Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 53 of 163
Found at i:13184815 original size:47 final size:47
Alignment explanation
Indices: 13184764--13184856 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
13184754 TTGACTTTGA
*
13184764 CCGTTGACTTTGACCTTTGACCACTGACCGTTGACTTTGACAGTTGT
1 CCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGACAGTTGT
*
13184811 CCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGACCGTTG
1 CCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGACAGTTG
13184857 ACTTTGATCG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.16, C:0.27, G:0.23, T:0.34
Consensus pattern (47 bp):
CCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGACAGTTGT
Found at i:13185925 original size:3 final size:3
Alignment explanation
Indices: 13185917--13185947 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
13185907 TAGAATATTC
13185917 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13185948 TTGGGATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13191402 original size:9 final size:10
Alignment explanation
Indices: 13191383--13191418 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
13191373 TGCCCCAAAC
13191383 CTTTTTCTTT
1 CTTTTTCTTT
13191393 CTTTTT-TTT
1 CTTTTTCTTT
13191402 CTTTTTCTTT
1 CTTTTTCTTT
13191412 CTTTTTC
1 CTTTTTC
13191419 CCTTGCCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:13191923 original size:21 final size:22
Alignment explanation
Indices: 13191887--13191932 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
13191877 ACTCATTAAG
13191887 CCCAAATCCTATTTAAACCAAA
1 CCCAAATCCTATTTAAACCAAA
*
13191909 CCCAAATTC-ATTTAAACCAAA
1 CCCAAATCCTATTTAAACCAAA
13191930 CCC
1 CCC
13191933 TTTTGAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (22 bp):
CCCAAATCCTATTTAAACCAAA
Found at i:13191996 original size:10 final size:10
Alignment explanation
Indices: 13191983--13192037 Score: 74
Period size: 10 Copynumber: 5.4 Consensus size: 10
13191973 AGTCAAACCA
13191983 TTGACCGACG
1 TTGACCGACG
*
13191993 TTGACCGGCG
1 TTGACCGACG
13192003 TTGACCGACG
1 TTGACCGACG
* *
13192013 TTGACCGGCA
1 TTGACCGACG
13192023 TTGACCGACCG
1 TTGACCGA-CG
13192034 TTGA
1 TTGA
13192038 TCGGTGTTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
10 33 0.87
11 5 0.13
ACGTcount: A:0.18, C:0.29, G:0.31, T:0.22
Consensus pattern (10 bp):
TTGACCGACG
Found at i:13192008 original size:20 final size:20
Alignment explanation
Indices: 13191981--13192037 Score: 96
Period size: 20 Copynumber: 2.8 Consensus size: 20
13191971 CAAGTCAAAC
13191981 CATTGACCGACGTTGACCGG
1 CATTGACCGACGTTGACCGG
*
13192001 CGTTGACCGACGTTGACCGG
1 CATTGACCGACGTTGACCGG
13192021 CATTGACCGACCGTTGA
1 CATTGACCGA-CGTTGA
13192038 TCGGTGTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 28 0.82
21 6 0.18
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.21
Consensus pattern (20 bp):
CATTGACCGACGTTGACCGG
Found at i:13192065 original size:13 final size:13
Alignment explanation
Indices: 13192047--13192175 Score: 135
Period size: 13 Copynumber: 10.2 Consensus size: 13
13192037 ATCGGTGTTG
13192047 TTTGACCGTTGAC
1 TTTGACCGTTGAC
13192060 TTTGACCGTTGAC
1 TTTGACCGTTGAC
*
13192073 TTTGACCTTTGACC
1 TTTGACCGTTGA-C
**
13192087 ACTGACCGTTGAC
1 TTTGACCGTTGAC
*
13192100 TTTGACAGTTG--
1 TTTGACCGTTGAC
13192111 --T--CCGTTGAC
1 TTTGACCGTTGAC
13192120 TTTGACCGTTGACC
1 TTTGACCGTTGA-C
**
13192134 ACTGACCGTTGAC
1 TTTGACCGTTGAC
13192147 TTTGACCGTTGAC
1 TTTGACCGTTGAC
*
13192160 TTTGATCGTTGAC
1 TTTGACCGTTGAC
13192173 TTT
1 TTT
13192176 TTTTCAAAAA
Statistics
Matches: 95, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
7 5 0.05
9 1 0.01
11 1 0.01
13 67 0.71
14 21 0.22
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (13 bp):
TTTGACCGTTGAC
Found at i:13192095 original size:40 final size:40
Alignment explanation
Indices: 13192049--13192172 Score: 167
Period size: 47 Copynumber: 2.9 Consensus size: 40
13192039 CGGTGTTGTT
*
13192049 TGACCGTTGACTTTGACCGTTGACTTTGACCTTTGACCAC
1 TGACCGTTGACTTTGACCGTTGACTTTGACCGTTGACCAC
13192089 TGACCGTTGACTTTGACAGTTGTCCGTTGACTTTGACCGTTGACCAC
1 TGACCGTTGACTTTG--A-----CCGTTGACTTTGACCGTTGACCAC
*
13192136 TGACCGTTGACTTTGACCGTTGACTTTGATCGTTGAC
1 TGACCGTTGACTTTGACCGTTGACTTTGACCGTTGAC
13192173 TTTTTTTCAA
Statistics
Matches: 75, Mismatches: 2, Indels: 14
0.82 0.02 0.15
Matches are distributed among these distances:
40 35 0.47
42 1 0.01
45 1 0.01
47 38 0.51
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (40 bp):
TGACCGTTGACTTTGACCGTTGACTTTGACCGTTGACCAC
Found at i:13192100 original size:27 final size:27
Alignment explanation
Indices: 13192047--13192159 Score: 134
Period size: 27 Copynumber: 4.5 Consensus size: 27
13192037 ATCGGTGTTG
**
13192047 TTTGACCGTTGA-CTTTGACCGTTGAC
1 TTTGACCGTTGACCACTGACCGTTGAC
*
13192073 TTTGACCTTTGACCACTGACCGTTGAC
1 TTTGACCGTTGACCACTGACCGTTGAC
*
13192100 TTTGACAGTTG-----T--CCGTTGAC
1 TTTGACCGTTGACCACTGACCGTTGAC
13192120 TTTGACCGTTGACCACTGACCGTTGAC
1 TTTGACCGTTGACCACTGACCGTTGAC
13192147 TTTGACCGTTGAC
1 TTTGACCGTTGAC
13192160 TTTGATCGTT
Statistics
Matches: 73, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
20 18 0.25
22 1 0.01
25 1 0.01
26 11 0.15
27 42 0.58
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (27 bp):
TTTGACCGTTGACCACTGACCGTTGAC
Found at i:13192116 original size:47 final size:47
Alignment explanation
Indices: 13192065--13192157 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
13192055 TTGACTTTGA
*
13192065 CCGTTGACTTTGACCTTTGACCACTGACCGTTGACTTTGACAGTTGT
1 CCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGACAGTTGT
*
13192112 CCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGACCGTTG
1 CCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGACAGTTG
13192158 ACTTTGATCG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.16, C:0.27, G:0.23, T:0.34
Consensus pattern (47 bp):
CCGTTGACTTTGACCGTTGACCACTGACCGTTGACTTTGACAGTTGT
Found at i:13193235 original size:3 final size:3
Alignment explanation
Indices: 13193223--13193267 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
13193213 TATTCTATTC
13193223 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13193268 TTGGGATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:13195335 original size:22 final size:23
Alignment explanation
Indices: 13195310--13195354 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
13195300 CATTCTTTTC
* *
13195310 AATTTTTT-TATAGTTTTTAAAT
1 AATTTTTTATAAAGTTTTAAAAT
13195332 AATTTTTTATAAAGTTTTAAAAT
1 AATTTTTTATAAAGTTTTAAAAT
13195355 TTTAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
AATTTTTTATAAAGTTTTAAAAT
Found at i:13195402 original size:17 final size:16
Alignment explanation
Indices: 13195373--13195410 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
13195363 ATTATTAACC
13195373 TTTTATATTTTTACAATA
1 TTTTATATTTTTA-AA-A
13195391 TTTTAT-TTTTTAAAA
1 TTTTATATTTTTAAAA
13195406 TTTTA
1 TTTTA
13195411 AAATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 2 0.10
17 6 0.30
18 6 0.30
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATATTTTTAAAA
Found at i:13202529 original size:13 final size:13
Alignment explanation
Indices: 13202511--13202535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13202501 TTCATACTCA
13202511 TTTATTTAGCTTG
1 TTTATTTAGCTTG
13202524 TTTATTTAGCTT
1 TTTATTTAGCTT
13202536 AAACGAACAA
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:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (13 bp):
TTTATTTAGCTTG
Found at i:13205022 original size:31 final size:30
Alignment explanation
Indices: 13204987--13205106 Score: 93
Period size: 30 Copynumber: 4.0 Consensus size: 30
13204977 TATTTTATCT
* *
13204987 AAAAATCACATTTTGACCCCTAAATTTCTCC
1 AAAAATTACATTTTAACCCCTAAATTTCT-C
* * *
13205018 AAAAATTAAAATTTAACTCCTAAACTTT-TC
1 AAAAATTACATTTTAACCCCTAAA-TTTCTC
* * *
13205048 TAAAATTACATTTTAACCTCC-AACTTTTTTC
1 AAAAATTACATTTTAACC-CCTAA-ATTTCTC
* *
13205079 -AAAATTACATTTTGACCCCTAAAATTCT
1 AAAAATTACATTTTAACCCCTAAATTTCT
13205107 TCATAACTTC
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
29 5 0.07
30 38 0.54
31 24 0.34
32 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCCTAAATTTCTC
Found at i:13215996 original size:40 final size:41
Alignment explanation
Indices: 13215938--13216063 Score: 148
Period size: 41 Copynumber: 3.1 Consensus size: 41
13215928 TTTCGCCTGA
* ** *
13215938 AAAAAATGATGATCGAGATGAAAACCCGTTAGGGGCGTCTTG
1 AAAAAA-GAGGATCGAGATGAAAACCCGCAAAGGGCGTCTTG
* * **
13215980 AAAAAA-AGGATCGAGATAAAAACTCC-CAAAGGGCATCTAA
1 AAAAAAGAGGATCGAGATGAAAAC-CCGCAAAGGGCGTCTTG
13216020 AAAAAAGAGGATCGAGATGAAAACCCGCAAAGGGCGTCTTG
1 AAAAAAGAGGATCGAGATGAAAACCCGCAAAGGGCGTCTTG
13216061 AAA
1 AAA
13216064 CCAAAGGGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
40 31 0.45
41 32 0.46
42 6 0.09
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.15
Consensus pattern (41 bp):
AAAAAAGAGGATCGAGATGAAAACCCGCAAAGGGCGTCTTG
Found at i:13217198 original size:75 final size:75
Alignment explanation
Indices: 13217064--13217203 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 75
13217054 TCACGGGGAA
*
13217064 GAGTGAAACTTCAAATGGTCATCTTCTTGATGAGATACAAAGAAGTAGACCAAAACAATAAAGTG
1 GAGTGAAACTTCAAAT-GCCATCTTCTTGATGAGATACAAAGAAGTAGACCAAAACAATAAAGTG
13217129 AAGCTCAATGT
65 AAGCTCAATGT
* * ** *
13217140 GAGTGAAACTTCAAACT-CCATCTT-TCTGATGAGATATAGAGAAGTAGGTCAAAGCAATAAAGT
1 GAGTGAAACTTCAAA-TGCCATCTTCT-TGATGAGATACAAAGAAGTAGACCAAAACAATAAAGT
13217203 G
64 G
13217204 GTCATCTTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
74 1 0.02
75 39 0.70
76 15 0.27
77 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (75 bp):
GAGTGAAACTTCAAATGCCATCTTCTTGATGAGATACAAAGAAGTAGACCAAAACAATAAAGTGA
AGCTCAATGT
Found at i:13217354 original size:123 final size:123
Alignment explanation
Indices: 13217206--13217487 Score: 411
Period size: 123 Copynumber: 2.3 Consensus size: 123
13217196 ATAAAGTGGT
* * *
13217206 CATCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAAAAATCATTTTCCTGATGAGAT
1 CATCTTCCTAATGAGATACAGAGAAGTGGATTAAAACAATGAAAAAATCATCTTCCTGATGAGAT
* * * * * *
13217271 ACAGATAAATAGACCAAATCAATGGAGCGAAGCTTAATATGAGTGAAACTTCAAACTC
66 ACAGAGAAATAGACCAAATCAATGAAGCGAAACTCAATATGAGAGAAACTTCAAACCC
* ** *
13217329 CATCTTCCTAATGAGATACAGAGAAGTGGATCAAAACAATGAAGCAGTCATCTTCCTGATGAGAT
1 CATCTTCCTAATGAGATACAGAGAAGTGGATTAAAACAATGAAAAAATCATCTTCCTGATGAGAT
* *
13217394 ACAGAGAAGTAGACCAAATCAATGAAGCGAAACTCAATATGAGAGAAACTTCCAACCC
66 ACAGAGAAATAGACCAAATCAATGAAGCGAAACTCAATATGAGAGAAACTTCAAACCC
* *
13217452 CATCTTCCTAATGAGATACAGAGAAGAGGACTAAAA
1 CATCTTCCTAATGAGATACAGAGAAGTGGATTAAAA
13217488 GATGAAGATA
Statistics
Matches: 141, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
123 141 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (123 bp):
CATCTTCCTAATGAGATACAGAGAAGTGGATTAAAACAATGAAAAAATCATCTTCCTGATGAGAT
ACAGAGAAATAGACCAAATCAATGAAGCGAAACTCAATATGAGAGAAACTTCAAACCC
Found at i:13217381 original size:171 final size:171
Alignment explanation
Indices: 13217082--13217403 Score: 457
Period size: 171 Copynumber: 1.9 Consensus size: 171
13217072 CTTCAAATGG
* * * *
13217082 TCATCTTCTTGATGAGATACAAAGAAGTAGACCAAAACAATAAAGTGAAGCTCAATGTGAGTGAA
