389 AATTACTTAATTATTTATTTT
1 AATTACTTAATTATTTATTTT
557410 CTGTTAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
19 2 0.05
20 6 0.16
21 11 0.30
22 4 0.11
23 11 0.30
24 3 0.08
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
AATTACTTAATTATTTATTTT
Found at i:558959 original size:120 final size:116
Alignment explanation
Indices: 558766--559090 Score: 410
Period size: 120 Copynumber: 2.8 Consensus size: 116
558756 GAGCAAATTG
* * * * *
558766 AGTTAAGAAAATCGTCTCATAATAAATCTTTATAATACATGATTTGAATTAATCGATAGGTTAGA
1 AGTTAAGAGAATCGTGTCACAATAAATCTTTATAATACATGA-TTGAATTAATTGGTAGGTTAGA
* * *
558831 AAATTAAAATAAATACTTTAAGATTAACCT-AAATGTGAATTGAGCAAACAA
65 AAATTAAAATAAATACTTTAAGATTAACCTAAAATATGAATAGAACAAACAA
* *
558882 AGTTAAGAGAATTGTCTGTCTTACAATAAATATTTATAATACATGATCTGAATTAATTGGTAGGT
1 AGTTAAGAGAATCG--TGTC--ACAATAAATCTTTATAATACATGAT-TGAATTAATTGGTAGGT
*
558947 TAGAAAATTAAAATAAATACTTTAAGATTAA-CTAAAATATGAATAGAACAAACTA
61 TAGAAAATTAAAATAAATACTTTAAGATTAACCTAAAATATGAATAGAACAAACAA
** * *
559002 AGTTAAGAGAATCGTGTCATGATAAATCTTTATAATAGATGA-T--ATGAA-TGGTAGGTTAGAA
1 AGTTAAGAGAATCGTGTCACAATAAATCTTTATAATACATGATTGAATTAATTGGTAGGTTAGAA
*
559063 AATCAAAATAAATACTTTAAGATTAACC
66 AATTAAAATAAATACTTTAAGATTAACC
559091 CACAATTTTA
Statistics
Matches: 184, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
111 38 0.21
112 5 0.03
114 1 0.01
116 32 0.17
118 7 0.04
119 3 0.02
120 98 0.53
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (116 bp):
AGTTAAGAGAATCGTGTCACAATAAATCTTTATAATACATGATTGAATTAATTGGTAGGTTAGAA
AATTAAAATAAATACTTTAAGATTAACCTAAAATATGAATAGAACAAACAA
Found at i:562908 original size:113 final size:113
Alignment explanation
Indices: 562750--563139 Score: 372
Period size: 114 Copynumber: 3.4 Consensus size: 113
562740 CTCCCAAGTT
* * * * **
562750 AGTCTTCTCCATTCATAATGTCAAAATTCAAACTCTCGAGTTTAATTAAGGAGCTTAACGTCTCA
1 AGTCTTCTCTATTCACAATGTCAAGATTCAAACTCTTGACCTTAATTAAGGAGCTTAACGTCTCA
* * * ** *
562815 TCTCGAGAGATATTGCAAAGA-TCTATTACGAGATAACCCTCTTGATCT
66 TCTCGATAGATATTGCAAAGACTC-ATTATGAGAAAACCCTCCCGATCC
* * * * * * * *
562863 AGTCTTCT-TCATTCACAATATCAAGATTCAAACTTTTGACCTTAATTAGGGAACCTAGCTTCCC
1 AGTCTTCTCT-ATTCACAATGTCAAGATTCAAACTCTTGACCTTAATTAAGGAGCTTAACGTCTC
* *
562927 ATCTCGATAAATATTGCAAAGACTCATTATGAGGAAAACCCTCCCGGTCC
65 ATCTCGATAGATATTGCAAAGACTCATTATGA-GAAAACCCTCCCGATCC
* * * * * * * * * *
562977 AATCTTCTCTATCCATAATGTCAGGATTCAAACTCCTAACCTTTATTAAAGAGCTTCATGTCTCA
1 AGTCTTCTCTATTCACAATGTCAAGATTCAAACTCTTGACCTTAATTAAGGAGCTTAACGTCTC-
* * *
563042 AT-TCGATAGATATTGTAATGACTCATTATGGGAACAACCCTCCCGATCC
65 ATCTCGATAGATATTGCAAAGACTCATTATGAGAA-AACCCTCCCGATCC
* * *
563091 AGTCTTCTCTATTCACAATGTTAAGATTCAAACTTTTGATCTTAATTAA
1 AGTCTTCTCTATTCACAATGTCAAGATTCAAACTCTTGACCTTAATTAA
563140 AAAAACTTAA
Statistics
Matches: 216, Mismatches: 55, Indels: 11
0.77 0.20 0.04
Matches are distributed among these distances:
113 78 0.36
114 135 0.62
115 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.33
Consensus pattern (113 bp):
AGTCTTCTCTATTCACAATGTCAAGATTCAAACTCTTGACCTTAATTAAGGAGCTTAACGTCTCA
TCTCGATAGATATTGCAAAGACTCATTATGAGAAAACCCTCCCGATCC
Found at i:563139 original size:114 final size:112
Alignment explanation
Indices: 562698--563140 Score: 349
Period size: 114 Copynumber: 3.9 Consensus size: 112
562688 ATCTAATGTA
* * * * * * * * * *
562698 TCATCTCGATAGATATTGTAGATACTTATGATGGGGACAAACCTCCCAAGT-TAGTCTTCTCCAT
1 TCATCTCGATAGATATTGCAAAGACTCATTATGGGAACAACCCTCCCGA-TCCAGTCTTCTCTAT
* * * ** *
562762 TCATAATGTCAAAATTCAAACTCTCGAGTTTAATTAAGGAGCTTAACGTC
65 TCACAATGTCAAGATTCAAACTCTTGACCTTAATTAAAGAGCTT-A-GTC
* * * * ** *
