Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 51 of 318
Found at i:18833828 original size:52 final size:51
Alignment explanation
Indices: 18833757--18834161 Score: 516
Period size: 52 Copynumber: 8.1 Consensus size: 51
18833747 ATCAAGTGAT
* **
18833757 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
18833809 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTG---A-T-
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
18833855 AAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
**
18833901 AAAGTGATAAGTGATAGCTTCACCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
18833953 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
18834005 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
18834056 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
** * *
18834103 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTG
18834155 ATAAGTG
1 A-AAGTG
18834162 GCTACACTTA
Statistics
Matches: 319, Mismatches: 18, Indels: 31
0.87 0.05 0.08
Matches are distributed among these distances:
46 127 0.40
48 1 0.00
49 1 0.00
51 1 0.00
52 184 0.58
53 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:18833957 original size:98 final size:98
Alignment explanation
Indices: 18833757--18834161 Score: 500
Period size: 98 Copynumber: 4.1 Consensus size: 98
18833747 ATCAAGTGAT
* ** *
18833757 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-----GAAAGTGATAAGTG
* *
18833822 ATAGCTTCGGCTATACTTATCTGATCAAGTG---A-T-
61 ATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
18833855 AAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGATCAAGTGAC-AAAGTGATAAGTGATAGC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACGAAAGTGATAAGTGATAGC
*
18833919 TTCACCTACACTTATCTGATCAAGTGACAAGTGG
66 TTCAGCTACACTTATCTGATCAAGTGACAAGT-G
18833953 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-----GAAAGTGATAAGTG
*
18834018 ATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
61 ATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
18834056 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-AAAGTGATAAGTGATAG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACGAAAGTGATAAGTGATAG
* * *
18834120 CTTTAGCTACACTTATCTAATCAAGAGACAAAGTG
65 CTTCAGCTACACTTATCTGATCAAGTGAC-AAGTG
18834155 ATAAGTG
1 A-AAGTG
18834162 GCTACACTTA
Statistics
Matches: 273, Mismatches: 19, Indels: 29
0.85 0.06 0.09
Matches are distributed among these distances:
92 40 0.15
95 1 0.00
96 1 0.00
98 128 0.47
99 10 0.04
103 1 0.00
104 92 0.34
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (98 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACGAAAGTGATAAGTGATAGC
TTCAGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:18834151 original size:46 final size:46
Alignment explanation
Indices: 18834057--18834161 Score: 174
Period size: 46 Copynumber: 2.3 Consensus size: 46
18834047 TGACAAGTGA
* * *
18834057 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTAATCAAGAGAC
*
18834103 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTAATCAAGAGAC
18834149 AAAGTGATAAGTG
1 AAAGTGATAAGTG
18834162 GCTACACTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTAATCAAGAGAC
Found at i:18834169 original size:37 final size:37
Alignment explanation
Indices: 18834125--18834234 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
18834115 GATAGCTTTA
*
18834125 GCTACACTTATCTAATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
18834162 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
18834199 GCTACACTTATCTGATCAAGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
18834235 ATCATACGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
36 12 0.17
37 57 0.83
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:18843894 original size:8 final size:8