1 TCATCTTCCTGATGAGATACAAAGAAATAGACCAAAACAATAAAGCGAAGCTCAATATGAGTGAA
* * * * **
13217147 ACTTCAAACTCCATCTTTCTGATGAGATATAGAGAAGTAGGTCAAAGCAATAAAGTGGTCATCTT
66 ACTTCAAACTCCATCTTCCTAATGAGATACAGAGAAGTAGGTCAAAACAATAAAGCAGTCATCTT
13217212 CCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAAAAA
131 CCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAAAAA
* * * * ** *
13217253 TCATTTTCCTGATGAGATACAGATAAATAGACCAAATCAATGGAGCGAAGCTTAATATGAGTGAA
1 TCATCTTCCTGATGAGATACAAAGAAATAGACCAAAACAATAAAGCGAAGCTCAATATGAGTGAA
*
13217318 ACTTCAAACTCCATCTTCCTAATGAGATACAGAGAAGT-GGATCAAAACAATGAAGCAGTCATCT
66 ACTTCAAACTCCATCTTCCTAATGAGATACAGAGAAGTAGG-TCAAAACAATAAAGCAGTCATCT
*
13217382 TCCTGATGAGATACAGAGAAGT
130 TCCTGATGAGATACAAAGAAGT
13217404 AGACCAAATC
Statistics
Matches: 131, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
170 2 0.02
171 129 0.98
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (171 bp):
TCATCTTCCTGATGAGATACAAAGAAATAGACCAAAACAATAAAGCGAAGCTCAATATGAGTGAA
ACTTCAAACTCCATCTTCCTAATGAGATACAGAGAAGTAGGTCAAAACAATAAAGCAGTCATCTT
CCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAAAAA
Found at i:13217400 original size:48 final size:48
Alignment explanation
Indices: 13217329--13217421 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
13217319 CTTCAAACTC
* *
13217329 CATCTTCCTAATGAGATACAGAGAAGTGGATCAAAACAATGAAGCAGT
1 CATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGCAGT
* *
13217377 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGC
1 CATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGC
13217422 GAAACTCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (48 bp):
CATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGCAGT
Found at i:13218338 original size:11 final size:11
Alignment explanation
Indices: 13218322--13218346 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13218312 TTTCGAATAA
13218322 ATATAAAAAAT
1 ATATAAAAAAT
13218333 ATATAAAAAAT
1 ATATAAAAAAT
13218344 ATA
1 ATA
13218347 ACCTAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATATAAAAAAT
Found at i:13219215 original size:30 final size:30
Alignment explanation
Indices: 13219140--13219319 Score: 140
Period size: 30 Copynumber: 6.1 Consensus size: 30
13219130 ATTTTATCTA
* * * **
13219140 AAAATAACATTTTGACCCCCTAAACTTCACC
1 AAAATTACTTTTTGA-CCCTTAAACTTTTCC
* *
13219171 AAAAATTA-TATTTGACCCTTAAACTTTTCT
1 -AAAATTACTTTTTGACCCTTAAACTTTTCC
* *
13219201 AAAA-TAGCTTTTTGACCCCTAAAGTTTTCC
1 AAAATTA-CTTTTTGACCCTTAAACTTTTCC
* *
13219231 AAAA-T--TGTTTGACCC-TAAACTTTTTC
1 AAAATTACTTTTTGACCCTTAAACTTTTCC
*
13219257 AAAATTACATTTTGACCCTTAAAC-TTTCC
1 AAAATTACTTTTTGACCCTTAAACTTTTCC
* * * *
13219286 AAAATTACGTTTTAACCCTTAAAATTCTCC
1 AAAATTACTTTTTGACCCTTAAACTTTTCC
13219316 AAAA
1 AAAA
13219320 CTTCATTTTT
Statistics
Matches: 120, Mismatches: 21, Indels: 16
0.76 0.13 0.10
Matches are distributed among these distances:
26 13 0.11
27 10 0.08
28 2 0.02
29 37 0.31
30 47 0.39
31 5 0.04
32 6 0.05
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAATTACTTTTTGACCCTTAAACTTTTCC
Found at i:13219255 original size:27 final size:26
Alignment explanation
Indices: 13219211--13219262 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
13219201 AAAATAGCTT
13219211 TTTGACCCCTAAAGTTTTCCAAAATTG
1 TTTGACCCCTAAAGTTTT-CAAAATTG
*
13219238 TTTGA-CCCTAAACTTTTTCAAAATT
1 TTTGACCCCTAAA-GTTTTCAAAATT
13219263 ACATTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (26 bp):
TTTGACCCCTAAAGTTTTCAAAATTG
Found at i:13223191 original size:20 final size:20
Alignment explanation
Indices: 13223150--13223204 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
13223140 GTTGGAGCAG
*
13223150 AACTATCGATACCATGAGGA
1 AACTATCGATACCATGACGA
* *
13223170 AACTATCGATACCTTTACGA
1 AACTATCGATACCATGACGA
*
13223190 AAGGTATCGATACCA
1 AA-CTATCGATACCA
13223205 GATTGATACT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
AACTATCGATACCATGACGA
Found at i:13227929 original size:73 final size:72
Alignment explanation
Indices: 13227797--13227964 Score: 221
Period size: 75 Copynumber: 2.3 Consensus size: 72
13227787 TTTGGGTGAA
* * *
13227797 TCAAGAGTAAGGCATGCCCACGCCTTATTATAGAACATCAAGAAGTACGACATTTTTTTTTCACA
1 TCAAGAATAAGGCATGCCCACGCCTTATTATAGAACATCAAGAAGTACAACA-TTTTTGTTCACA
*
13227862 GAAGAAAT
65 GAAGAAAC
*
13227870 TCAAGAATAAGGCATGCCCACGTCTTATTATTGTAGAACAT-AAGGAAGTACAACATTTTTGTTC
1 TCAAGAATAAGGCATGCCCACGCCTTATTA---TAGAACATCAA-GAAGTACAACATTTTTGTTC
13227934 ACAGAAGAAAC
62 ACAGAAGAAAC
* *
13227945 TCAAAAATAAGGCGTGCCCA
1 TCAAGAATAAGGCATGCCCA
13227965 TAACTTATTC
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
73 28 0.33
75 38 0.45
76 18 0.21
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (72 bp):
TCAAGAATAAGGCATGCCCACGCCTTATTATAGAACATCAAGAAGTACAACATTTTTGTTCACAG
AAGAAAC
Found at i:13234010 original size:20 final size:21
Alignment explanation
Indices: 13233985--13234030 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
13233975 CTCACGTCAC
13233985 AAAATAATTT-AAAATTATAA-
1 AAAATAATTTCAAAATTA-AAG
13234005 AAAAT-ATTTCAAAATTAAAG
1 AAAATAATTTCAAAATTAAAG
13234025 AAAATA
1 AAAATA
13234031 TATAAGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATAATTTCAAAATTAAAG
Found at i:13242773 original size:25 final size:25
Alignment explanation
Indices: 13242744--13242812 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
13242734 ATACTAGTTA
*
13242744 AACTCTGTCTGGGCTCGTAAGAGCT
1 AACTCTATCTGGGCTCGTAAGAGCT
* *
13242769 AACTCTATTTGGGCTTGTAAGAGCT
1 AACTCTATCTGGGCTCGTAAGAGCT
* *
13242794 AACCCTATCTAGGCTCGTA
1 AACTCTATCTGGGCTCGTA
13242813 TAAGCCAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (25 bp):
AACTCTATCTGGGCTCGTAAGAGCT
Found at i:13257023 original size:5 final size:5
Alignment explanation
Indices: 13257013--13257084 Score: 72
Period size: 5 Copynumber: 14.2 Consensus size: 5
13257003 ATGGGGGTAG
* * * * *
13257013 GATAT GATAT GATAT GATAC GTTAT AATAT GATAA GATAT GATTT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
* *
13257063 GAAATT GATAC GATAT GATAT G
1 GATA-T GATAT GATAT GATAT G
13257085 TTATAAGATA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
5 48 0.92
6 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (5 bp):
GATAT
Found at i:13276293 original size:12 final size:12
Alignment explanation
Indices: 13276256--13276303 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
13276246 GAAATGAGGC
13276256 AGAGAAGGAAGAA
1 AGAGAAGGAAG-A
*
13276269 AAAGAA-GAAGA
1 AGAGAAGGAAGA
*
13276280 AGAGAAGGATGA
1 AGAGAAGGAAGA
13276292 AGAGAAGGAAGA
1 AGAGAAGGAAGA
13276304 TGCCCCAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 6 0.20
12 19 0.63
13 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (12 bp):
AGAGAAGGAAGA
Found at i:13276746 original size:17 final size:18
Alignment explanation
Indices: 13276703--13276756 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
13276693 ATGCATAGCA
*
13276703 TTTAGTTGTCATTACATT
1 TTTAGTTGTCACTACATT
* *
13276721 TTTAATTGTCACTGCA-T
1 TTTAGTTGTCACTACATT
* *
13276738 TTTAGTTGTTAGTACATT
1 TTTAGTTGTCACTACATT
13276756 T
1 T
13276757 GCATCGTAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (18 bp):
TTTAGTTGTCACTACATT
Found at i:13286794 original size:23 final size:20
Alignment explanation
Indices: 13286766--13286806 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
13286756 TCAGTTCCAT
13286766 GATCCATTGTTGTTTCTACATTG
1 GATCCA-TGTT-TTTC-ACATTG
13286789 GATCCATGTTTTTCACAT
1 GATCCATGTTTTTCACAT
13286807 CTGGTTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 4 0.22
23 6 0.33
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (20 bp):
GATCCATGTTTTTCACATTG
Found at i:13291274 original size:23 final size:20
Alignment explanation
Indices: 13291246--13291286 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
13291236 TCAGTTCCAT
13291246 GATCCATTGTTGTTTCTACATTG
1 GATCCA-TGTT-TTTC-ACATTG
13291269 GATCCATGTTTTTCACAT
1 GATCCATGTTTTTCACAT
13291287 CTGGTTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 4 0.22
23 6 0.33
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (20 bp):
GATCCATGTTTTTCACATTG
Found at i:13295755 original size:23 final size:20
Alignment explanation
Indices: 13295727--13295767 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
13295717 TCAGTTCCAT
13295727 GATCCATTGTTGTTTCTACATTG
1 GATCCA-TGTT-TTTC-ACATTG
13295750 GATCCATGTTTTTCACAT
1 GATCCATGTTTTTCACAT
13295768 CTGGTTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 4 0.22
23 6 0.33
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (20 bp):
GATCCATGTTTTTCACATTG
Found at i:13300235 original size:23 final size:20
Alignment explanation
Indices: 13300207--13300247 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
13300197 TCAGTTCCAT
13300207 GATCCATTGTTGTTTCTACATTG
1 GATCCA-TGTT-TTTC-ACATTG
13300230 GATCCATGTTTTTCACAT
1 GATCCATGTTTTTCACAT
13300248 CTGGTTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 4 0.22
23 6 0.33
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (20 bp):
GATCCATGTTTTTCACATTG
Found at i:13304713 original size:23 final size:20
Alignment explanation
Indices: 13304685--13304725 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
13304675 TCAGTTCCAT
13304685 GATCCATTGTTGTTTCTACATTG
1 GATCCA-TGTT-TTTC-ACATTG
13304708 GATCCATGTTTTTCACAT
1 GATCCATGTTTTTCACAT
13304726 CTTTGCTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 4 0.22
23 6 0.33
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (20 bp):
GATCCATGTTTTTCACATTG
Found at i:13312545 original size:5 final size:5
Alignment explanation
Indices: 13312531--13312567 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
13312521 ACATATATCT
13312531 TTTTC TTTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
13312568 CTTTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:13318331 original size:20 final size:21
Alignment explanation
Indices: 13318285--13318335 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
13318275 ATTCCTGCAT
13318285 AAAAT-TGAAAAGGAAAGAAG
1 AAAATGTGAAAAGGAAAGAAG
*
13318305 TAAATGTGAAAA-GATAA-AAG
1 AAAATGTGAAAAGGA-AAGAAG
13318325 AAAATGT-AAAA
1 AAAATGTGAAAA
13318336 TGCATTGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 15 0.56
21 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.16
Consensus pattern (21 bp):
AAAATGTGAAAAGGAAAGAAG
Found at i:13330306 original size:19 final size:19
Alignment explanation
Indices: 13330282--13330344 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
13330272 AGCAATAATG
13330282 TGCAAGCGTACACTGTCGA
1 TGCAAGCGTACACTGTCGA
** * *
13330301 TGCAAGTATAGCAATAAT-G-
1 TGCAAGCGTA-CACT-GTCGA
13330320 TGCAAGCGTACACTGTCGA
1 TGCAAGCGTACACTGTCGA
13330339 TGCAAG
1 TGCAAG
13330345 TATAGTAGAC
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 1 0.03
18 4 0.12
19 22 0.69
20 4 0.12
21 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (19 bp):
TGCAAGCGTACACTGTCGA
Found at i:13330321 original size:38 final size:38
Alignment explanation
Indices: 13330270--13330349 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
13330260 TATGAACGTC
13330270 ATAGCAATAATGTGCAAGCGTACACTGTCGATGCAAGT
1 ATAGCAATAATGTGCAAGCGTACACTGTCGATGCAAGT
13330308 ATAGCAATAATGTGCAAGCGTACACTGTCGATGCAAGT