562812 TCATCTCGAGAGATATTGCAAAGA-TCTATTACGAG-ATAACCCTCTTGATCTAGTCTTCT-TCA
1 TCATCTCGATAGATATTGCAAAGACTC-ATTATGGGAACAACCCTCCCGATCCAGTCTTCTCT-A
* * ** * *
562874 TTCACAATATCAAGATTCAAACTTTTGACCTTAATTAGGGAACCTAGCTTC
64 TTCACAATGTCAAGATTCAAACTCTTGACCTTAATTAAAGAGCTTAG--TC
* * * *
562925 CCATCTCGATAAATATTGCAAAGACTCATTATGAGGAA-AACCCTCCCGGTCCAATCTTCTCTAT
1 TCATCTCGATAGATATTGCAAAGACTCATTATG-GGAACAACCCTCCCGATCCAGTCTTCTCTAT
* * * * * *
562989 CCATAATGTCAGGATTCAAACTCCTAACCTTTATTAAAGAGCTTCATGTC
65 TCACAATGTCAAGATTCAAACTCTTGACCTTAATTAAAGAGCTT-A-GTC
* *
563039 TCAAT-TCGATAGATATTGTAATGACTCATTATGGGAACAACCCTCCCGATCCAGTCTTCTCTAT
1 TC-ATCTCGATAGATATTGCAAAGACTCATTATGGGAACAACCCTCCCGATCCAGTCTTCTCTAT
* * *
563103 TCACAATGTTAAGATTCAAACTTTTGATCTTAATTAAA
65 TCACAATGTCAAGATTCAAACTCTTGACCTTAATTAAA
563141 AAAACTTAAT
Statistics
Matches: 255, Mismatches: 61, Indels: 26
0.75 0.18 0.08
Matches are distributed among these distances:
111 1 0.00
112 2 0.01
113 86 0.34
114 160 0.63
115 5 0.02
116 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (112 bp):
TCATCTCGATAGATATTGCAAAGACTCATTATGGGAACAACCCTCCCGATCCAGTCTTCTCTATT
CACAATGTCAAGATTCAAACTCTTGACCTTAATTAAAGAGCTTAGTC
Found at i:563943 original size:3 final size:3
Alignment explanation
Indices: 563930--563959 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
563920 TTTAAGTATA
563930 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
563960 ATGACAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:567439 original size:36 final size:36
Alignment explanation
Indices: 567398--567500 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
567388 AGTTGAGTAT
567398 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
567434 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
567470 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
567501 CCAGCACCGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:568967 original size:14 final size:14
Alignment explanation
Indices: 568950--568983 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
568940 ATAGAGAAAG
*
568950 AAAAAGGGAAAAAT
1 AAAAAAGGAAAAAT
*
568964 AAAAAATGAAAAAT
1 AAAAAAGGAAAAAT
568978 AAAAAA
1 AAAAAA
568984 AGATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (14 bp):
AAAAAAGGAAAAAT
Found at i:585408 original size:12 final size:12
Alignment explanation
Indices: 585379--585428 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
585369 AATTATTAGC
585379 ATATTTAA-AAT
1 ATATTTAATAAT
*
585390 ATATTTATTAAT
1 ATATTTAATAAT
*
585402 ATTTTTAATAAT
1 ATATTTAATAAT
*
585414 ATAATATAATAAT
1 AT-ATTTAATAAT
585427 AT
1 AT
585429 TATTATTACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 7 0.22
12 15 0.47
13 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:585843 original size:22 final size:20
Alignment explanation
Indices: 585791--585844 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
585781 ATTATTCTAA
*
585791 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
585811 TAAGTTTTTATAATAAATAATAT
1 T-A-TTTTTATAAT-AATAATAT
585834 TATTTATTATA
1 TATTT-TTATA
585845 TTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 15 0.52
23 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:588857 original size:19 final size:19
Alignment explanation
Indices: 588799--588859 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
588789 TATTAATTAT
*
588799 TTTTAAATATTTTTCAATTTA
1 TTTTAAATA--TTTAAATTTA
*
588820 TTTT--ATATTCATAATTTTA
1 TTTTAAATATT--TAAATTTA
588839 TTTTAAATATTTAAATTTA
1 TTTTAAATATTTAAATTTA
588858 TT
1 TT
588860 ATGTTCATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
17 2 0.06
19 22 0.67
21 9 0.27