Alignment explanation
Indices: 18843881--18843910 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
18843871 AAAATAGGCT
18843881 TAAAATGA
1 TAAAATGA
18843889 TAAAATGA
1 TAAAATGA
18843897 TAAAATGA
1 TAAAATGA
18843905 TAAAAT
1 TAAAAT
18843911 TCGGTCCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (8 bp):
TAAAATGA
Found at i:18855687 original size:42 final size:45
Alignment explanation
Indices: 18855635--18855721 Score: 108
Period size: 47 Copynumber: 1.9 Consensus size: 45
18855625 AAATATTTTT
* *
18855635 TTAAAGAATTATATT-T-AAATATATATTTAATTTT-AACAAAGA
1 TTAAAAAATTAAATTGTGAAATATATATTTAATTTTGAACAAAGA
18855677 TTAAAAAATTAAATTGGAGTGAAATATATATTTAATTTTGAACAA
1 TTAAAAAATTAAATT---GTGAAATATATATTTAATTTTGAACAA
18855722 TTATATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
42 13 0.35
46 1 0.03
47 18 0.49
48 5 0.14
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.40
Consensus pattern (45 bp):
TTAAAAAATTAAATTGTGAAATATATATTTAATTTTGAACAAAGA
Found at i:18862189 original size:6 final size:6
Alignment explanation
Indices: 18862178--18862204 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18862168 AAAAATCCAT
18862178 TCTCCC TCTCCC TCTCCC TCTCCC TCT
1 TCTCCC TCTCCC TCTCCC TCTCCC TCT
18862205 TGTATTATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
TCTCCC
Found at i:18865585 original size:13 final size:13
Alignment explanation
Indices: 18865567--18865592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18865557 TCCGTACAGT
18865567 CCACAGCTTCAGA
1 CCACAGCTTCAGA
18865580 CCACAGCTTCAGA
1 CCACAGCTTCAGA
18865593 TGTTTTACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.15, T:0.15
Consensus pattern (13 bp):
CCACAGCTTCAGA
Found at i:18867218 original size:22 final size:23
Alignment explanation
Indices: 18867185--18867232 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
18867175 AGGTGTAACT
18867185 TAATAAACAAATGT-AT-ATAAAA
1 TAATAAACAAAT-TAATAATAAAA
18867207 TAAT-AACAAAATTAATAATAAAA
1 TAATAAAC-AAATTAATAATAAAA
18867230 TAA
1 TAA
18867233 GAGTTATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 10 0.43
23 9 0.39
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
TAATAAACAAATTAATAATAAAA
Found at i:18867531 original size:28 final size:26
Alignment explanation
Indices: 18867492--18867549 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
18867482 TTAAATTAAT
* *
18867492 AAAAATAAATTTTATTTTAATCTTTCTA
1 AAAAACAAATTTTAATTTAAT-TTT-TA
18867520 AAAAACAAATTTTAATTTAATTTTTA
1 AAAAACAAATTTTAATTTAATTTTTA
18867546 AAAA
1 AAAA
18867550 TTATAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 6 0.21
27 3 0.11
28 19 0.68
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (26 bp):
AAAAACAAATTTTAATTTAATTTTTA
Found at i:18875919 original size:12 final size:12
Alignment explanation
Indices: 18875879--18875913 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
18875869 CTTTCCGGCT
18875879 ATCCTTCTTCTC
1 ATCCTTCTTCTC
*
18875891 ATCCTTATTCTC
1 ATCCTTCTTCTC
18875903 ATCCTTCTTCT
1 ATCCTTCTTCT
18875914 TCTCCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.11, C:0.37, G:0.00, T:0.51
Consensus pattern (12 bp):
ATCCTTCTTCTC
Found at i:18881907 original size:22 final size:21
Alignment explanation
Indices: 18881882--18881931 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 21
18881872 AAATATTTCA
18881882 TTTTATATTGCAATTTT-AATTT
1 TTTTATATT-C-ATTTTAAATTT
18881904 TTTTAATATTCATTTTAAATTT
1 TTTT-ATATTCATTTTAAATTT
18881926 TCTTTA
1 T-TTTA
18881932 ATTATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 5 0.20
22 12 0.48
23 8 0.32
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATATTCATTTTAAATTT
Found at i:18884664 original size:21 final size:21
Alignment explanation