1 ATAGCAATAATGTGCAAGCGTACACTGTCGATGCAAGT
13330346 ATAG
1 ATAG
13330350 TAGACAGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (38 bp):
ATAGCAATAATGTGCAAGCGTACACTGTCGATGCAAGT
Found at i:13337643 original size:19 final size:20
Alignment explanation
Indices: 13337619--13337662 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
13337609 AAAACACCTA
*
13337619 AAAAGAAATTTGGAA-AAAT
1 AAAAGAAATTAGGAACAAAT
* *
13337638 AAAAGAGATTAGTAACAAAT
1 AAAAGAAATTAGGAACAAAT
13337658 AAAAG
1 AAAAG
13337663 TCAGAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.64, C:0.02, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGAAATTAGGAACAAAT
Found at i:13340675 original size:17 final size:17
Alignment explanation
Indices: 13340638--13340733 Score: 104
Period size: 17 Copynumber: 5.7 Consensus size: 17
13340628 GAACTCATTT
* **
13340638 TTTAAATTTGTTTTAGG
1 TTTAAATTTATTTTAAA
* *
13340655 TTTAGATTTATTGTAAA
1 TTTAAATTTATTTTAAA
* *
13340672 TTTAAATTAATTTTAAG
1 TTTAAATTTATTTTAAA
13340689 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
13340706 TTTAAAATTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
13340722 TTTGAATTTATT
1 TTTAAATTTATT
13340734 CAAATCTAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
16 14 0.22
17 50 0.78
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:13340677 original size:6 final size:6
Alignment explanation
Indices: 13340668--13340731 Score: 55
Period size: 6 Copynumber: 11.3 Consensus size: 6
13340658 AGATTTATTG
* * * *
13340668 TAAATT TAAA-T TAATTT TAAGTT TAAATT T-ATTT TAAATT TAAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
13340714 T--ATT TAAATT TGAATT TA
1 TAAATT TAAATT TAAATT TA
13340732 TTCAAATCTA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
4 3 0.07
5 8 0.18
6 34 0.76
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:13340721 original size:16 final size:16
Alignment explanation
Indices: 13340662--13340745 Score: 71
Period size: 16 Copynumber: 5.1 Consensus size: 16
13340652 AGGTTTAGAT
13340662 TTATTGTAAATTT-AAA
1 TTATT-TAAATTTAAAA
* *
13340678 TTAATTTTAAGTTTAAAT
1 TT-A-TTTAAATTTAAAA
13340696 TTATTTTAAATTTAAAA
1 TTA-TTTAAATTTAAAA
* *
13340713 TTATTTAAATTTGAAT
1 TTATTTAAATTTAAAA
* *
13340729 TTATTCAAATCTAAAA
1 TTATTTAAATTTAAAA
13340745 T
1 T
13340746 AAATAATGTC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
16 26 0.47
17 23 0.42
18 6 0.11
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (16 bp):
TTATTTAAATTTAAAA
Found at i:13342282 original size:29 final size:29
Alignment explanation
Indices: 13342196--13342611 Score: 253
Period size: 29 Copynumber: 14.1 Consensus size: 29
13342186 CTCAGAAGGT
*
13342196 CCCT-AAACTTCTCAAAAATTACATTTTTG
1 CCCTCAAACTTC-CAAAAATTACATTTTTA
* ** ** * *
13342225 GCCTCGACCCTCTAAAAAAAATACATTTTTG
1 CCCTC-AAACT-TCCAAAAATTACATTTTTA
* *
13342256 CCCTCAAACTTCCAAAAATTATATTTTTT
1 CCCTCAAACTTCCAAAAATTACATTTTTA
*
13342285 CCCTCGAACTTCCAAAAAATTACCA-TTTTA
1 CCCTCAAACTTCC-AAAAATTA-CATTTTTA
* * *
13342315 CCCTCGAACATCCAAAAATTACCA-TTTTG
1 CCCTCAAACTTCCAAAAATTA-CATTTTTA
* * * * *
13342344 CCCCCGAGCATCCAAAAAATACCATTTTTA
1 CCCTCAAACTTCCAAAAATTA-CATTTTTA
* * * *
13342374 CCCTTAAACTTCCAAAAATGACAGTTTCA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
13342403 CCCTCAAACTTCCAAAAATTACATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
*
13342432 CTCC-CAAACATCCAAAAATTATCA-TTTTA
1 C-CCTCAAACTTCCAAAAATTA-CATTTTTA
* *
13342461 CCC-CTGAACATCCAAAAATTACCA-TTTTA
1 CCCTC-AAACTTCCAAAAATTA-CATTTTTA
* * * *
13342490 CCCTTAAACTTCTCAAAAATCAAAATTTTGA
1 CCCTCAAACTTC-CAAAAAT-TACATTTTTA
* * *
13342521 CCC-CGAACTTCTCAAAAATCACATTTTGGA
1 CCCTCAAACTTC-CAAAAATTACATTTT-TA
* **
13342551 CCCT-AAACTTTTTC-AAAATTACCGTTTTA
1 CCCTCAAAC--TTCCAAAAATTACATTTTTA
13342580 CCC-CTAAACTTCCAAAAATTACCA-TTTTA
1 CCCTC-AAACTTCCAAAAATTA-CATTTTTA
13342609 CCC
1 CCC
13342612 CCGAGCATCC
Statistics
Matches: 309, Mismatches: 57, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
28 6 0.02
29 174 0.56
30 94 0.30
31 32 0.10
32 3 0.01
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.31
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTTA
Found at i:13342332 original size:59 final size:59
Alignment explanation
Indices: 13342208--13342635 Score: 254
Period size: 59 Copynumber: 7.2 Consensus size: 59
13342198 CTAAACTTCT
** * * * * * *
13342208 CAAAAATTACATTTTTGGCCTCGACCCTCTAAAAAAAATA-CATTTTTGCCCTCAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACATC--CAAAAATTACCATTTTTACCCTCAAACATC
* * * *
13342268 CAAAAATTATATTTTTTCCCTCGAACTTCCAAAAAATTACCA-TTTTACCCTCGAACATC
1 CAAAAATTACATTTTTACCCTCGAACATCC-AAAAATTACCATTTTTACCCTCAAACATC
* * * * * *
13342327 CAAAAATTACCA-TTTTGCCCCCGAGCATCCAAAAAATACCATTTTTACCCTTAAACTTC
1 CAAAAATTA-CATTTTTACCCTCGAACATCCAAAAATTACCATTTTTACCCTCAAACATC
* * * * *
13342386 CAAAAATGACAGTTTCACCCTCAAACTTCCAAAAATTA-CATTTTTACTCC-CAAACATC
1 CAAAAATTACATTTTTACCCTCGAACATCCAAAAATTACCATTTTTAC-CCTCAAACATC
* *
13342444 CAAAAATTATCA-TTTTACCC-CTGAACATCCAAAAATTACCA-TTTTACCCTTAAACTTC
1 CAAAAATTA-CATTTTTACCCTC-GAACATCCAAAAATTACCATTTTTACCCTCAAACATC
* * * * * * * *
13342502 TCAAAAATCAAAATTTTGACCC-CGAACTTCTCAAAAATCA-CATTTTGGACCCT-AAACTTTTT
1 -CAAAAAT-TACATTTTTACCCTCGAACATC-CAAAAATTACCATTTT-TACCCTCAAAC--ATC
** * * * * *
13342564 C-AAAATTACCGTTTTACCC-CTAAACTTCCAAAAATTACCA-TTTTACCCCCGAGCATC
1 CAAAAATTACATTTTTACCCTC-GAACATCCAAAAATTACCATTTTTACCCTCAAACATC
*
13342621 CAAAAGTTACCATTT
1 CAAAAATTA-CATTT
13342636 ACCCTCAATT
Statistics
Matches: 287, Mismatches: 58, Indels: 47
0.73 0.15 0.12
Matches are distributed among these distances:
57 5 0.02
58 78 0.27
59 132 0.46
60 64 0.22
61 6 0.02
62 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCTCGAACATCCAAAAATTACCATTTTTACCCTCAAACATC
Found at i:13342509 original size:30 final size:29
Alignment explanation
Indices: 13342251--13342653 Score: 288
Period size: 29 Copynumber: 13.8 Consensus size: 29
13342241 AAAAATACAT
* *
13342251 TTTTGCCCTCAAACTTCCAAAAATTA-TA
1 TTTTACCCTCAAACTTCCAAAAATTACCA
* *
13342279 TTTTTTCCCTCGAACTTCCAAAAAATTACCA
1 -TTTTACCCTCAAACTTCC-AAAAATTACCA
* *
13342310 TTTTACCCTCGAACATCCAAAAATTACCA
1 TTTTACCCTCAAACTTCCAAAAATTACCA
* * * * * *
13342339 TTTTGCCCCCGAGCATCCAAAAAATACCA
1 TTTTACCCTCAAACTTCCAAAAATTACCA
* *
13342368 TTTTTACCCTTAAACTTCCAAAAATGA-CA
1 -TTTTACCCTCAAACTTCCAAAAATTACCA
*
13342397 GTTTCACCCTCAAACTTCCAAAAATTA-CA
1 -TTTTACCCTCAAACTTCCAAAAATTACCA
* *
13342426 TTTTTACTCC-CAAACATCCAAAAATTATCA
1 -TTTTAC-CCTCAAACTTCCAAAAATTACCA
* *
13342456 TTTTACCC-CTGAACATCCAAAAATTACCA
1 TTTTACCCTC-AAACTTCCAAAAATTACCA
* * **
13342485 TTTTACCCTTAAACTTCTCAAAAATCAAAA
1 TTTTACCCTCAAACTTC-CAAAAATTACCA
* *
13342515 TTTTGACCC-CGAACTTCTCAAAAATCA-CA
1 TTTT-ACCCTCAAACTTC-CAAAAATTACCA
* *
13342544 TTTTGGACCCT-AAACTTTTTC-AAAATTACCG
1 TTTT--ACCCTCAAAC--TTCCAAAAATTACCA
13342575 TTTTACCC-CTAAACTTCCAAAAATTACCA
1 TTTTACCCTC-AAACTTCCAAAAATTACCA
* * * * *
13342604 TTTTACCCCCGAGCATCCAAAAGTTACCA
1 TTTTACCCTCAAACTTCCAAAAATTACCA
**
13342633 -TTTACCCTCAATTTTCCAAAA
1 TTTTACCCTCAAACTTCCAAAA
13342654 GTTTGACTTC
Statistics
Matches: 306, Mismatches: 50, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
28 22 0.07
29 177 0.58
30 94 0.31
31 11 0.04
32 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (29 bp):
TTTTACCCTCAAACTTCCAAAAATTACCA
Found at i:13355041 original size:39 final size:39
Alignment explanation
Indices: 13354987--13356205 Score: 624
Period size: 39 Copynumber: 31.2 Consensus size: 39
13354977 TGAAGATTCG
* * *
13354987 ATCTCTTACCCCGAGCATGGGACAGGTCATCACCAGTTA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* ** ** *
13355026 ATCTCTTACCCCGAGCCTAGGGTA-A-ATCATCATTAACCG
1 ATCTCTTACCCCGAG-CTTGGG-ACAGATCATCACCAGTCA
* * ** * *
13355065 ATCTAC-TACCCCGAGCCTAGGACAGATTGTAACC-GCTCG
1 ATCT-CTTACCCCGAGCTTGGGACAGATCATCACCAG-TCA
* **
13355104 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATTAGTCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * * **
13355143 ATTTCTTACCTCGAGCTTTGGG-TAGATCATCACCAACCA
1 ATCTCTTACCCCGAGC-TTGGGACAGATCATCACCAGTCA
** ** * * *
13355182 ATCTCTTACCCCGAGCCTAAGG-CAGATTGTAACCATTCG
1 ATCTCTTACCCCGAG-CTTGGGACAGATCATCACCAGTCA
*
13355221 ATCTCTTACCCCGAG-TATGGGACAGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCT-TGGGACAGATCATCACCAGTCA
* * * *
13355260 ATCTCTTACCCCGAGCTTGGGGCAGAT--TGCAGCTGCTCG
1 ATCTCTTACCCCGAGCTTGGGACAGATCAT-CACCAG-TCA
* * * * *
13355299 ATCTCTTACCTCGAGCTTGGGGCAAATCATCATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * * *
13355338 ATCTCTTATCCCGAGCTTGGGGCAGAT--TGCAACCATTCG
1 ATCTCTTACCCCGAGCTTGGGACAGATCAT-C-ACCAGTCA
*
13355377 ATCTCTTACCCCGAGCATGGGACAGATCATCACCAGTCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * * * *
13355416 ATCTCTTACCCCGAGCTTTGGGATAAATTA-CAACCATTCG
1 ATCTCTTACCCCGAGC-TTGGGACAGATCATC-ACCAGTCA
* * * *
13355456 ATCTCTTATCCCGAGCATAGGATAGATCATCACCAGTCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* ** * * *
13355495 ATCTCTTACCTCGAGCTTGGGGTAGAT--TGCAGTCATTCG
1 ATCTCTTACCCCGAGCTTGGGACAGATCAT-CA-CCAGTCA
* * * * *
13355534 ATCTCTTACCCCAAGCCTGAGGTA-A-ATCATAATCAGTAA
1 ATCTCTTACCCCGAGCTTG-GG-ACAGATCATCACCAGTCA
* ** * * *
13355573 ATCTCTTACCCCGAGCCTAGGG-CAGATTGTAACCATTCG
1 ATCTCTTACCCCGAG-CTTGGGACAGATCATCACCAGTCA
* ** * *
13355612 ATCTCTTACCCCGAGCCTGGGGTAGATCATCACCAATCG
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * * *
13355651 ATCTAC-CACCCTGAGCTTGGGGCAGAT--TGCAGCC-GCTCG
1 ATCT-CTTACCCCGAGCTTGGGACAGATCAT-CA-CCAG-TCA
* * * * * *
13355690 ATCTCTTACCTCGAGCCTGGGGCAAATCATCATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * * * * *
13355729 ATCTCTTATCCTGAGCCTAGGG-CAGATTA-CAGCCATTCG
1 ATCTCTTACCCCGAG-CTTGGGACAGATCATCA-CCAGTCA
* * * ** *
13355768 ATTTCTTACTCCGAGCCTGGGGTAGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * * *
13355807 ATCTCTTACCCTGAGCCTAGGG-CAGAT--TGCAATCAGCCA
1 ATCTCTTACCCCGAG-CTTGGGACAGATCAT-C-ACCAGTCA
* *
13355846 ATCTCTTACCCCGAGCATGGGACAGATCATCACCA-ACA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * *
13355884 GATCTAC-TACCCCGAGCTTGGGGCAGAT--TGCAACCATTCG
1 -ATCT-CTTACCCCGAGCTTGGGACAGATCAT-C-ACCAGTCA
* **
13355924 ATCTCTTACCCCGAGCATGGGACAGATCATCACCAACCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * * * * *
13355963 ATCTCTTACTCTGAGTTTGGGGCAGAT--TGCAGCCATTCG
1 ATCTCTTACCCCGAGCTTGGGACAGATCAT-CA-CCAGTCA
* * ** *
13356002 ATTTCTTACTCCGAGCTTGGGGTAGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * *
13356041 ATCTCTTACCCTGAGCCTCGCG-CAGAT--TGCAACCAGTCA
1 ATCTCTTACCCCGAG-CTTGGGACAGATCAT-C-ACCAGTCA
* * *
13356080 ATCTCTTACCCCGAGCATGGGACAGATCATCACAAGCCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
* * *
13356119 ATCTCTTACCCTGAGCTTGAGG-CAGAT--TGCAACCATTCG
1 ATCTCTTACCCCGAGCTTG-GGACAGATCAT-C-ACCAGTCA
* * *
13356158 ATCTCTTACCCCGAGCATAGGACAGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
13356197 ATCTCTTAC
1 ATCTCTTAC
13356206 TTCGAGTCTG
Statistics
Matches: 886, Mismatches: 218, Indels: 152
0.71 0.17 0.12
Matches are distributed among these distances:
37 11 0.01
38 46 0.05
39 735 0.83
40 84 0.09
41 10 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGACAGATCATCACCAGTCA
Found at i:13356224 original size:78 final size:77
Alignment explanation
Indices: 13354982--13356256 Score: 1138