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAATATTTAAATTTA
Found at i:589198 original size:2 final size:2
Alignment explanation
Indices: 589191--589232 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
589181 AAATATTTTA
589191 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
589233 TAAAAAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:591348 original size:15 final size:15
Alignment explanation
Indices: 591328--591359 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
591318 ATTTATTTCG
591328 CCAGAATCAATCTCA
1 CCAGAATCAATCTCA
591343 CCAGAATCAATCTCA
1 CCAGAATCAATCTCA
591358 CC
1 CC
591360 GTCCATCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.38, G:0.06, T:0.19
Consensus pattern (15 bp):
CCAGAATCAATCTCA
Found at i:594917 original size:19 final size:19
Alignment explanation
Indices: 594881--594918 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
594871 ATTCGACTAC
*
594881 TAATTTATAATGATAATTA
1 TAATTTAAAATGATAATTA
594900 TAATTTAAAGATGA-AATTA
1 TAATTTAAA-ATGATAATTA
594919 GAATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
TAATTTAAAATGATAATTA
Found at i:595472 original size:13 final size:15
Alignment explanation
Indices: 595439--595475 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
595429 TGAAGATAAC
595439 TTTAATTTACTATCTT
1 TTTAATTTAC-ATCTT
595455 TTTAATTTA-ATC-T
1 TTTAATTTACATCTT
595468 TTTAATTT
1 TTTAATTT
595476 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.43
14 3 0.14
16 9 0.43
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTAATTTACATCTT
Found at i:595657 original size:2 final size:2
Alignment explanation
Indices: 595652--595677 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
595642 GTAAAAAAGA
595652 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
595678 GAAGAGTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:597355 original size:21 final size:21
Alignment explanation
Indices: 597329--597373 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
597319 TTGAAATAAT
597329 TTTTTTATAAAATAATCAACC
1 TTTTTTATAAAATAATCAACC
597350 TTTTTTATAAAATAATCAACC
1 TTTTTTATAAAATAATCAACC
597371 TTT
1 TTT
597374 ATTGTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTTTATAAAATAATCAACC
Found at i:597425 original size:19 final size:18
Alignment explanation
Indices: 597393--597438 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
597383 AAATCATTTT
*
597393 CATATGTATGTAATAACTA
1 CATATATATGTAATAA-TA
*
597412 CATATATATTTAATAATA
1 CATATATATGTAATAATA
*
597430 TATATATAT
1 CATATATAT
597439 ATATATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (18 bp):
CATATATATGTAATAATA
Found at i:601497 original size:28 final size:28
Alignment explanation
Indices: 601444--601498 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
601434 CCGCTGTTAC
* * *
601444 TTTCAAGCACTGGCTCGCCAGCATAATA
1 TTTCAAGCACTAGCTCGACAGAATAATA
*
601472 TTTCAAGCACTAGCTCGATAGAATAAT
1 TTTCAAGCACTAGCTCGACAGAATAAT
601499 GTAAATAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCGACAGAATAATA
Found at i:602748 original size:28 final size:28
Alignment explanation
Indices: 602717--602771 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
602707 ACATAGACAC
*
602717 ATGCATGCATACA-AGCAAACATACATGT
1 ATGCATGCACACATA-CAAACATACATGT
*
602745 ATGCATGCACACATACAAACATGCATG
1 ATGCATGCACACATACAAACATACATG
602772 GACACAGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.20
Consensus pattern (28 bp):
ATGCATGCACACATACAAACATACATGT
Found at i:608939 original size:23 final size:23
Alignment explanation
Indices: 608913--608961 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