Indices: 18884640--18884691 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
18884630 CATTGTTTCG
* * *
18884640 AATCTCACTGCTACAGTATCT
1 AATCTCACCGCTACAATAACT
*
18884661 AATCTTACCGCTACAATAACT
1 AATCTCACCGCTACAATAACT
18884682 AATCTCACCG
1 AATCTCACCG
18884692 TCACCGCTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.29
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACT
Found at i:18889708 original size:43 final size:41
Alignment explanation
Indices: 18889614--18889780 Score: 169
Period size: 43 Copynumber: 4.0 Consensus size: 41
18889604 ATTGAGATAT
* *
18889614 GATTACATGTAAGACCATGTCT-GGACATTGGCATTGTATT
1 GATTTCATGTAAGACCATGTCTGGGACATTGGCATTGTATC
18889654 GATATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTAATC
1 GAT-TT-CATGTAAGACCATGTCTGGGACATTGGCATTG-T-ATC
* *
18889699 GATTTCATGTAAGACCCTGTCTGGGACAGTGGCATCGATGTAT-
1 GATTTCATGTAAGACCATGTCTGGGACATTGGCAT---TGTATC
** * * *
18889742 GATAACATGTAAGACCATATCTAGGATA-TGGCATTGTAT
1 GATTTCATGTAAGACCATGTCTGGGACATTGGCATTGTAT
18889781 AAGCTTATGT
Statistics
Matches: 109, Mismatches: 10, Indels: 17
0.80 0.07 0.12
Matches are distributed among these distances:
39 5 0.05
40 3 0.03
41 1 0.01
42 23 0.21
43 64 0.59
44 5 0.05
45 6 0.06
46 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (41 bp):
GATTTCATGTAAGACCATGTCTGGGACATTGGCATTGTATC
Found at i:18889776 original size:85 final size:84
Alignment explanation
Indices: 18889614--18889778 Score: 210
Period size: 86 Copynumber: 1.9 Consensus size: 84
18889604 ATTGAGATAT
* * *
18889614 GATTACATGTAAGACCATGTCTGGACATTGGCATTGTATTGATATTACATGTAAGACCATGTCTG
1 GATTACATGTAAGACCATGTCTGGACAGTGGCATTGTATTGATA-TACATGTAAGACCATATCTA
18889679 GGACATTGGCATTGTTAATC
65 GGACATTGGCATTGTTAATC
* *
18889699 GATTTCATGTAAGACCCTGTCTGGGACAGTGGCATCGATGTA-TGATA-ACATGTAAGACCATAT
1 GATTACATGTAAGACCATGTCT-GGACAGTGGCAT---TGTATTGATATACATGTAAGACCATAT
*
18889762 CTAGGATA-TGGCATTGT
62 CTAGGACATTGGCATTGT
18889779 ATAAGCTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
85 29 0.41
86 32 0.46
88 5 0.07
89 4 0.06
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (84 bp):
GATTACATGTAAGACCATGTCTGGACAGTGGCATTGTATTGATATACATGTAAGACCATATCTAG
GACATTGGCATTGTTAATC
Found at i:18892422 original size:46 final size:46
Alignment explanation
Indices: 18892353--18892478 Score: 166
Period size: 46 Copynumber: 2.7 Consensus size: 46
18892343 ATAATCTCAC
*
18892353 CCATAATGAACTCGGAACGCAACTCAACGAGCTTGAG-TG-TTCACAT
1 CCATAATGAACTCGGAACGCAACTCAACGAG-TTCAGATGCTT-ACAT
* *
18892399 CCATAATGAACTCGGAACACAACTCAACGAGTTCAGATGCTTGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGCTTACAT
* *
18892445 CCATAGGTGAACTCGAAACGCAACTCAACGAGTT
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTT
18892479 TGGATTCCTC
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
45 4 0.06
46 40 0.56
47 27 0.38
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGCTTACAT
Found at i:18893148 original size:20 final size:21
Alignment explanation
Indices: 18893114--18893167 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
18893104 TGATGATATC
*
18893114 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
18893135 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
18893155 TTTTATTATTTTA
1 TTATATTATTTTA
18893168 TTATTATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:18893171 original size:3 final size:3
Alignment explanation
Indices: 18893153--18893201 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
18893143 TTTAATGAGA
*
18893153 TAT T-T TAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
18893198 TAT T
1 TAT T
18893202 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:18893173 original size:11 final size:11
Alignment explanation