Period size: 78 Copynumber: 16.3 Consensus size: 77
13354972 TAGATTGAAG
* ** *
13354982 ATTCGATCTCTTACCCCGAGCATGGGACAGGTCATCACCAGTTAATCTCTTACCCCGAGCCTAGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAG-CTGGG
* * *
13355047 GTA-AAT-C-ATC
65 GCAGATTGCAACC
* * ** * *
13355057 ATTAACCGATCTAC-TACCCCGAGCCTAGGACAGATTGTAACC-GCTCGATCTCTTACCCCGAGC
1 ATT---CGATCT-CTTACCCCGAGCATGGGACAGATCATCACCAGC-CAATCTCTTACCCCGAGC
*
13355120 TTGGGGCAGA-T-C-ATC
61 -TGGGGCAGATTGCAACC
* * * * * *
13355135 ATTAGTCAATTTCTTACCTCGAGCTTTGGG-TAGATCATCACCAACCAATCTCTTACCCCGAGCC
1 A-T--TCGATCTCTTACCCCGAGC-ATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAG-C
** *
13355199 TAAGGCAGATTGTAACC
61 TGGGGCAGATTGCAACC
*
13355216 ATTCGATCTCTTACCCCGAGTATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAGCTTGGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAGC-TGGG
* *
13355281 GCAGATTGCAGCT
65 GCAGATTGCAACC
** * * * * * *
13355294 GCTCGATCTCTTACCTCGAGCTTGGGGCAAATCATCATCAGCCAATCTCTTATCCCGAGCTTGGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAGC-TGGG
13355359 GCAGATTGCAACC
65 GCAGATTGCAACC
*
13355372 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGTCAATCTCTTACCCCGAGCTTTGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAGC--TGG
** * *
13355437 GATAAATTACAACC
64 GGCAGATTGCAACC
* * * * *
13355451 ATTCGATCTCTTATCCCGAGCATAGGATAGATCATCACCAGTCAATCTCTTACCTCGAGCTTGGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAGC-TGGG
* **
13355516 GTAGATTGCAGTC
65 GCAGATTGCAACC
* * * * ** *
13355529 ATTCGATCTCTTACCCCAAGCCTGAGGTA-A-ATCATAATCAGTAAATCTCTTACCCCGAGCCTA
1 ATTCGATCTCTTACCCCGAGCATG-GG-ACAGATCATCACCAGCCAATCTCTTACCCCGAG-CTG
*
13355592 GGGCAGATTGTAACC
63 GGGCAGATTGCAACC
* ** ** * * *
13355607 ATTCGATCTCTTACCCCGAGCCTGGGGTAGATCATCACCAATCGATCTAC-CACCCTGAGCTTGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCT-CTTACCCCGAGC-TGG
*
13355671 GGCAGATTGCAGCC
64 GGCAGATTGCAACC
** * * * * * * * *
13355685 GCTCGATCTCTTACCTCGAGCCTGGGGCAAATCATCATCAGCCAATCTCTTATCCTGAGCCTAGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAG-CTGGG
* *
13355750 GCAGATTACAGCC
65 GCAGATTGCAACC
* * * ** * *
13355763 ATTCGATTTCTTACTCCGAGCCTGGGGTAGATCATCACCAGCCAATCTCTTACCCTGAGCCTAGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAG-CTGGG
*
13355828 GCAGATTGCAATC
65 GCAGATTGCAACC
** * *
13355841 AGCCAATCTCTTACCCCGAGCATGGGACAGATCATCACCA-ACAGATCTAC-TACCCCGAGCTTG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCA-ATCT-CTTACCCCGAGC-TG
13355904 GGGCAGATTGCAACC
63 GGGCAGATTGCAACC
* * * *
13355919 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAACCAATCTCTTACTCTGAGTTTGGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAG-CTGGG
*
13355984 GCAGATTGCAGCC
65 GCAGATTGCAACC
* * * ** * * *
13355997 ATTCGATTTCTTACTCCGAGCTTGGGGTAGATCATCACCAGCCAATCTCTTACCCTGAGCCTCGC
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAG-CTGGG
13356062 GCAGATTGCAACC
65 GCAGATTGCAACC
* * * * *
13356075 AGTCAATCTCTTACCCCGAGCATGGGACAGATCATCACAAGCCAATCTCTTACCCTGAGCTTGAG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAGC-TGGG
13356140 GCAGATTGCAACC
65 GCAGATTGCAACC
* **
13356153 ATTCGATCTCTTACCCCGAGCATAGGACAGATCATCACCAGCCAATCTCTTACTTCGAGTCTGGG
1 ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAG-CTGGG
* *
13356218 GTAGATTGCAGCC
65 GCAGATTGCAACC
* ** *
13356231 GTTTAATCTCTTACCCCGAGCTTGGG
1 ATTCGATCTCTTACCCCGAGCATGGG
13356257 GCAAATTGCA
Statistics
Matches: 984, Mismatches: 179, Indels: 71
0.80 0.15 0.06
Matches are distributed among these distances:
75 3 0.00
77 18 0.02
78 868 0.88
79 89 0.09
80 2 0.00
81 4 0.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (77 bp):
ATTCGATCTCTTACCCCGAGCATGGGACAGATCATCACCAGCCAATCTCTTACCCCGAGCTGGGG
CAGATTGCAACC
Found at i:13356257 original size:39 final size:39
Alignment explanation
Indices: 13355104--13356344 Score: 203
Period size: 39 Copynumber: 31.8 Consensus size: 39
13355094 TAACCGCTCG
* *
13355104 ATCTCTTACCCCGAGCTTGGGGCAGA-T-C-ATCATTAGTCA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATT--T-A
* * * ***
13355143 ATTTCTTACCTCGAGCTTTGGGTAGA-T-CATCACCAACCA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
* * ** * **
13355182 ATCTCTTACCCCGAGCCTAAGGCAGATTGTAACCATTCG
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * ***
13355221 ATCTCTTACCCCGAG-TATGGGACAGA-T-CATCACCAGCCA
1 ATCTCTTACCTCGAGCT-TGGGGCAGATTGCA--ACCATTTA
* * *** **
13355260 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCTGCTCG
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * ***
13355299 ATCTCTTACCTCGAGCTTGGGGCA-AAT-CATCATCAGCCA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
**
13355338 ATCTCTTATCC-CGAGCTTGGGGCAGATTGCAACCATTCG
1 ATCTCTTA-CCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * * * *
13355377 ATCTCTTACCCCGAGCATGGGACAGA-T-CATCACCAGTCA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
* ** * * **
13355416 ATCTCTTACCCCGAGCTTTGGGATAAATTACAACCATTCG
1 ATCTCTTACCTCGAGC-TTGGGGCAGATTGCAACCATTTA
* * ** * *
13355456 ATCTCTTATCC-CGAGCATAGGATAGA-T-CATCACCAGTCA
1 ATCTCTTA-CCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
* ** **
13355495 ATCTCTTACCTCGAGCTTGGGGTAGATTGCAGTCATTCG
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * * * * * *** * * *
13355534 ATCTCTTACCCCAAGCCTGAGGTAAATCATAATCAGTAA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * * * **
13355573 ATCTCTTACCCCGAGCCTAGGGCAGATTGTAACCATTCG
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * * * **
13355612 ATCTCTTACCCCGAGCCTGGGGTAGA-T-CATCACCAATCG
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
* * ** **
13355651 ATCTAC-CACC-CTGAGCTTGGGGCAGATTGCAGCCGCTCG
1 ATCT-CTTACCTC-GAGCTTGGGGCAGATTGCAACCATTTA
* * * ***
13355690 ATCTCTTACCTCGAGCCTGGGGCA-AAT-CATCATCAGCCA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
* * * * **
13355729 ATCTCTTATCCT-GAGCCTAGGGCAGATTACAGCCATTCG
1 ATCTCTTA-CCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * * ***
13355768 ATTTCTTA-CTCCGAGCCTGGGGTAGA-T-CATCACCAGCCA
1 ATCTCTTACCT-CGAGCTTGGGGCAGATTGCA--ACCATTTA
* * * ***
13355807 ATCTCTTACC-CTGAGCCTAGGGCAGATTGCAATCAGCCA
1 ATCTCTTACCTC-GAGCTTGGGGCAGATTGCAACCATTTA
* * * **
13355846 ATCTCTTACCCCGAGCATGGGACAGA-T-CATCACCA-ACA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
* **
13355884 GATCTAC-TACCCCGAGCTTGGGGCAGATTGCAACCATTCG
1 -ATCT-CTTACCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * * ***
13355924 ATCTCTTACCCCGAGCATGGGACAGA-T-CATCACCAACCA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
* * **
13355963 ATCTCTTA-CTCTGAGTTTGGGGCAGATTGCAGCCATTCG
1 ATCTCTTACCTC-GAGCTTGGGGCAGATTGCAACCATTTA
* * ***
13356002 ATTTCTTA-CTCCGAGCTTGGGGTAGA-T-CATCACCAGCCA
1 ATCTCTTACCT-CGAGCTTGGGGCAGATTGCA--ACCATTTA
* * * * *
13356041 ATCTCTTACC-CTGAGCCTCGCGCAGATTGCAACCAGTCA
1 ATCTCTTACCTC-GAGCTTGGGGCAGATTGCAACCATTTA
* * * * ***
13356080 ATCTCTTACCCCGAGCATGGGACAGA-T-CATCACAAGCCA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
* **
13356119 ATCTCTTACC-CTGAGCTTGAGGCAGATTGCAACCATTCG
1 ATCTCTTACCTC-GAGCTTGGGGCAGATTGCAACCATTTA
* * * * ***
13356158 ATCTCTTACCCCGAGCATAGGACAGA-T-CATCACCAGCCA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA--ACCATTTA
* * * *
13356197 ATCTCTTACTTCGAG-TCTGGGGTAGATTGCAGCCGTTTA
1 ATCTCTTACCTCGAGCT-TGGGGCAGATTGCAACCATTTA
* * *
13356236 ATCTCTTACCCCGAGCTTGGGGCAAATTGCAACCATTTT
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * * * * ***
13356275 ATCTTTTACGTCGAGCTTGGGGCAGATTACCATCAGCAA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATTTA
* * *
13356314 ATCTCTTACCCCGATCATGGGGCAGATTGCA
1 ATCTCTTACCTCGAGCTTGGGGCAGATTGCA
13356345 GTCATTCGAA
Statistics
Matches: 900, Mismatches: 219, Indels: 166
0.70 0.17 0.13
Matches are distributed among these distances:
37 24 0.03
38 28 0.03
39 760 0.84
40 57 0.06
41 26 0.03
42 5 0.01
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCTCGAGCTTGGGGCAGATTGCAACCATTTA
Found at i:13356290 original size:117 final size:117
Alignment explanation
Indices: 13355181--13356345 Score: 406
Period size: 117 Copynumber: 9.9 Consensus size: 117
13355171 ATCACCAACC
* * * * * *
13355181 AATCTCTTACCCCGAGCCTAAGGCAGATTGTAACCATTCGATCTCTTACCCCGAGTATGGGACAG
1 AATCTCTTACCCCGAGCTTGAGGCAAATTGCAACCATTCGATCTCTTACCCCGAGCATAGGACAG
* * * * * * *
13355246 ATCATCACCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCTGCTC
66 ATCACCACCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCGTTT
* * * * ** * * * * *
13355298 GATCTCTTACCTCGAGCTTGGGGCAAA-T-CATCATCAGCCAATCTCTTATCCCGAGCTTGGGGC
1 AATCTCTTACCCCGAGCTTGAGGCAAATTGCA--ACCATTCGATCTCTTACCCCGAGCATAGGAC
** * * * * * *
13355361 AGATTGCAACCATTC-GATCTCTTACCCCGAGCATGGGACAGATCAT-CA-CCAG-TC
64 AGATCACCACCA-GCAAATCTCTTACCCCGATCATGGGGCAGAT--TGCAGCC-GTTT
* * * *
13355415 AATCTCTTACCCCGAGCTTTG-GGATAAATTACAACCATTCGATCTCTTATCCCGAGCATAGGAT
1 AATCTCTTACCCCGAGC-TTGAGG-CAAATTGCAACCATTCGATCTCTTACCCCGAGCATAGGAC
* * * * * * * *
13355479 AGATCATCACCAGTC-AATCTCTTACCTCGAGCTTGGGGTAGATTGCAGTCATTC
64 AGATCACCACCAG-CAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCGTTT
* * * * *** * * ** * *
13355533 GATCTCTTACCCCAAGCCTGAGGTAAATCATAATCAGTAAATCTCTTACCCCGAGCCTAGGGCAG
1 AATCTCTTACCCCGAGCTTGAGGCAAATTGCAACCATTCGATCTCTTACCCCGAGCATAGGACAG
**** * * * * * ** *
13355598 ATTGTAACCATTC-GATCTCTTACCCCGAGCCTGGGGTAGATCAT-CA-CCAATC
66 ATCACCACCA-GCAAATCTCTTACCCCGATCATGGGGCAGAT--TGCAGCCGTTT
* * * * * * ** * * * *
13355650 GATCTAC-CACCCTGAGCTTGGGGCAGATTGCAGCCGCTCGATCTCTTACCTCGAGCCTGGGGCA
1 AATCT-CTTACCCCGAGCTTGAGGCAAATTGCAACCATTCGATCTCTTACCCCGAGCATAGGACA
* * * * * * * * * * * *
13355714 AATCATCATCAGCCAATCTCTTATCCTGAGCCTAGGGCAGATTACAGCCATTC
65 GATCACCACCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCGTTT
* * * * * * * ** * * * *
13355767 GATTTCTTACTCCGAGCCTGGGGTAGA-T-CATCACCAGCCAATCTCTTACCCTGAGCCTAGGGC
1 AATCTCTTACCCCGAGCTTGAGGCAAATTGCA--ACCATTCGATCTCTTACCCCGAGCATAGGAC
** * * * * * ***
13355830 AGATTGCAATCAGCCAATCTCTTACCCCGAGCATGGGACAGATCAT-CA-CC-AAC
64 AGATCACCACCAGCAAATCTCTTACCCCGATCATGGGGCAGAT--TGCAGCCGTTT
* * *
13355883 AGATCTAC-TACCCCGAGCTTGGGGCAGATTGCAACCATTCGATCTCTTACCCCGAGCATGGGAC
1 A-ATCT-CTTACCCCGAGCTTGAGGCAAATTGCAACCATTCGATCTCTTACCCCGAGCATAGGAC
* * * * * * * *
13355947 AGATCATCACCAACCAATCTCTTACTCTGAGT-TTGGGGCAGATTGCAGCCATTC
64 AGATCACCACCAGCAAATCTCTTACCCCGA-TCATGGGGCAGATTGCAGCCGTTT
* * * * * * ** * * * *
13356001 GATTTCTTACTCCGAGCTTGGGGTAGA-T-CATCACCAGCCAATCTCTTACCCTGAGCCTCGCG-
1 AATCTCTTACCCCGAGCTTGAGGCAAATTGCA--ACCATTCGATCTCTTACCCCGAGCATAG-GA
** * * * *
13356063 CAGATTGCAACCAGTC-AATCTCTTACCCCGAGCATGGGACAGATCATCACAAGCC----
63 CAGATCACCACCAG-CAAATCTCTTACCCCGATCATGGGGCAGAT--T-GC-AGCCGTTT
* *
13356118 AATCTCTTACCCTGAGCTTGAGGCAGATTGCAACCATTCGATCTCTTACCCCGAGCATAGGACAG
1 AATCTCTTACCCCGAGCTTGAGGCAAATTGCAACCATTCGATCTCTTACCCCGAGCATAGGACAG
* * ** *
13356183 ATCATCACCAGCCAATCTCTTACTTCGAGTC-TGGGGTAGATTGCAGCCGTTT
66 ATCACCACCAGCAAATCTCTTACCCCGA-TCATGGGGCAGATTGCAGCCGTTT
* ** * ** * * *
13356235 AATCTCTTACCCCGAGCTTGGGGCAAATTGCAACCATTTTATCTTTTACGTCGAGCTTGGGGCAG
1 AATCTCTTACCCCGAGCTTGAGGCAAATTGCAACCATTCGATCTCTTACCCCGAGCATAGGACAG
* *
13356300 ATTACCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAG
66 ATCACCACCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAG
13356346 TCATTCGAAG
Statistics
Matches: 782, Mismatches: 211, Indels: 110
0.71 0.19 0.10
Matches are distributed among these distances:
113 4 0.01
114 1 0.00
115 8 0.01
116 16 0.02
117 640 0.82
118 97 0.12
119 9 0.01
120 3 0.00
121 4 0.01
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (117 bp):
AATCTCTTACCCCGAGCTTGAGGCAAATTGCAACCATTCGATCTCTTACCCCGAGCATAGGACAG
ATCACCACCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCGTTT
Found at i:13356771 original size:17 final size:17
Alignment explanation
Indices: 13356749--13356828 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
13356739 GAACTCATTT
* **
13356749 TTTAAATTTGTTTTAGG
1 TTTAAATTTATTTTAAA
13356766 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
13356783 TTTAAATTAATTTTAAG
1 TTTAAATTTATTTTAAA
13356800 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
13356817 TTTAAATTTATT
1 TTTAAATTTATT
13356829 CAAATCTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:13356780 original size:11 final size:11
Alignment explanation
Indices: 13356766--13356820 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
13356756 TTGTTTTAGG
13356766 TTTAAATTTAT
1 TTTAAATTTAT
*
13356777 TTTAAATTTAA
1 TTTAAATTTAT
* * *
13356788 ATTAATTTTAAG
1 TTTAAATTT-AT
13356800 TTTAAATTTAT
1 TTTAAATTTAT
13356811 TTTAAATTTA
1 TTTAAATTTA
13356821 AATTTATTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 28 0.78
12 8 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:13356787 original size:34 final size:34
Alignment explanation
Indices: 13356749--13356828 Score: 133
Period size: 34 Copynumber: 2.4 Consensus size: 34
13356739 GAACTCATTT
* *
13356749 TTTAAATTTGTTTTAGGTTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAGTTTAAATTTATTTTAAA
*
13356783 TTTAAATTAATTTTAAGTTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAGTTTAAATTTATTTTAAA
13356817 TTTAAATTTATT
1 TTTAAATTTATT
13356829 CAAATCTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGTTTAAATTTATTTTAAA
Found at i:13356792 original size:5 final size:6
Alignment explanation
Indices: 13356766--13356826 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
13356756 TTGTTTTAGG
* * * *
13356766 TTTAAA TTT-AT TTTAAA TTTAAA -TTAAT TTTAAG TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
13356811 TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
13356827 TTCAAATCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 12 0.27
6 33 0.73
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:13356838 original size:16 final size:17
Alignment explanation
Indices: 13356768--13356839 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 17
13356758 GTTTTAGGTT
* *
13356768 TAAATTTATTTTAAATT
1 TAAATTTATTTCAAATC
* * * *
13356785 TAAATTAATTTTAAGTT
1 TAAATTTATTTCAAATC
* *
13356802 TAAATTTATTTTAAATT
1 TAAATTTATTTCAAATC
13356819 TAAATTTA-TTCAAATC
1 TAAATTTATTTCAAATC
13356835 TAAAT
1 TAAAT
13356840 AAATAATGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 11 0.22
17 38 0.78
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (17 bp):
TAAATTTATTTCAAATC
Found at i:13357529 original size:15 final size:14
Alignment explanation
Indices: 13357509--13357542 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
13357499 TTGAAACTGA
13357509 AAATATTAAATAATT
1 AAATATTAAAT-ATT
13357524 AAATATTAAATATT
1 AAATATTAAATATT
13357538 AAATA
1 AAATA
13357543 GAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATTAAATATT
Found at i:13357531 original size:7 final size:7
Alignment explanation
Indices: 13357509--13357542 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
13357499 TTGAAACTGA
13357509 AAATATT
1 AAATATT
13357516 AAATAATT
1 AAAT-ATT
13357524 AAATATT
1 AAATATT
13357531 AAATATT
1 AAATATT
13357538 AAATA
1 AAATA
13357543 GAAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:13358601 original size:29 final size:28
Alignment explanation
Indices: 13358566--13358791 Score: 197
Period size: 29 Copynumber: 7.7 Consensus size: 28
13358556 CTGAACTTCT
* * *
13358566 CAAAAATTACATTTTTGCCGCCGAACTTA
1 CAAAAATTACATTTTTACC-CCGAACATC
*
13358595 CAAAAATTACCA-TTTTACCCCCAAACATC
1 CAAAAATTA-CATTTTTA-CCCCGAACATC
* *
13358624 CAAAAATTACCA-TTTTGCCCTCGAGCATC
1 CAAAAATTA-CATTTTTACCC-CGAACATC
*
13358653 AAAAAATTATCATTTTTACTCCCGAACATC
1 CAAAAATTA-CATTTTTAC-CCCGAACATC
* * *
13358683 CAAAAATAACATTTTCACCCTCGAACTTC
1 CAAAAATTACATTTTTACCC-CGAACATC
13358712 CAAAAATTACATTTTTACTCCCGAACATC
1 CAAAAATTACATTTTTAC-CCCGAACATC
* *
13358741 TAAAAATTAC-TATTTTACCCTCGAACTTC
1 CAAAAATTACAT-TTTTACCC-CGAACATC
*
13358770 TCAAAAATCACATTTTTGACCC
1 -CAAAAATTACATTTTT-ACCC
13358792 TAAACTTTTC
Statistics
Matches: 163, Mismatches: 22, Indels: 22
0.79 0.11 0.11
Matches are distributed among these distances:
28 8 0.05
29 111 0.68
30 37 0.23
31 7 0.04
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.31
Consensus pattern (28 bp):
CAAAAATTACATTTTTACCCCGAACATC
Found at i:13358683 original size:59 final size:58
Alignment explanation
Indices: 13358596--13358786 Score: 224
Period size: 59 Copynumber: 3.3 Consensus size: 58
13358586 CCGAACTTAC
* * * *
13358596 AAAAATTACCA-TTTTACCCCCAAACATCCAAAAATTACCATTTTGCCCTCGAGCATCA
1 AAAAATTA-CATTTTTACTCCCGAACATCCAAAAATTACCATTTTACCCTCGAACATCA
* * *
13358654 AAAAATTATCATTTTTACTCCCGAACATCCAAAAA-TAACATTTTCACCCTCGAACTTCC
1 AAAAATTA-CATTTTTACTCCCGAACATCCAAAAATTACCATTTT-ACCCTCGAACATCA
* * * *
13358713 AAAAATTACATTTTTACTCCCGAACATCTAAAAATTACTATTTTACCCTCGAACTTCTC
1 AAAAATTACATTTTTACTCCCGAACATCCAAAAATTACCATTTTACCCTCGAACATC-A
*
13358772 AAAAATCACATTTTT
1 AAAAATTACATTTTT
13358787 GACCCTAAAC
Statistics
Matches: 117, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
58 56 0.48
59 61 0.52
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (58 bp):
AAAAATTACATTTTTACTCCCGAACATCCAAAAATTACCATTTTACCCTCGAACATCA
Found at i:13358844 original size:28 final size:29
Alignment explanation
Indices: 13358789--13358847 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
13358779 ACATTTTTGA
** *
13358789 CCCTAAACTTTTCCAAAATTACCGTTTTAC
1 CCCTAAAC-TTTCCAAAACCACCATTTTAC
13358819 CCCTAAAC-TTCCAAAACCACCATTTTAC
1 CCCTAAACTTTCCAAAACCACCATTTTAC
13358847 C
1 C
13358848 TTTGAGTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 18 0.69
30 8 0.31
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.31
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAACCACCATTTTAC
Found at i:13358888 original size:29 final size:29
Alignment explanation
Indices: 13358742--13358891 Score: 92
Period size: 29 Copynumber: 5.1 Consensus size: 29
13358732 CCGAACATCT
* * *
13358742 AAAAATTACTATTTTACCCTCGAA-CTTCTC
1 AAAAATTACCATTTTACCCT-TAATTTTC-C
* *
13358772 AAAAATCA-CATTTTTGACCCTAAACTTTTCC
1 AAAAATTACCA-TTTT-ACCCTTAA-TTTTCC
* * **
13358803 -AAAATTACCGTTTTACCCCTAAACTTCC
1 AAAAATTACCATTTTACCCTTAATTTTCC
** * * * *
13358831 -AAAACCACCATTTTACCTTTGAGTATCC
1 AAAAATTACCATTTTACCCTTAATTTTCC
13358859 AAAAATTACCATTTTACCCTTAATTTTCC
1 AAAAATTACCATTTTACCCTTAATTTTCC
13358888 AAAA
1 AAAA
13358892 GTTTGACTTC
Statistics
Matches: 89, Mismatches: 25, Indels: 13
0.70 0.20 0.10
Matches are distributed among these distances:
28 23 0.26
29 33 0.37
30 23 0.26
31 7 0.08
32 3 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTTAATTTTCC
Found at i:13364847 original size:24 final size:24
Alignment explanation
Indices: 13364813--13364860 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
13364803 GTTCACGAAC
* * *
13364813 AAGCTCGTTTATTGGCTTGTTTAT
1 AAGCTCATTTACTGACTTGTTTAT
13364837 AAGCTCATTTACTGACTTGTTTAT
1 AAGCTCATTTACTGACTTGTTTAT
13364861 TTATTAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
AAGCTCATTTACTGACTTGTTTAT
Found at i:13364984 original size:24 final size:23
Alignment explanation
Indices: 13364951--13365038 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
13364941 TCATTAATAT
*
13364951 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
* *
13364975 TGTTTATGAACATGTTCATTTAA
1 TGTTCATGAACATGTTCAATTAA
* *
13364998 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCAATTAA
* *
13365021 -GTTAAATGAATATGTTCA
1 TGTT-CATGAACATGTTCA
13365039 TGAACATTCA
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
22 3 0.06
23 30 0.58
24 19 0.37
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:13367521 original size:32 final size:32
Alignment explanation
Indices: 13367485--13367547 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
13367475 TCTTTGGGGA
* *
13367485 GAGGAAAGTCTTCTGGTTCATCATTTTCTTGT
1 GAGGAAAGTCTTCTAGTTCATCATATTCTTGT
13367517 GAGGAAAGTCTTCTAGTTCATCATATTCTTG
1 GAGGAAAGTCTTCTAGTTCATCATATTCTTG
13367548 GTTTTCTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (32 bp):
GAGGAAAGTCTTCTAGTTCATCATATTCTTGT
Found at i:13375513 original size:27 final size:28
Alignment explanation
Indices: 13375461--13375515 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
13375451 TTGAATCCTT
* *
13375461 TTAATTTTTTATTTTAAGTTCTTTTTTC
1 TTAATTTTTTATTATAAGTTATTTTTTC
*
13375489 TTAA-TTTTTATTATAATTATATTTTTT
1 TTAATTTTTTATTATAAGT-TATTTTTT
13375516 AAAACTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (28 bp):
TTAATTTTTTATTATAAGTTATTTTTTC
Found at i:13382336 original size:2 final size:2
Alignment explanation
Indices: 13382329--13382355 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13382319 AAGACTTGAT
13382329 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13382356 TTGAATTACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13399575 original size:4 final size:4
Alignment explanation
Indices: 13399566--13399597 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
13399556 TGTGGGTCTT
13399566 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
13399598 AAATTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:13401030 original size:13 final size:13
Alignment explanation
Indices: 13401012--13401042 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
13401002 AAAATTTGAT
13401012 GTCTATCTTTCGA
1 GTCTATCTTTCGA
13401025 GTCTATCTTTCGA
1 GTCTATCTTTCGA
13401038 GTCTA
1 GTCTA
13401043 GTTAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.45
Consensus pattern (13 bp):
GTCTATCTTTCGA
Found at i:13406540 original size:14 final size:14
Alignment explanation
Indices: 13406521--13406547 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13406511 TAAATTTATA
13406521 AAAAAATTAAATTG
1 AAAAAATTAAATTG
13406535 AAAAAATTAAATT
1 AAAAAATTAAATT
13406548 TGCGAGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (14 bp):
AAAAAATTAAATTG
Found at i:13407315 original size:22 final size:20
Alignment explanation
Indices: 13407267--13407326 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
13407257 AAAATAATCC
* *
13407267 CATTTTCTTATAAATTAATT
1 CATTTTCTTAAAAATTAAAT
*
13407287 TATTTTCTTGAAAAATATAAAT
1 CATTTTCTT-AAAAAT-TAAAT
13407309 CATTTTCTCATAAAAATT
1 CATTTTCT--TAAAAATT
13407327 TAACTTGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 8 0.25
21 5 0.16
22 12 0.38
23 6 0.19
24 1 0.03
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (20 bp):
CATTTTCTTAAAAATTAAAT
Found at i:13407841 original size:18 final size:17
Alignment explanation
Indices: 13407795--13407848 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