608903 GAACCGTTAT
608913 AGTCTCATAAGTAACCAATTAAA
1 AGTCTCATAAGTAACCAATTAAA
608936 AGTCTCATAAGTAACCAATTAAA
1 AGTCTCATAAGTAACCAATTAAA
608959 AGT
1 AGT
608962 ATTACAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (23 bp):
AGTCTCATAAGTAACCAATTAAA
Found at i:614062 original size:35 final size:35
Alignment explanation
Indices: 614016--614091 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
614006 AAAACAATCC
* *
614016 TCAATTTCATTCTAAACCC-CAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCTAAATTT-CAAAATAAT
614051 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
614086 TCAATT
1 TCAATT
614092 AAATTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
Found at i:614641 original size:130 final size:130
Alignment explanation
Indices: 614488--614735 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
614478 TATTTATATA
* **
614488 ATCAATTTGATCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
614553 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
614618 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * * *
614683 TTAACGCATGATCATGATATATGTTATTGGTGACACATGTCATCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
614736 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:614766 original size:130 final size:129
Alignment explanation
Indices: 614502--614766 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
614492 ATTTGATCCT
* ** *
614502 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
614567 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
614632 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACGCATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
614697 TGATATATGTTATTGGTGACACATGTCATCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
614761 -A
128 CA
614762 AAATT
1 AAATT
614767 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:615094 original size:28 final size:27
Alignment explanation
Indices: 615063--615125 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
615053 AGTTGATACA
*
615063 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
615091 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
615119 ATATTTT
1 ATATTTT
615126 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:615226 original size:16 final size:18
Alignment explanation
Indices: 615205--615238 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
615195 ATTTCTTATT
615205 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
615221 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
615239 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:615791 original size:32 final size:32
Alignment explanation
Indices: 615742--615803 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
615732 TGCGGAGGAC
* * *
615742 TAAAGTCATAAATTTACTTAAGTTTGAGGGAT
1 TAAAGTCATAAAATTACTGAAGTTTAAGGGAT
*
615774 TAAATTCATAAAATTACTGAAGTTTAAGGG
1 TAAAGTCATAAAATTACTGAAGTTTAAGGG
615804 TTGATTACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (32 bp):
TAAAGTCATAAAATTACTGAAGTTTAAGGGAT
Found at i:623435 original size:6 final size:6
Alignment explanation
Indices: 623421--623458 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
623411 TACTACCTTA
*
623421 CCTCCC CCTCAC CCTCAC CCTCAC CCTCAC CCTCAC CC
1 CCTCAC CCTCAC CCTCAC CCTCAC CCTCAC CCTCAC CC
623459 CATTACATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.13, C:0.71, G:0.00, T:0.16
Consensus pattern (6 bp):
CCTCAC
Found at i:627573 original size:8 final size:8
Alignment explanation
Indices: 627560--627586 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
627550 TCACTGTATG
627560 ATATACAT
1 ATATACAT