Indices: 18893157--18893195 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
18893147 ATGAGATATT
18893157 TTATTATTTTA
1 TTATTATTTTA
*
18893168 TTATTATTTCA
1 TTATTATTTTA
18893179 TTATTATTTTA
1 TTATTATTTTA
18893190 TTATTA
1 TTATTA
18893196 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:18893181 original size:19 final size:19
Alignment explanation
Indices: 18893153--18893194 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
18893143 TTTAATGAGA
*
18893153 TATTTTATTATT-TTATTAT
1 TATTTCATTATTATT-TTAT
18893172 TATTTCATTATTATTTTAT
1 TATTTCATTATTATTTTAT
18893191 TATT
1 TATT
18893195 AATTATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTCATTATTATTTTAT
Found at i:18895427 original size:46 final size:46
Alignment explanation
Indices: 18895305--18895616 Score: 493
Period size: 46 Copynumber: 6.8 Consensus size: 46
18895295 GCTCTCTGAA
* * *
18895305 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** *
18895351 ATGAAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
18895396 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
18895442 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** *
18895488 ATGAAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
18895533 ATGAAATGTGCAAGACCATGGTTGAAAGATACCATGGAAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
18895579 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
18895617 TGTAATGACC
Statistics
Matches: 246, Mismatches: 18, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
45 82 0.33
46 164 0.67
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:18895501 original size:91 final size:92
Alignment explanation
Indices: 18895305--18895616 Score: 493
Period size: 91 Copynumber: 3.4 Consensus size: 92
18895295 GCTCTCTGAA
* * * **
18895305 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACGTGACATGAAA-GAATAAGACCAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCAT
*
18895369 GGTTGAAAGATACCATGGCAACGTGAT
66 GGTTGAAAGATACCATGGCAACATGAT
18895396 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCAT
*
18895461 GGTTGAAAGATACCATGGCAACATGAC
66 GGTTGAAAGATACCATGGCAACATGAT
** * *
18895488 ATGAAA-GAATAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGCAAGACCAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCAT
* *
18895552 GGTTGAAAGATACCATGGAAACCTGAT
66 GGTTGAAAGATACCATGGCAACATGAT
18895579 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
18895617 TGTAATGACC
Statistics
Matches: 203, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
91 133 0.66
92 70 0.34
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (92 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCAT
GGTTGAAAGATACCATGGCAACATGAT
Found at i:18895551 original size:137 final size:137
Alignment explanation
Indices: 18895305--18895616 Score: 570
Period size: 137 Copynumber: 2.3 Consensus size: 137
18895295 GCTCTCTGAA
* *
18895305 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACGTGACATGAAAGAATAAGACCATG
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAGAATAAGACCATG
* * *
18895370 GTTGAAAGATACCATGGCAACGTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
66 GTTGAAAGATACCATGGCAACCTGATATGAAATGTGCAAGACCATGGTTGAAAGATACCATGGAA
18895435 ACATGAT
131 ACATGAT
18895442 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAGAATAAGACCATG
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAGAATAAGACCATG
18895507 GTTGAAAGATACCATGGCAACCTGATATGAAATGTGCAAGACCATGGTTGAAAGATACCATGGAA
66 GTTGAAAGATACCATGGCAACCTGATATGAAATGTGCAAGACCATGGTTGAAAGATACCATGGAA
*
18895572 ACCTGAT
131 ACATGAT
18895579 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
18895617 TGTAATGACC
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 169 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (137 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAGAATAAGACCATG
GTTGAAAGATACCATGGCAACCTGATATGAAATGTGCAAGACCATGGTTGAAAGATACCATGGAA
ACATGAT
Found at i:18896120 original size:20 final size:20
Alignment explanation
Indices: 18896095--18896134 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18896085 ATTTAAGTAT
18896095 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
18896115 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
18896135 AATAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TAAAAGATATTTATTAATTA
Found at i:18898573 original size:25 final size:25
Alignment explanation
Indices: 18898545--18898678 Score: 159
Period size: 25 Copynumber: 5.5 Consensus size: 25
18898535 TAGCACATTT
18898545 GTGCTCTCTGATATTTAGCACGCCA
1 GTGCTCTCTGATATTTAGCACGCCA
* ****
18898570 GTGCTCACTG--A-TTAGCACATTT
1 GTGCTCTCTGATATTTAGCACGCCA
18898592 GTGCTCTCTGATATTTAGCACGCCA
1 GTGCTCTCTGATATTTAGCACGCCA
* *
18898617 GTGCTCTCTGAT-TACTAGCACGCTA
1 GTGCTCTCTGATAT-TTAGCACGCCA
*
18898642 GTGCTCTCTGATATTTAGCACGTCA
1 GTGCTCTCTGATATTTAGCACGCCA
18898667 GTGCTCTCTGAT
1 GTGCTCTCTGAT
18898679 TAGCACATTT
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
22 16 0.18
23 1 0.01
24 2 0.02
25 69 0.78
26 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.34
Consensus pattern (25 bp):
GTGCTCTCTGATATTTAGCACGCCA
Found at i:18898593 original size:47 final size:47
Alignment explanation
Indices: 18898524--18898720 Score: 283
Period size: 47 Copynumber: 4.2 Consensus size: 47
18898514 GACTTCAGCA
18898524 TGCTCTCTGATTAGCACATTTGTGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTGATTAGCACATTTGTGCTCTCTGATATTTAGCACGCCAG
*
18898571 TGCTCACTGATTAGCACATTTGTGCTCTCTGATATTTAGCACGCCAG
1 TGCTCTCTGATTAGCACATTTGTGCTCTCTGATATTTAGCACGCCAG
** * *
18898618 TGCTCTCTGATTACTAGCACGCTAGTGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTGA-T--TAGCACATTTGTGCTCTCTGATATTTAGCACGCCAG
**
18898668 TGCTCTCTGATTAGCACATTTGTGCTCTCTG-TA--TAGCACTTCAG
1 TGCTCTCTGATTAGCACATTTGTGCTCTCTGATATTTAGCACGCCAG
18898712 TGCTCTCTG
1 TGCTCTCTG
18898721 TTCATTAGTG
Statistics
Matches: 137, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
44 19 0.14
46 2 0.01
47 72 0.53
48 1 0.01
49 1 0.01
50 42 0.31
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (47 bp):
TGCTCTCTGATTAGCACATTTGTGCTCTCTGATATTTAGCACGCCAG
Found at i:18898653 original size:97 final size:94
Alignment explanation
Indices: 18898545--18898720 Score: 289
Period size: 97 Copynumber: 1.8 Consensus size: 94
18898535 TAGCACATTT
18898545 GTGCTCTCTGATATTTAGCACGCCAGTGCTCACTGATTAGCACATTTGTGCTCTCTGATATTTAG
1 GTGCTCTCTGATATTTAGCACGCCAGTGCTCACTGATTAGCACATTTGTGCTCTCTG-TA--TAG
18898610 CACGCCAGTGCTCTCTGATTACTAGCACGCTA
63 CACGCCAGTGCTCTCTGATTACTAGCACGCTA
* *
18898642 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTGTGCTCTCTGTATAGCAC
1 GTGCTCTCTGATATTTAGCACGCCAGTGCTCACTGATTAGCACATTTGTGCTCTCTGTATAGCAC
**
18898707 TTCAGTGCTCTCTG
66 GCCAGTGCTCTCTG
18898721 TTCATTAGTG
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
94 18 0.24
96 2 0.03
97 55 0.73
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (94 bp):
GTGCTCTCTGATATTTAGCACGCCAGTGCTCACTGATTAGCACATTTGTGCTCTCTGTATAGCAC
GCCAGTGCTCTCTGATTACTAGCACGCTA
Found at i:18901330 original size:53 final size:53
Alignment explanation
Indices: 18901174--18901339 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
18901164 TGATAAAAAT
* **
18901174 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
18901226 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
18901279 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
18901333 TATGTGA
1 -ATGTGA
18901340 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:18904868 original size:237 final size:237