13407785 GATTGTTTAT
*
13407795 TATTAAGTTA-TATGATA
1 TATTAA-TTATTATGAAA
13407812 TATTAATTATTATGAAA
1 TATTAATTATTATGAAA
* *
13407829 TATTATTTTATTATAAAA
1 TATTA-ATTATTATGAAA
13407847 TA
1 TA
13407849 AATTTTGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 3 0.09
17 17 0.53
18 12 0.38
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TATTAATTATTATGAAA
Found at i:13409793 original size:19 final size:19
Alignment explanation
Indices: 13409766--13409807 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13409756 ACGAAAATTA
* * *
13409766 TAATGTTTAGGTTTATGAT
1 TAATATTTAGATTAATGAT
13409785 TAATATTTAGATTAATGAT
1 TAATATTTAGATTAATGAT
13409804 TAAT
1 TAAT
13409808 GGTTTGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (19 bp):
TAATATTTAGATTAATGAT
Found at i:13410750 original size:18 final size:18
Alignment explanation
Indices: 13410729--13410787 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
13410719 CACTAATGCC
13410729 TTTTATTACCTTGTATAT
1 TTTTATTACCTTGTATAT
*
13410747 TTTTCATT-CAC-TG-ATGCCT
1 TTTT-ATTAC-CTTGTAT--AT
13410766 TTTTATTACCTTGTATAT
1 TTTTATTACCTTGTATAT
13410784 TTTT
1 TTTT
13410788 CATTCACTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
17 2 0.06
18 16 0.50
19 12 0.38
20 2 0.06
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (18 bp):
TTTTATTACCTTGTATAT
Found at i:13410779 original size:37 final size:37
Alignment explanation
Indices: 13410699--13410814 Score: 207
Period size: 37 Copynumber: 3.2 Consensus size: 37
13410689 GCTCATCATG
*
13410699 TACCTTGTATATTTTTCATTCACTAATGCC-TTTTAT
1 TACCTTGTATATTTTTCATTCACTGATGCCTTTTTAT
13410735 TACCTTGTATATTTTTCATTCACTGATGCCTTTTTAT
1 TACCTTGTATATTTTTCATTCACTGATGCCTTTTTAT
13410772 TACCTTGTATATTTTTCATTCACTGATGCCTTTTTAT
1 TACCTTGTATATTTTTCATTCACTGATGCCTTTTTAT
*
13410809 TTCCTT
1 TACCTT
13410815 TTACTTTCTC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
36 29 0.38
37 48 0.62
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.54
Consensus pattern (37 bp):
TACCTTGTATATTTTTCATTCACTGATGCCTTTTTAT
Found at i:13410787 original size:19 final size:19
Alignment explanation
Indices: 13410729--13410787 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
13410719 CACTAATGCC
13410729 TTTTATTACCTTGTATATT
1 TTTTATTACCTTGTATATT
* **
13410748 TTTCATT-CAC-TG-ATGCCT
1 TTTTATTAC-CTTGTAT-ATT
13410766 TTTTATTACCTTGTATATT
1 TTTTATTACCTTGTATATT
13410785 TTT
1 TTT
13410788 CATTCACTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
17 2 0.07
18 11 0.38
19 14 0.48
20 2 0.07
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTTATTACCTTGTATATT
Found at i:13410805 original size:18 final size:18
Alignment explanation
Indices: 13410747--13410805 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
13410737 CCTTGTATAT
13410747 TTTTCATTCACTGATGCC
1 TTTTCATTCACTGATGCC
* **
13410765 TTTTTATT-ACCTTGTAT-AT
1 TTTTCATTCA-C-TG-ATGCC
13410784 TTTTCATTCACTGATGCC
1 TTTTCATTCACTGATGCC
13410802 TTTT
1 TTTT
13410806 TATTTCCTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 3 0.10
18 14 0.47
19 10 0.33
20 3 0.10
ACGTcount: A:0.17, C:0.20, G:0.08, T:0.54
Consensus pattern (18 bp):
TTTTCATTCACTGATGCC
Found at i:13410805 original size:19 final size:19
Alignment explanation
Indices: 13410746--13410806 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
13410736 ACCTTGTATA
13410746 TTTTTCATTCACTGATGCC
1 TTTTTCATTCACTGATGCC
*
13410765 TTTTT-ATT-ACCTTGTAT--A
1 TTTTTCATTCA-C-TG-ATGCC
13410783 TTTTTCATTCACTGATGCC
1 TTTTTCATTCACTGATGCC
13410802 TTTTT
1 TTTTT
13410807 ATTTCCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
17 3 0.09
18 11 0.33
19 16 0.48
20 3 0.09
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (19 bp):
TTTTTCATTCACTGATGCC
Found at i:13419940 original size:36 final size:39
Alignment explanation
Indices: 13419892--13419973 Score: 116
Period size: 36 Copynumber: 2.2 Consensus size: 39
13419882 TAATATAACG
*
13419892 AAAAAAATAATGATATTTAAAAT-ATT-TTACATATT-T
1 AAAATAATAATGATATTTAAAATGATTATTACATATTAT
* *
13419928 AAAATAATAATGATATTTAAAATGATTATTTCATTTTAT
1 AAAATAATAATGATATTTAAAATGATTATTACATATTAT
13419967 AAAATAA
1 AAAATAA
13419974 AATATTACCG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
36 22 0.55
37 3 0.08
38 7 0.17
39 8 0.20
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (39 bp):
AAAATAATAATGATATTTAAAATGATTATTACATATTAT
Found at i:13419943 original size:18 final size:18
Alignment explanation
Indices: 13419892--13419950 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
13419882 TAATATAACG
*
13419892 AAAAAAATAATGATATTT
1 AAAATAATAATGATATTT
** *
13419910 AAAAT-ATTTTACATATTT
1 AAAATAATAAT-GATATTT
13419928 AAAATAATAATGATATTT
1 AAAATAATAATGATATTT
13419946 AAAAT
1 AAAAT
13419951 GATTATTTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 3 0.09
18 26 0.81
19 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAATAATAATGATATTT
Found at i:13426907 original size:3 final size:3
Alignment explanation
Indices: 13426899--13426970 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
13426889 TTTTACTTAT
* * * * *
13426899 ATA ATA ATA ATA ATA ATA ATA A-A ATA TTT AT- ATT TTAA ATA ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
*
13426943 ATT A-A ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13426971 TTTATATTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
2 7 0.12
3 48 0.86
4 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:13426939 original size:26 final size:26
Alignment explanation
Indices: 13426910--13426996 Score: 87
Period size: 26 Copynumber: 3.6 Consensus size: 26
13426900 TAATAATAAT
13426910 AATAATAATAAAATATTTATATTTTA
1 AATAATAATAAAATATTTATATTTTA
* * *
13426936 AATAATTATTAAATA---ATA--AT-
1 AATAATAATAAAATATTTATATTTTA
13426956 AATAATAATAAAATATTTATATTTTA
1 AATAATAATAAAATATTTATATTTTA
* *
13426982 AATAATTATTAAATA
1 AATAATAATAAAATA
13426997 ATAATTATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
20 13 0.28
21 1 0.02
23 6 0.13
25 1 0.02
26 26 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAATAATAAAATATTTATATTTTA
Found at i:13427017 original size:46 final size:46
Alignment explanation
Indices: 13426901--13427001 Score: 202
Period size: 46 Copynumber: 2.2 Consensus size: 46
13426891 TTACTTATAT
13426901 AATAATAATAATAATAATAAAATATTTATATTTTAAATAATTATTA
1 AATAATAATAATAATAATAAAATATTTATATTTTAAATAATTATTA
13426947 AATAATAATAATAATAATAAAATATTTATATTTTAAATAATTATTA
1 AATAATAATAATAATAATAAAATATTTATATTTTAAATAATTATTA
13426993 AATAATAAT
1 AATAATAAT
13427002 TATTTAATGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (46 bp):
AATAATAATAATAATAATAAAATATTTATATTTTAAATAATTATTA
Found at i:13428349 original size:3 final size:3
Alignment explanation
Indices: 13428341--13428381 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
13428331 TTTTACTTAT
13428341 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13428382 CTTATATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13429407 original size:15 final size:16
Alignment explanation
Indices: 13429387--13429417 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13429377 TTAATACTTG
13429387 AAAATT-TGGGTACCC
1 AAAATTGTGGGTACCC
13429402 AAAATTGTGGGTACCC
1 AAAATTGTGGGTACCC
13429418 GATTATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (16 bp):
AAAATTGTGGGTACCC
Found at i:13431528 original size:52 final size:52
Alignment explanation
Indices: 13431449--13431687 Score: 370
Period size: 52 Copynumber: 4.6 Consensus size: 52
13431439 TAAATGAAAA
* * *
13431449 AGGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGAATATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
13431501 AGGTCTGATTACTATGTGTCATTGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
13431553 AGGTTCGATGATTATGTGTCATCTTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
13431605 AGGTCCGATGACTATATGTCATCGTGAGTATATGATTCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
13431657 AGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
13431688 TAAATGAAAT
Statistics
Matches: 167, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 167 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:13438745 original size:52 final size:52
Alignment explanation
Indices: 13438564--13438745 Score: 244
Period size: 52 Copynumber: 3.6 Consensus size: 52
13438554 TAAATGAAAA
13438564 AGGTCCGATGACTATGTGTCATCGTGAG--TA-GAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATG
* *
13438613 AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATG
* * * * * *
13438665 AGGTCCGATGACAATGTATCATCGTGAGCATATGATTCTTTTACGAATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATG
* * *
13438717 AGGTTCGGTGACTATGTGTCATCATGAGC
1 AGGTCCGATGACTATGTGTCATCGTGAGC
13438746 CTTAAATGAA
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
49 27 0.23
51 2 0.02
52 87 0.75
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATG
Found at i:13439515 original size:21 final size:21
Alignment explanation
Indices: 13439491--13439530 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13439481 CAGTAGAAGA
*
13439491 GTCACTTGTATTGGTAAAACT
1 GTCACTTGTATCGGTAAAACT
13439512 GTCACTTGTATCGGTAAAA
1 GTCACTTGTATCGGTAAAA
13439531 GTCTACACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (21 bp):
GTCACTTGTATCGGTAAAACT
Found at i:13445136 original size:19 final size:20
Alignment explanation
Indices: 13445112--13445159 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13445102 TTATAATGGT
*
13445112 TATATTTTA-ATATTTAAAA
1 TATATTTTATATATTCAAAA
*
13445131 TATATTTTATATATTCAAAT
1 TATATTTTATATATTCAAAA
*
13445151 TAAATTTTA
1 TATATTTTA
13445160 CAAATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTTTATATATTCAAAA
Found at i:13446394 original size:24 final size:24
Alignment explanation
Indices: 13446367--13446414 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
13446357 GAAGATTAGT
**
13446367 ATTTATTAGTATAATATATTTGAC
1 ATTTATTAACATAATATATTTGAC
*
13446391 ATTTATTAACATAATTTATTTGAC
1 ATTTATTAACATAATATATTTGAC
13446415 CTAAGATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (24 bp):
ATTTATTAACATAATATATTTGAC
Found at i:13448904 original size:32 final size:33
Alignment explanation
Indices: 13448835--13448907 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
13448825 TAGAGGAAAC
13448835 TTTTTTTTCTTTTTGAATAAGATTGAAAGGAAG
1 TTTTTTTTCTTTTTGAATAAGATTGAAAGGAAG
* *
13448868 TTTTTTTTCTTTTTTAATAAGATT-AAGAGG-AT
1 TTTTTTTTCTTTTTGAATAAGATTGAA-AGGAAG
13448900 TTTTTTTT
1 TTTTTTTT
13448908 ATTCAGAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 11 0.30
33 26 0.70
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.58
Consensus pattern (33 bp):
TTTTTTTTCTTTTTGAATAAGATTGAAAGGAAG
Found at i:13450206 original size:15 final size:15
Alignment explanation
Indices: 13450186--13450215 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13450176 ATTTGTGATC
13450186 CTTTGCATTTTATTG
1 CTTTGCATTTTATTG
13450201 CTTTGCATTTTATTG
1 CTTTGCATTTTATTG
13450216 TATGTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (15 bp):
CTTTGCATTTTATTG
Found at i:13456284 original size:49 final size:50
Alignment explanation
Indices: 13456212--13456348 Score: 150
Period size: 49 Copynumber: 2.7 Consensus size: 50
13456202 AACACATCGC
* * **