627568 ATATACAT
1 ATATACAT
627576 ATATACAT
1 ATATACAT
627584 ATA
1 ATA
627587 ATTCGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATACAT
Found at i:627823 original size:21 final size:19
Alignment explanation
Indices: 627793--627832 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
627783 TTAAAAAAAT
* *
627793 AAAATTAAAAATCAATATTA
1 AAAAATAAAAAACAA-ATTA
627813 AAAAATAAAAAACAAATTA
1 AAAAATAAAAAACAAATTA
627832 A
1 A
627833 TTTCTGAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATAAAAAACAAATTA
Found at i:634093 original size:2 final size:2
Alignment explanation
Indices: 634086--634131 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
634076 TTCAAACATA
634086 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
634128 AT AT
1 AT AT
634132 GTGGTGTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:643327 original size:22 final size:22
Alignment explanation
Indices: 643283--643342 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
643273 TTGGTGCAGA
*
643283 GGGAATCGA-TCCCCCCTTGA-
1 GGGAACCGATTCCCCCCTTGAG
* *
643303 GGGAACCGATTTCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTG-AG
643326 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
643343 ACAGGGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 8 0.25
21 8 0.25
22 1 0.03
23 15 0.47
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTGAG
Found at i:647378 original size:32 final size:32
Alignment explanation
Indices: 647342--647456 Score: 124
Period size: 32 Copynumber: 3.6 Consensus size: 32
647332 AAGATTCAAT
*
647342 AATTTAATGACCATTTTGTAACAATTTGATAA
1 AATTTAATGACTATTTTGTAACAATTTGATAA
* *
647374 AATTTAATGACTACTTTGTAACAGTTTGATAA
1 AATTTAATGACTATTTTGTAACAATTTGATAA
* * * * *
647406 AATTCAATAATTATTTTATAACAA-TCGATAA
1 AATTTAATGACTATTTTGTAACAATTTGATAA
* * *
647437 AATTTATTAAATATTTTGTA
1 AATTTAATGACTATTTTGTA
647457 CTAGCTCGAT
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
31 22 0.32
32 47 0.68
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.43
Consensus pattern (32 bp):
AATTTAATGACTATTTTGTAACAATTTGATAA
Found at i:648054 original size:31 final size:30
Alignment explanation
Indices: 647979--648054 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 30
647969 GTAACTTTAG
*
647979 ATATAATTTAAAAAATAATTAAGTCCCAAAA
1 ATATAATTT-AAAAATAATTAAGTACCAAAA
* ** * *
648010 ATAGAACCGTAAAAATAATTAAGTAACTAAAT
1 ATATAA-TTTAAAAATAATTAAGT-ACCAAAA
648042 ATATAATTTAAAA
1 ATATAATTTAAAA
648055 TATTTATATT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (30 bp):
ATATAATTTAAAAATAATTAAGTACCAAAA
Found at i:649623 original size:28 final size:27
Alignment explanation
Indices: 649559--649624 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
649549 CCTAAACCCG
*
649559 AACCGACCCAAATATCACACTTAAAAA
1 AACCGACCCGAATATCACACTTAAAAA
* *
649586 ATCCGGCCCGAATATCACACTTAAAAA
1 AACCGACCCGAATATCACACTTAAAAA
649613 AACTCGACCCGA
1 AAC-CGACCCGA
649625 CCCCGTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 26 0.79
28 7 0.21
ACGTcount: A:0.44, C:0.32, G:0.09, T:0.15
Consensus pattern (27 bp):
AACCGACCCGAATATCACACTTAAAAA
Found at i:649669 original size:33 final size:32
Alignment explanation
Indices: 649608--649685 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
649598 TATCACACTT
*
649608 AAAAAAACT-CGACCCGACCCCGTATTTTTTG
1 AAAAAAAATCCGACCCGACCCCGTATTTTTTG
* * * *
649639 GAAAAAAATCCGACCCGATCCCGATTTTTTTTT
1 AAAAAAAATCCGACCCGACCCCG-TATTTTTTG
649672 AAAAAAAATCCGAC
1 AAAAAAAATCCGAC
649686 TCGAATACCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 7 0.18
32 12 0.31
33 20 0.51
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (32 bp):