Alignment explanation
Indices: 18904453--18904926 Score: 939
Period size: 237 Copynumber: 2.0 Consensus size: 237
18904443 GTACTTTGAA
18904453 ATTGTATATAAATGTTTATATCAGATACAGATACCTTTAGAACTGTTACAACTAGAAAGGATTTC
1 ATTGTATATAAATGTTTATATCAGATACAGATACCTTTAGAACTGTTACAACTAGAAAGGATTTC
18904518 AGAATGGAAATGGGATATAATTTCTATGGGTTTGAATTGGAATTATCTCGATCTTCGAAAAAGAA
66 AGAATGGAAATGGGATATAATTTCTATGGGTTTGAATTGGAATTATCTCGATCTTCGAAAAAGAA
18904583 AGACGGTATTTAAATAATCGTCGAAAGTATGGTAAAGTCTGCATATTCTATTCAGGTATGACTAC
131 AGACGGTATTTAAATAATCGTCGAAAGTATGGTAAAGTCTGCATATTCTATTCAGGTATGACTAC
18904648 ATTTCTTACTTAATAATTGTCTAAAATATGGGTTTCTGAGGT
196 ATTTCTTACTTAATAATTGTCTAAAATATGGGTTTCTGAGGT
18904690 ATTGTATATAAATGTTTATATCAGATACAGATACCTTTAGAACTGTTACAACTAGAAAGGATTTC
1 ATTGTATATAAATGTTTATATCAGATACAGATACCTTTAGAACTGTTACAACTAGAAAGGATTTC
*
18904755 AGAATGGAAATGGGATATAATTTCTATGGGTTTGAATTGGAATTATCTTGATCTTCGAAAAAGAA
66 AGAATGGAAATGGGATATAATTTCTATGGGTTTGAATTGGAATTATCTCGATCTTCGAAAAAGAA
18904820 AGACGGTATTTAAATAATCGTCGAAAGTATGGTAAAGTCTGCATATTCTATTCAGGTATGACTAC
131 AGACGGTATTTAAATAATCGTCGAAAGTATGGTAAAGTCTGCATATTCTATTCAGGTATGACTAC
18904885 ATTTCTTACTTAATAATTGTCTAAAATATGGGTTTCTGAGGT
196 ATTTCTTACTTAATAATTGTCTAAAATATGGGTTTCTGAGGT
18904927 TGTTAGATCA
Statistics
Matches: 236, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
237 236 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (237 bp):
ATTGTATATAAATGTTTATATCAGATACAGATACCTTTAGAACTGTTACAACTAGAAAGGATTTC
AGAATGGAAATGGGATATAATTTCTATGGGTTTGAATTGGAATTATCTCGATCTTCGAAAAAGAA
AGACGGTATTTAAATAATCGTCGAAAGTATGGTAAAGTCTGCATATTCTATTCAGGTATGACTAC
ATTTCTTACTTAATAATTGTCTAAAATATGGGTTTCTGAGGT
Found at i:18905765 original size:35 final size:35
Alignment explanation
Indices: 18905714--18905873 Score: 227
Period size: 35 Copynumber: 4.7 Consensus size: 35
18905704 TAAATATTTA
*
18905714 AGGAAAGATTCCCTGCAACAAAATAATGTGTGAAC
1 AGGAAAGATTCCCTGCAACAAAATAATGCGTGAAC
*
18905749 AGGAGAGATTCCCTGCAACAAAATAATGCGTGAAC
1 AGGAAAGATTCCCTGCAACAAAATAATGCGTGAAC
* * *
18905784 AGGAGAGATTCCCTGCAA-GAAATGAT--GTGAAC
1 AGGAAAGATTCCCTGCAACAAAATAATGCGTGAAC
*
18905816 AGGAAAGATTCCCTGCAACAGAATAATGCGTGAAC
1 AGGAAAGATTCCCTGCAACAAAATAATGCGTGAAC
* *
18905851 AGGAAATATTCCCTGCAAGAAAA
1 AGGAAAGATTCCCTGCAACAAAA
18905874 GACAAGTGAA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
32 23 0.21
33 5 0.05
34 6 0.05
35 77 0.69
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (35 bp):
AGGAAAGATTCCCTGCAACAAAATAATGCGTGAAC
Found at i:18905825 original size:67 final size:68
Alignment explanation
Indices: 18905714--18905872 Score: 239
Period size: 67 Copynumber: 2.3 Consensus size: 68
18905704 TAAATATTTA
* *
18905714 AGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 AGGAAAGATTCCCTGCAA-GAAATAA-GTGTGAACAGGAAAGATTCCCTGCAACAAAATAATGCG
18905779 TGAAC
64 TGAAC
* * *
18905784 AGGAGAGATTCCCTGCAAGAAATGA-TGTGAACAGGAAAGATTCCCTGCAACAGAATAATGCGTG
1 AGGAAAGATTCCCTGCAAGAAATAAGTGTGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTG
18905848 AAC
66 AAC
*
18905851 AGGAAATATTCCCTGCAAGAAA
1 AGGAAAGATTCCCTGCAAGAAA
18905873 AGACAAGTGA
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
67 60 0.73
69 5 0.06
70 17 0.21
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (68 bp):
AGGAAAGATTCCCTGCAAGAAATAAGTGTGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTG
AAC
Found at i:18907900 original size:21 final size:22
Alignment explanation
Indices: 18907876--18907920 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
18907866 AGAAAAAGAG
18907876 AAATACAAAAAAG-AATAG-ATC
1 AAATA-AAAAAAGAAATAGAATC
*
18907897 AAATAAAAAAGGAAATAGAATC
1 AAATAAAAAAAGAAATAGAATC
18907919 AA
1 AA
18907921 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATAAAAAAAGAAATAGAATC
Found at i:18908757 original size:20 final size:20
Alignment explanation
Indices: 18908732--18908771 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18908722 ATTTAAGTAT
18908732 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
18908752 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
18908772 AATAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TAAAAGATATTTATTAATTA
Found at i:18908788 original size:15 final size:16
Alignment explanation
Indices: 18908770--18908810 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
18908760 ATTTATTAAT
*
18908770 TAAATA-ATTATATTA
1 TAAATATATTATATGA
*
18908785 TAAA-ATTTTATATGA
1 TAAATATATTATATGA
18908800 TAAATATATTA
1 TAAATATATTA
18908811 GATAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 15 0.71
16 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TAAATATATTATATGA
Found at i:18909015 original size:19 final size:19
Alignment explanation
Indices: 18908985--18909025 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
18908975 GAAAAGAAAG
18908985 AAAGAAAGGAAGAAAGGAGA
1 AAAGAAAGGAAGAAAGG-GA
18909005 AAAGAAA-GAAGAAAGGGA
1 AAAGAAAGGAAGAAAGGGA
18909023 AAA
1 AAA
18909026 TTGAAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 9 0.43
20 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AAAGAAAGGAAGAAAGGGA
Found at i:18910637 original size:46 final size:46
Alignment explanation
Indices: 18910563--18910711 Score: 192
Period size: 46 Copynumber: 3.2 Consensus size: 46
18910553 GGGTATTACA
* *
18910563 ATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
1 ATGGCAACATGATATGAAATGAGTAAGACCATGGTTGAAAGATACC
* **
18910609 ATGGCAACGTGATATGAAATGAACAAGACCATGGTTGAAAGATACC
1 ATGGCAACATGATATGAAATGAGTAAGACCATGGTTGAAAGATACC
* * * *
18910655 ATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACT
1 ATGGCAACATGATATG-AAATGAGTAAGACCATGGTTGAAAGATACC
*
18910701 ATGGCATCATG
1 ATGGCAACATG
18910712 CAAAGATAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
45 1 0.01
46 89 0.99
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGGCAACATGATATGAAATGAGTAAGACCATGGTTGAAAGATACC
Found at i:18914888 original size:44 final size:42
Alignment explanation
Indices: 18914834--18914994 Score: 125
Period size: 44 Copynumber: 3.8 Consensus size: 42
18914824 CTGATATGCG
* *
18914834 ATTTCATGTAAGATCACGTCTGGGACATTGGCATCGATTTGA
1 ATTTAATGTAAGATCATGTCTGGGACATTGGCATCGATTTGA
* * * *
18914876 GATTTAAGTGTAAGACCATGTCTAGGACATTAGCATCTTATTTGA
1 -ATTTAA-TGTAAGATCATGTCTGGGACATTGGCATC-GATTTGA
* * * *
18914921 TTTTAA-GTAGGATCATGTCTGGGATAGTGGCATCGATATTTG-
1 ATTTAATGTAAGATCATGTCTGGGACATTGGCATCG--ATTTGA
* *
18914963 A-TTACATGTAAGA-C-TGTCTAGGACGTTGGCAT
1 ATTTA-ATGTAAGATCATGTCTGGGACATTGGCAT
18914995 TGTACGAGCT
Statistics
Matches: 92, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
41 17 0.18
42 24 0.26
43 15 0.16
44 30 0.33
45 6 0.07
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (42 bp):
ATTTAATGTAAGATCATGTCTGGGACATTGGCATCGATTTGA
Found at i:18916640 original size:15 final size:15
Alignment explanation
Indices: 18916620--18916648 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18916610 TAGGAATAGT
18916620 TAGGACATTGGCATC
1 TAGGACATTGGCATC
18916635 TAGGACATTGGCAT
1 TAGGACATTGGCAT
18916649 TGACTTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (15 bp):
TAGGACATTGGCATC
Found at i:18916765 original size:43 final size:42
Alignment explanation
Indices: 18916682--18916777 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 42
18916672 CCATGTTTGA
* * * *
18916682 GACATTGGCATCGTATTTGATTTCGTTTAAAACCCTGTCTGG
1 GACAGTGGCATCGTATTTGATTACATGTAAAACCCTGTCTGG
*
18916724 GACAGTGGCATCGATATTTGATTACATGTAATACCAC-GTCTGG
1 GACAGTGGCATCG-TATTTGATTACATGTAAAACC-CTGTCTGG