13456212 CTAAAAAAAAGTTTGAGTTGAAAACTTGAAAGGGGGGCTCAAACTAG-AA
1 CTAAAAAAAAGTTCGAGTTGAAAACCTGAAAGGGCAGCTCAAACTAGCAA
*
13456261 CTAAAAAAAAGTTCGGGTTGAAAACCTGAAAGGGCAGCTCAAACTAGCAA
1 CTAAAAAAAAGTTCGAGTTGAAAACCTGAAAGGGCAGCTCAAACTAGCAA
** * * *
13456311 AAAAAAAAGAAGGGTCGAGATGAAAACCCGCAAAGGGC
1 CTAAAAAA-AA-GTTCGAGTTGAAAACCTG-AAAGGGC
13456349 GTCTTGAAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 42 0.58
50 8 0.11
51 2 0.03
52 14 0.19
53 7 0.10
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.15
Consensus pattern (50 bp):
CTAAAAAAAAGTTCGAGTTGAAAACCTGAAAGGGCAGCTCAAACTAGCAA
Found at i:13457598 original size:97 final size:96
Alignment explanation
Indices: 13457367--13457598 Score: 225
Period size: 97 Copynumber: 2.4 Consensus size: 96
13457357 TCATAAAGTT
* * * *
13457367 TGAAGAAGGATAGGTTGAAA-TCGCAATGACGAACCTAACATCCTAAAATCGAAGAGGGAAAGGT
1 TGAAG-AGGATAGGTT-AAAGTCGCAATGACGAACCT-ACACCCAAAAATCGAAAAGGGAAAGAT
* * * *
13457431 TGAAGCCGTAATGGTGAACCTTACTCCTTAAAAC
63 TGAAGCCGTAACGATGAACCTTACACCCTAAAAC
* * * *
13457465 TGAAGAGGGATAAGTTGAAGCCGCAACGACGAACCTACACCCAAAAATCGAAAAGGGAAAGATTG
1 TGAAGA-GGATAGGTTAAAGTCGCAATGACGAACCTACACCCAAAAATCGAAAAGGGAAAGATTG
*** * *
13457530 AATTTGTAACGATGGATCTTACACCCTAAAA-
65 AAGCCGTAACGATGAACCTTACACCCTAAAAC
* *
13457561 TCGAAGAGGAATAGGTTAAAGTCACAATGACGGACCTA
1 T-GAAGAGG-ATAGGTTAAAGTCGCAATGACGAACCTA
13457599 ATGCCCTAAA
Statistics
Matches: 107, Mismatches: 23, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
96 3 0.03
97 77 0.72
98 27 0.25
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (96 bp):
TGAAGAGGATAGGTTAAAGTCGCAATGACGAACCTACACCCAAAAATCGAAAAGGGAAAGATTGA
AGCCGTAACGATGAACCTTACACCCTAAAAC
Found at i:13457730 original size:49 final size:49
Alignment explanation
Indices: 13457367--13457868 Score: 251
Period size: 49 Copynumber: 10.2 Consensus size: 49
13457357 TCATAAAGTT
* ** *
13457367 TGAAGAAGGATAGGTTGAAATCGCAATGACGAACCTAACATCC-TAAAA-
1 TGAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACA-CCTTAAAAC
* * * ** * *
13457415 TCGAAGAGGGAAAGGTTGAAGCCGTAATGGTGAACCTTACTCCTTAAAAC
1 T-GAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAC
* * *
13457465 TGAAGAGGGATAAGTTGAAGCCGCAACGACGAACCT-ACACC-CAAAAA
1 TGAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAC
* * * *** * * * * * *
13457512 TCGAAAAGGGAAAGATTGAATTTGTAACGATGGATCTTACACCCTAAAA-
1 T-GAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAC
* * * * * * ** *
13457561 TCGAAGAGGAATAGGTTAAAGTCACAATGACGGACCTAATGCCCTAAAAC
1 T-GAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAC
** * * * * * * * *
13457611 CAAAAAGGAATCGATTGAAGTCGCAACGGC-ATATCTAACACCCTAAAAC
1 TGAAGAGGGATAGGTTGAAGCCGCAACGACGA-ACCTAACACCTTAAAAC
** * * * * *
13457660 CAAATAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTACACCTTAAAAC
1 TGAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAC
* * * *
13457709 TGAAGAGGGATAGGTTAAAGCCACAACGGCGGACCTAACACCTTAAAAC
1 TGAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAC
* * * * * * *
13457758 ATGACGAGGGAAAGATTGAAGTCGCAACGACGGATCTTACACCTTAAAAC
1 -TGAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAC
* * * * * * * * *
13457808 AGAAAAGGAATAGGTTGAAGCTGCGACGGCGGACCTAATACCTTAAAAA
1 TGAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAC
*
13457857 TGAAGAAGGATA
1 TGAAGAGGGATA
13457869 TATTGAATTC
Statistics
Matches: 340, Mismatches: 104, Indels: 19
0.73 0.22 0.04
Matches are distributed among these distances:
47 5 0.01
48 31 0.09
49 258 0.76
50 46 0.14
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (49 bp):
TGAAGAGGGATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAC
Found at i:13457800 original size:99 final size:98
Alignment explanation
Indices: 13457665--13457859 Score: 255
Period size: 99 Copynumber: 2.0 Consensus size: 98
13457655 AAAACCAAAT
* * * * * *
13457665 AGGGAAAGGTTGAAGCCGCAATGGCGAACCTTACACCTTAAAACTGAAGAGGGATAGGTTAAAGC
1 AGGGAAAGATTGAAGCCGCAACGACGAACCTTACACCTTAAAACAGAAAAGGAATAGGTTAAAGC
13457730 CACAACGGCGGACCTAACACCTTAAAACATGACG
66 CACAACGGCGGACCTAACACCTTAAAA-ATGACG
* * * *
13457764 AGGGAAAGATTGAAGTCGCAACGACGGATCTTACACCTTAAAACAGAAAAGGAATAGGTTGAAGC
1 AGGGAAAGATTGAAGCCGCAACGACGAACCTTACACCTTAAAACAGAAAAGGAATAGGTTAAAGC
** * *
13457829 TGCGACGGCGGACCTAATACCTTAAAAATGA
66 CACAACGGCGGACCTAACACCTTAAAAATGA
13457860 AGAAGGATAT
Statistics
Matches: 82, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
98 4 0.05
99 78 0.95
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.16
Consensus pattern (98 bp):
AGGGAAAGATTGAAGCCGCAACGACGAACCTTACACCTTAAAACAGAAAAGGAATAGGTTAAAGC
CACAACGGCGGACCTAACACCTTAAAAATGACG
Found at i:13457895 original size:148 final size:148
Alignment explanation
Indices: 13457623--13457900 Score: 317
Period size: 148 Copynumber: 1.9 Consensus size: 148
13457613 AAAAGGAATC
* * * *
13457623 GATTGAAGTCGCAACGGCATATCTAACACCCTAAAACCAAATAGGGAAAGGTTGAAGCCGCAATG
1 GATTGAAGTCGCAACGACAGATCTAACACCCTAAAACCAAATAAGGAAAGGTTGAAGCCGCAACG
* * * * *
13457688 GCGAACCTTACACCTTAAAACTGAAGAGGGATAGGTTAAAGCCACAACGGCGGACCTAACACCTT
66 GCGAACCTAACACCTTAAAAATGAAGAAGGATAGATTAAAGCCACAACGGCAGACCTAACACCTT
13457753 AAAACATGACGAGGGAAA
131 AAAACATGACGAGGGAAA
* * * * *
13457771 GATTGAAGTCGCAACGACGGATCTTACACCTTAAAA-CAGAA-AAGGAATAGGTTGAAGCTGCGA
1 GATTGAAGTCGCAACGACAGATCTAACACCCTAAAACCA-AATAAGGAA-AGGTTGAAGCCGCAA
* * * * ** * * *
13457834 CGGCGGACCTAATACCTTAAAAATGAAGAAGGATATATTGAATTCACGACGGTAGATCTAACACC
64 CGGCGAACCTAACACCTTAAAAATGAAGAAGGATAGATTAAAGCCACAACGGCAGACCTAACACC
13457899 TT
129 TT
13457901 GAAATAAAAA
Statistics
Matches: 105, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
147 7 0.07
148 98 0.93
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (148 bp):
GATTGAAGTCGCAACGACAGATCTAACACCCTAAAACCAAATAAGGAAAGGTTGAAGCCGCAACG
GCGAACCTAACACCTTAAAAATGAAGAAGGATAGATTAAAGCCACAACGGCAGACCTAACACCTT
AAAACATGACGAGGGAAA
Found at i:13458506 original size:33 final size:32
Alignment explanation
Indices: 13458464--13458543 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
13458454 AATGTATAGA
13458464 AGGAGGTTTTTTTTATTTTTGAATAAGATTGAG
1 AGGAGG-TTTTTTTATTTTTGAATAAGATTGAG
*
13458497 AGGAGGTTTTTTTCTTTTTGAATAAGATTGAG
1 AGGAGGTTTTTTTATTTTTGAATAAGATTGAG
**
13458529 A-GAAATTTTTTTATT
1 AGGAGGTTTTTTTATT
13458544 CAGAGAAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 11 0.26
32 26 0.60
33 6 0.14
ACGTcount: A:0.28, C:0.01, G:0.21, T:0.50
Consensus pattern (32 bp):
AGGAGGTTTTTTTATTTTTGAATAAGATTGAG
Found at i:13458515 original size:32 final size:33
Alignment explanation
Indices: 13458464--13458530 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
13458454 AATGTATAGA
13458464 AGGAGGTTTTTTTTATTTTTGAATAAGATTGAG
1 AGGAGGTTTTTTTTATTTTTGAATAAGATTGAG
*
13458497 AGGAGG-TTTTTTTCTTTTTGAATAAGATTGAG
1 AGGAGGTTTTTTTTATTTTTGAATAAGATTGAG
13458529 AG
1 AG
13458531 AAATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 27 0.82
33 6 0.18
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.46
Consensus pattern (33 bp):
AGGAGGTTTTTTTTATTTTTGAATAAGATTGAG
Found at i:13458550 original size:18 final size:18
Alignment explanation
Indices: 13458527--13458578 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
13458517 AATAAGATTG
13458527 AGAGAAATTTTTTTATTC
1 AGAGAAATTTTTTTATTC
*
13458545 AGAGAAGGATTTTTTTGTTC
1 AGAGAA--ATTTTTTTATTC
*
13458565 AGAGGGAATTTTTT
1 AGA-GAAATTTTTT
13458579 AATGAGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 14 0.48
21 2 0.07
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (18 bp):
AGAGAAATTTTTTTATTC
Found at i:13460392 original size:13 final size:14
Alignment explanation
Indices: 13460374--13460414 Score: 66
Period size: 13 Copynumber: 2.9 Consensus size: 14
13460364 TTTGTGATCA
13460374 TTTGCATTTTATT-
1 TTTGCATTTTATTC
13460387 TTTGCATTTTATTGC
1 TTTGCATTTTATT-C
13460402 TTTGCATTTTATT
1 TTTGCATTTTATT
13460415 GTATGTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.66
Consensus pattern (14 bp):
TTTGCATTTTATTC
Found at i:13460407 original size:15 final size:14
Alignment explanation
Indices: 13460374--13460416 Score: 70
Period size: 15 Copynumber: 3.1 Consensus size: 14
13460364 TTTGTGATCA
13460374 TTTGCATTTTATT-
1 TTTGCATTTTATTG
13460387 TTTGCATTTTATTG
1 TTTGCATTTTATTG
13460401 CTTTGCATTTTATTG
1 -TTTGCATTTTATTG
13460416 T
1 T
13460417 ATGTATATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.46
14 1 0.04
15 14 0.50
ACGTcount: A:0.14, C:0.09, G:0.12, T:0.65
Consensus pattern (14 bp):
TTTGCATTTTATTG
Found at i:13468281 original size:49 final size:49
Alignment explanation
Indices: 13468209--13468719 Score: 352
Period size: 49 Copynumber: 10.4 Consensus size: 49
13468199 CATAAAGTTT
* * *
13468209 GAAGAAGGATAGGTTGAAGCCGCAACGGCGGACCTAACATCC-TAAAATC
1 GAAGAGGGAAAGGTTGAAGCCGCAACGACGGACCTAACA-CCTTAAAATC
* * * * * *
13468258 GAAGAGGGAAAGGTTGAAGCCGCAATGGCGAACCTTACTCCTTAAAATT
1 GAAGAGGGAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * **
13468307 GAAGAGGGATAGGTTGAAGCTGTAACGACGGACTTAACACCCAAAAATC
1 GAAGAGGGAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * * *
13468356 GAAAAGGGAAAGATTGAAGTCGCAACGACGGATCTTACACCTTAAAATT
1 GAAGAGGGAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* ** * * * *
13468405 GAAGAGGGATAGGTTGAAGTTGCAATGACAGACCTAATACCCTAAAATC
1 GAAGAGGGAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * ** ** * ** * *
13468454 AAATA-AAAATAAATTGAAGCCGTAACGGTGGATCTAACACCTTAAAACC
1 GAAGAGGGAA-AGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * * *
13468503 AAATAGAGAAAGGTTGAAGCCGCAACGACGGACCTTACAGCTTAAAATT
1 GAAGAGGGAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * *
13468552 GAAGAGGGATAGGTTAAAGCCGCAAC-AGCAGACCTAACTCCTTAAAACAC
1 GAAGAGGGAAAGGTTGAAGCCGCAACGA-CGGACCTAACACCTTAAAA-TC
* * * * * * * *
13468602 GATA-AGAGAAAGATTGAAGTCGCAACGACAGATCTTACACCTTGAAATA
1 GA-AGAGGGAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * *
13468651 GAA-AAGGAATAGGTTGAAGCCGCGACGGCGGACCTAACACCTTGAAAAT-
1 GAAGAGGGAA-AGGTTGAAGCCGCAACGACGGACCTAACACCTT-AAAATC
*
13468700 GAAGAGGGATA-GTTGAAGCC
1 GAAGAGGGAAAGGTTGAAGCC
13468720 ACGACGGTAG
Statistics
Matches: 347, Mismatches: 105, Indels: 21
0.73 0.22 0.04
Matches are distributed among these distances:
48 18 0.05
49 282 0.81
50 45 0.13
51 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (49 bp):
GAAGAGGGAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
Found at i:13468598 original size:147 final size:144
Alignment explanation
Indices: 13468213--13468719 Score: 447
Period size: 147 Copynumber: 3.5 Consensus size: 144
13468203 AAGTTTGAAG
* * * *
13468213 AAGGATAGGTTGAAGCCGCAACGGCGGACCTAACATCC-TAAAATCGAAGAGGGAAAGGTTGAAG
1 AAGGAAAGGTTGAAGCCGCAACGACGGACCTAACA-CCTTAAAATTGAAGAGGGATAGGTTGAAG
* * ** * *** * *
13468277 CCGCAATGGC-GAACCTTACTCCTTAAAATTGAAGAGGGATAGGTTGAAGCTGTAACGACGGA-C
65 CCGCAA-AGCAG-ACCTAACTCCTTAAAATCAAATAAAAATAGATTGAAGCCGTAACGACGGATC
**
13468340 TTAACACCCAAAAATCGAA
128 -TAACACCTTAAAA-CGAA
* * * *
13468359 AAGGGAAAGATTGAAGTCGCAACGACGGATCTTACACCTTAAAATTGAAGAGGGATAGGTTGAAG
1 AA-GGAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATTGAAGAGGGATAGGTTGAAG
** * * * **
13468424 TTGCAATGACAGACCTAA-TACCCTAAAATCAAATAAAAATAAATTGAAGCCGTAACGGTGGATC