AAAAAAAATCCGACCCGACCCCGTATTTTTTG
Found at i:649676 original size:31 final size:33
Alignment explanation
Indices: 649606--649678 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
649596 AATATCACAC
649606 TTAAAAAAACTCGACCCGACCCCGTATTTTTTG
1 TTAAAAAAACTCGACCCGACCCCGTATTTTTTG
* * *
649639 -GAAAAAAA-TCCGACCCGATCCCG-ATTTTTTT
1 TTAAAAAAACT-CGACCCGACCCCGTATTTTTTG
649670 TTAAAAAAA
1 TTAAAAAAA
649679 ATCCGACTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
31 8 0.24
32 26 0.76
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (33 bp):
TTAAAAAAACTCGACCCGACCCCGTATTTTTTG
Found at i:656857 original size:297 final size:297
Alignment explanation
Indices: 656323--656913 Score: 1146
Period size: 297 Copynumber: 2.0 Consensus size: 297
656313 ACAATTCGGC
* *
656323 AAGAATGATGGTATTCTTTTCAGATGTTGTTAAATGATCTAACCAGCGGAGGCAAATAGGAGGGT
1 AAGAATGATGGCATTCTTTTCAGATGTTGTTAAATGATCTAACCAGCAGAGGCAAATAGGAGGGT
656388 TTTAGTAAGCTAATATATATTTAAGGAAGATCAGATCCCCTTTATTGATAATTTTAAAGAGTCCT
66 TTTAGTAAGCTAATATATATTTAAGGAAGATCAGATCCCCTTTATTGATAATTTTAAAGAGTCCT
656453 TATAGGGCCACATTCAGTAAAATGTCAGTGCATTGAGAATAAATCCCCACCGTCCCAGGGCCACT
131 TATAGGGCCACATTCAGTAAAATGTCAGTGCATTGAGAATAAATCCCCACCGTCCCAGGGCCACT
*
656518 CTCGATTAGTACCTTAATGAGGGATGAGGTAATGCTACAACTAGGTATACAAGACAGCCCTTTTT
196 CACGATTAGTACCTTAATGAGGGATGAGGTAATGCTACAACTAGGTATACAAGACAGCCCTTTTT
656583 CACTTGAGCATTTTGGTGGGAGTCACATTAGTAGTAT
261 CACTTGAGCATTTTGGTGGGAGTCACATTAGTAGTAT
656620 AAGAATGATGGCATTCTTTTCAGATGTTGTTAAATGATCTAACCAGCAGAGGCAAATAGGAGGGT
1 AAGAATGATGGCATTCTTTTCAGATGTTGTTAAATGATCTAACCAGCAGAGGCAAATAGGAGGGT
656685 TTTAGTAAGCTAATATATATTTAAGGAAGATCAGATCCCCTTTATTGATAATTTTAAAGAGTCCT
66 TTTAGTAAGCTAATATATATTTAAGGAAGATCAGATCCCCTTTATTGATAATTTTAAAGAGTCCT
656750 TATAGGGCCACATTCAGTAAAATGTCAGTGCATTGAGAATAAATCCCCACCGTCCCAGGGCCACT
131 TATAGGGCCACATTCAGTAAAATGTCAGTGCATTGAGAATAAATCCCCACCGTCCCAGGGCCACT
*
656815 CACGATTAGTGCCTTAATGAGGGATGAGGTAATGCTACAACTAGGTATACAAGACAGCCCTTTTT
196 CACGATTAGTACCTTAATGAGGGATGAGGTAATGCTACAACTAGGTATACAAGACAGCCCTTTTT
656880 CACTTGAGCATTTTGGTGGGAGTCACATTAGTAG
261 CACTTGAGCATTTTGGTGGGAGTCACATTAGTAG
656914 CATGTGCTTG
Statistics
Matches: 290, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
297 290 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (297 bp):
AAGAATGATGGCATTCTTTTCAGATGTTGTTAAATGATCTAACCAGCAGAGGCAAATAGGAGGGT
TTTAGTAAGCTAATATATATTTAAGGAAGATCAGATCCCCTTTATTGATAATTTTAAAGAGTCCT
TATAGGGCCACATTCAGTAAAATGTCAGTGCATTGAGAATAAATCCCCACCGTCCCAGGGCCACT
CACGATTAGTACCTTAATGAGGGATGAGGTAATGCTACAACTAGGTATACAAGACAGCCCTTTTT
CACTTGAGCATTTTGGTGGGAGTCACATTAGTAGTAT
Found at i:663193 original size:4 final size:4
Alignment explanation
Indices: 663184--663209 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
663174 GCAAACCGAC
663184 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
663210 ATCCCCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:664648 original size:13 final size:13
Alignment explanation
Indices: 664610--664654 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
664600 TTCATGTTTA
664610 TAATATCATTAAT
1 TAATATCATTAAT
* *
664623 TAAT-CCAAATAAT
1 TAATATC-ATTAAT
664636 TAATATCATTAAT
1 TAATATCATTAAT
664649 TAATAT
1 TAATAT
664655 AGAGCAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATATCATTAAT
Found at i:666704 original size:4 final size:4
Alignment explanation
Indices: 666695--666725 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
666685 TTCAATTGAT
666695 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
666726 TATATTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Done.