65 CCGCAAAG-CAGACCTAACT-CCTTAAAATCAAATAAAAATAGATTGAAGCCGTAACGACGGATC
*
13468488 TAACACCTTAAAACCAA
128 TAACACCTTAAAACGAA
* * *
13468505 ATAGAGAAAGGTTGAAGCCGCAACGACGGACCTTACAGCTTAAAATTGAAGAGGGATAGGTTAAA
1 A-AG-GAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATTGAAGAGGGATAGGTTGAA
* * * *
13468570 GCCGCAACAGCAGACCTAACTCCTTAAAA-CACGATAAGAGAA-AGATTGAAGTCGCAACGACAG
64 GCCGCAA-AGCAGACCTAACTCCTTAAAATCA-AATAA-A-AATAGATTGAAGCCGTAACGACGG
*
13468633 ATCTTACACCTTGAAATA-GAA
125 ATCTAACACCTT-AAA-ACGAA
* *
13468654 AAGGAATAGGTTGAAGCCGCGACGGCGGACCTAACACCTTGAAAA-TGAAGAGGGATA-GTTGAA
1 AAGGAA-AGGTTGAAGCCGCAACGACGGACCTAACACCTT-AAAATTGAAGAGGGATAGGTTGAA
13468717 GCC
64 GCC
13468720 ACGACGGTAG
Statistics
Matches: 294, Mismatches: 50, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
146 13 0.04
147 194 0.66
148 74 0.25
149 12 0.04
150 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (144 bp):
AAGGAAAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATTGAAGAGGGATAGGTTGAAGC
CGCAAAGCAGACCTAACTCCTTAAAATCAAATAAAAATAGATTGAAGCCGTAACGACGGATCTAA
CACCTTAAAACGAA
Found at i:13468639 original size:99 final size:100
Alignment explanation
Indices: 13468487--13468698 Score: 252
Period size: 99 Copynumber: 2.1 Consensus size: 100
13468477 AACGGTGGAT
* * * *
13468487 CTAACACCTT-AAAAC-C-AAATAGAGAAAGGTTGAAGCCGCAACGACGGACCTTACAGCTTAAA
1 CTAACACCTTGAAAACACGATA-AGAGAAAGATTGAAGCCGCAACGACAGACCTTACACCTTAAA
* * *
13468549 ATTGAAGAGGGATAGGTTAAAGCCGCAACAGCAGAC
65 ATAGAAAAGGAATAGGTTAAAGCCGCAACAGCAGAC
* * * *
13468585 CTAACTCCTT-AAAACACGATAAGAGAAAGATTGAAGTCGCAACGACAGATCTTACACCTTGAAA
1 CTAACACCTTGAAAACACGATAAGAGAAAGATTGAAGCCGCAACGACAGACCTTACACCTTAAAA
* * * *
13468649 TAGAAAAGGAATAGGTTGAAGCCGCGACGGCGGAC
66 TAGAAAAGGAATAGGTTAAAGCCGCAACAGCAGAC
13468684 CTAACACCTTGAAAA
1 CTAACACCTTGAAAA
13468699 TGAAGAGGGA
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
98 14 0.15
99 75 0.79
100 6 0.06
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.17
Consensus pattern (100 bp):
CTAACACCTTGAAAACACGATAAGAGAAAGATTGAAGCCGCAACGACAGACCTTACACCTTAAAA
TAGAAAAGGAATAGGTTAAAGCCGCAACAGCAGAC
Found at i:13468725 original size:48 final size:50
Alignment explanation
Indices: 13468513--13468745 Score: 145
Period size: 49 Copynumber: 4.7 Consensus size: 50
13468503 AAATAGAGAA
* * * * * * * * *
13468513 AGGTTGAAGCCGCAACGACGGACCTTACAGCTT-AAAATTGAAGAGGGAT
1 AGGTTGAAGCCACGACGGCAGACCTAACACCTTGAAAATAGAAAAGGAAT
* * * * * * *
13468562 AGGTTAAAGCCGCAACAGCAGACCTAACTCCTT-AAAACACGATAAGAGAA-
1 AGGTTGAAGCCACGACGGCAGACCTAACACCTTGAAAATA-GAAAAG-GAAT
* * * * * * *
13468612 AGATTGAAGTCGCAACGACAGATCTTACACCTTG-AAATAGAAAAGGAAT
1 AGGTTGAAGCCACGACGGCAGACCTAACACCTTGAAAATAGAAAAGGAAT
* * * *
13468661 AGGTTGAAGCCGCGACGGCGGACCTAACACCTTGAAAAT-GAAGAGGGAT
1 AGGTTGAAGCCACGACGGCAGACCTAACACCTTGAAAATAGAAAAGGAAT
* *
13468710 A-GTTGAAGCCACGACGGTAGATCTAACACCTTGAAA
1 AGGTTGAAGCCACGACGGCAGACCTAACACCTTGAAA
13468746 TAAAAAAAAA
Statistics
Matches: 144, Mismatches: 35, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
48 34 0.24
49 71 0.49
50 37 0.26
51 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.17
Consensus pattern (50 bp):
AGGTTGAAGCCACGACGGCAGACCTAACACCTTGAAAATAGAAAAGGAAT
Found at i:13469381 original size:33 final size:33
Alignment explanation
Indices: 13469313--13469383 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
13469303 TAGAAGGAGG
**
13469313 TTTTTTTCTTTTTGAATAAGATTGAGAGGGGTT
1 TTTTTTTCTTTTTGAATAAGATTGAGAGAAGTT
13469346 TTTTTTTCTTTTTGAATAAGATTGAGAGAA-TT
1 TTTTTTTCTTTTTGAATAAGATTGAGAGAAGTT
13469378 TTTTTT
1 TTTTTT
13469384 ATTCAGAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.23, C:0.03, G:0.18, T:0.56
Consensus pattern (33 bp):
TTTTTTTCTTTTTGAATAAGATTGAGAGAAGTT
Found at i:13475159 original size:20 final size:21
Alignment explanation
Indices: 13475115--13475159 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
13475105 TAAGCTTTTA
* *
13475115 AAAATACATTTTTAAATATTT
1 AAAATACATTATTAAATAATT
*
13475136 AAAATATATTATTAAA-AATT
1 AAAATACATTATTAAATAATT
13475156 AAAA
1 AAAA
13475160 GTTTTTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATACATTATTAAATAATT
Found at i:13477431 original size:40 final size:40
Alignment explanation
Indices: 13477387--13477495 Score: 164
Period size: 40 Copynumber: 2.7 Consensus size: 40
13477377 GTGTAACTTT
13477387 GCAGTGTTTACAATGTCACTGCCAGTTCAGTTGTAATATC
1 GCAGTGTTTACAATGTCACTGCCAGTTCAGTTGTAATATC
* *
13477427 GCAGTGTTTACAGTGTCACTGTCAGTTCAGTTGTAATATC
1 GCAGTGTTTACAATGTCACTGCCAGTTCAGTTGTAATATC
* * * *
13477467 GTAGTGTTTACATTGTCACTACCATTTCA
1 GCAGTGTTTACAATGTCACTGCCAGTTCA
13477496 TACAGTCCCA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (40 bp):
GCAGTGTTTACAATGTCACTGCCAGTTCAGTTGTAATATC
Found at i:13484704 original size:3 final size:3
Alignment explanation
Indices: 13484696--13484724 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13484686 CACTTCAAAT
13484696 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13484725 TTCTTGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13485377 original size:18 final size:21
Alignment explanation
Indices: 13485334--13485379 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
13485324 ACAATTTCAC
13485334 TATTTTCATTATTAAAAAATA
1 TATTTTCATTATTAAAAAATA
*
13485355 TATTTTCA-T-TTAATAAA-A
1 TATTTTCATTATTAAAAAATA
13485373 TATTTTC
1 TATTTTC
13485380 CAAATTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 7 0.29
20 1 0.04
21 8 0.33
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTCATTATTAAAAAATA
Found at i:13486199 original size:21 final size:23
Alignment explanation
Indices: 13486166--13486213 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
13486156 TGTTTATTTT
13486166 TTATATTTAAAAT-T-TCAAAAA
1 TTATATTTAAAATCTATCAAAAA
*
13486187 TTATAATTT-AAATCTATCAAATA
1 TTAT-ATTTAAAATCTATCAAAAA
13486210 TTAT
1 TTAT
13486214 GTTTGTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 8 0.35
22 5 0.22
23 10 0.43
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATATTTAAAATCTATCAAAAA
Found at i:13497161 original size:22 final size:22
Alignment explanation
Indices: 13497129--13497172 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13497119 CAAGACAACC
13497129 ATTTGGCGGATTTCTAAAAACT
1 ATTTGGCGGATTTCTAAAAACT
*
13497151 ATTTGGTGGATTTCTAAAAACT
1 ATTTGGCGGATTTCTAAAAACT
13497173 GTCTCTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
ATTTGGCGGATTTCTAAAAACT
Found at i:13499231 original size:3 final size:3
Alignment explanation
Indices: 13499223--13499250 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13499213 GTAAAAGGTG
13499223 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
13499251 CTAATCTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13504335 original size:129 final size:130
Alignment explanation
Indices: 13504100--13504338 Score: 297
Period size: 129 Copynumber: 1.8 Consensus size: 130
13504090 TTTAGTATCT
* * * * *
13504100 TTTATGTAACAGTAATAATATTGATTGTCAAATATTATTTTGTAATAATATTTTAATTGGTTGTG
1 TTTATGTAACAATAATAATATTGATTGTCAAATATTATCTTGCAACAATATTTCAATTGGTTGTG
* * * *
13504165 TGTTACATTGTACATCGATGATATGCTATTGTCAAAAATTTATTTTAAATGTGATTATCAAATCA
66 TATAACATTGCACAACGATGATATGCTATTGTCAAAAATTTATTTTAAATGTGATTATCAAATCA
* *
13504230 TTTATGTAACAATAAT-ATCATTGGTTG-CAAATATTATCTTGCAACGATATTTCAATCT-GTTG
1 TTTATGTAACAATAATAAT-ATTGATTGTCAAATATTATCTTGCAACAATATTTCAAT-TGGTTG
* * *
13504292 TGTATAACATTGCGCAACGATTATATG-TCATTGTCAAATATTTATTT
64 TGTATAACATTGCACAACGATGATATGCT-ATTGTCAAAAATTTATTT
13504339 AACAATCATA
Statistics
Matches: 92, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
128 1 0.01
129 68 0.74
130 23 0.25
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (130 bp):
TTTATGTAACAATAATAATATTGATTGTCAAATATTATCTTGCAACAATATTTCAATTGGTTGTG
TATAACATTGCACAACGATGATATGCTATTGTCAAAAATTTATTTTAAATGTGATTATCAAATCA
Found at i:13509280 original size:24 final size:24
Alignment explanation
Indices: 13509253--13509335 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
13509243 ATCAAATATG
13509253 CGAGCATAAACGTATAGTGGCTGA
1 CGAGCATAAACGTATAGTGGCTGA
* **
13509277 CGAGTATAAATTTATAGTGGCTGA
1 CGAGCATAAACGTATAGTGGCTGA
* * *
13509301 CGAGCATAAACGTATAGCGACTAA
1 CGAGCATAAACGTATAGTGGCTGA
*
13509325 CGAACATAAAC
1 CGAGCATAAAC
13509336 ATACGTTCTC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.22
Consensus pattern (24 bp):
CGAGCATAAACGTATAGTGGCTGA
Found at i:13510537 original size:3 final size:3
Alignment explanation
Indices: 13510526--13510585 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
13510516 GACGACGACG
* * * *
13510526 ACA AAA ACA ACA ACA ACA ATA GA-A GCA ACA ACA ACA ATA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA -ACA ACA ACA ACA ACA ACA ACA ACA
*
13510571 ACA ACA ACA ATA ACA
1 ACA ACA ACA ACA ACA
13510586 TGGAATAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
3 45 0.98
4 1 0.02
ACGTcount: A:0.67, C:0.25, G:0.03, T:0.05
Consensus pattern (3 bp):
ACA
Found at i:13510556 original size:18 final size:18
Alignment explanation
Indices: 13510531--13510585 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
13510521 CGACGACAAA
13510531 AACAACAACAACAATAGA-
1 AACAACAACAACAATA-AC
*
13510549 AGCAACAACAACAATAAC
1 AACAACAACAACAATAAC
13510567 AACAACAACAACAATAAC
1 AACAACAACAACAATAAC
13510585 A
1 A
13510586 TGGAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.65, C:0.25, G:0.04, T:0.05
Consensus pattern (18 bp):
AACAACAACAACAATAAC
Found at i:13510853 original size:7 final size:7
Alignment explanation
Indices: 13510835--13510910 Score: 50
Period size: 7 Copynumber: 10.6 Consensus size: 7
13510825 ACCAAACCTC
13510835 AAACTCT
1 AAACTCT
13510842 AAAACTCT
1 -AAACTCT
*
13510850 AAACTCA
1 AAACTCT
13510857 AAAC-CT
1 AAACTCT
13510863 AGAAC-CT
1 A-AACTCT
*
13510870 CAAACCCT
1 -AAACTCT
13510878 AAACTC-
1 AAACTCT
*
13510884 ACAACCCT
1 A-AACTCT
*
13510892 AAACCTTT
1 AAA-CTCT
13510900 AAACTCT
1 AAACTCT
13510907 AAAC
1 AAAC
13510911 CTTAATTCCA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
6 3 0.05
7 36 0.65
8 16 0.29
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (7 bp):
AAACTCT
Found at i:13510853 original size:15 final size:15
Alignment explanation
Indices: 13510835--13510895 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 15
13510825 ACCAAACCTC
*
13510835 AAACTCTAAAACTCT
1 AAACTCTAAAACCCT
13510850 AAACTC-AAAA-CCT
1 AAACTCTAAAACCCT
*
13510863 AGAAC-CTCAAACCCT
1 A-AACTCTAAAACCCT
*
13510878 AAACTC-ACAACCCT
1 AAACTCTAAAACCCT
13510892 AAAC
1 AAAC
13510896 CTTTAAACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
13 4 0.11
14 23 0.61
15 11 0.29
ACGTcount: A:0.48, C:0.34, G:0.02, T:0.16
Consensus pattern (15 bp):
AAACTCTAAAACCCT
Found at i:13510889 original size:14 final size:13
Alignment explanation
Indices: 13510843--13510895 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
13510833 TCAAACTCTA
*
13510843 AAACTCTAAACTC
1 AAACCCTAAACTC
*
13510856 AAAACCTAGAACCTC
1 AAACCCTA-AA-CTC
13510871 AAACCCTAAACTC
1 AAACCCTAAACTC
13510884 ACAACCCTAAAC
1 A-AACCCTAAAC
13510896 CTTTAAACTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 10 0.29
14 14 0.41
15 10 0.29
ACGTcount: A:0.47, C:0.36, G:0.02, T:0.15
Consensus pattern (13 bp):
AAACCCTAAACTC
Done.