18916767 GAC-GTTGGCAT
1 GACAG-TGGCAT
18916778 TGTACGAGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 13 0.28
43 32 0.70
44 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (42 bp):
GACAGTGGCATCGTATTTGATTACATGTAAAACCCTGTCTGG
Found at i:18918648 original size:46 final size:46
Alignment explanation
Indices: 18918590--18918757 Score: 200
Period size: 46 Copynumber: 3.6 Consensus size: 46
18918580 TACATCTCAC
* *
18918590 GAACTCAGACTCAACTCAATGAGTTCAGACGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGT
* * * * *
18918636 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C-TCA-C
1 GAACTCGGACTCAACTCAACGAGTTC--A-GAC--GTTCGCATCCATAAGT
18918683 GAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGT
18918729 GAACTCGGACTCAACTCAACGAGTTCAGA
1 GAACTCGGACTCAACTCAACGAGTTCAGA
18918758 TGCCCAAATA
Statistics
Matches: 101, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 3 0.03
45 3 0.03
46 52 0.51
47 25 0.25
48 3 0.03
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCATCCATAAGT
Found at i:18918650 original size:93 final size:93
Alignment explanation
Indices: 18918535--18918763 Score: 404
Period size: 93 Copynumber: 2.5 Consensus size: 93
18918525 TGTAACGCGC
*
18918535 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTTACATCTCACGAACTCAGAC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTTACATCTCACGAACTCAGAC
*
18918600 TCAACTCAATGAGTTCAGACGTTCGCAT
66 TCAACTCAACGAGTTCAGACGTTCGCAT
* *
18918628 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACGAACTCGGAC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTTACATCTCACGAACTCAGAC
18918693 TCAACTCAACGAGTTCAGACGTTCGCAT
66 TCAACTCAACGAGTTCAGACGTTCGCAT
* *
18918721 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCA
18918764 AATATCCGAA
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (93 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTTACATCTCACGAACTCAGAC
TCAACTCAACGAGTTCAGACGTTCGCAT
Found at i:18918694 original size:47 final size:46
Alignment explanation
Indices: 18918542--18918705 Score: 183
Period size: 47 Copynumber: 3.5 Consensus size: 46
18918532 CGCCCATAAG
18918542 CGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTTACATCTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGATG-CCAGTTACATCTCA
* * * * * *
18918589 CGAACTCAGACTCAACTCAATGAGTTC--A-GAC-GTTCGCATCCATAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGATGCCAGTT-ACAT-C-TCA
*
18918634 GTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCA
1 -CGAACTCGGACTCAACTCAACGAGCTCGGATGCC-AGTTACATCTCA
18918682 CGAACTCGGACTCAACTCAACGAG
1 CGAACTCGGACTCAACTCAACGAG
18918706 TTCAGACGTT
Statistics
Matches: 94, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
44 2 0.02
45 3 0.03
46 23 0.24
47 47 0.50
48 3 0.03
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (46 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGATGCCAGTTACATCTCA
Found at i:18925204 original size:13 final size:13
Alignment explanation
Indices: 18925186--18925212 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18925176 AGTTTATCGG
18925186 AATTATTATAATT
1 AATTATTATAATT
18925199 AATTATTATAATT
1 AATTATTATAATT
18925212 A
1 A
18925213 TGATTTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATTATAATT
Found at i:18926058 original size:28 final size:28
Alignment explanation
Indices: 18926026--18926084 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
18926016 TAAATTATTG
18926026 ATAGTTGAATGTTAGTTTTAAAGAATGA
1 ATAGTTGAATGTTAGTTTTAAAGAATGA
18926054 ATAGTTGAATGTTAGTTTTAAAGAATGA
1 ATAGTTGAATGTTAGTTTTAAAGAATGA
18926082 ATA
1 ATA
18926085 ATTGTGATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (28 bp):
ATAGTTGAATGTTAGTTTTAAAGAATGA
Found at i:18928461 original size:38 final size:38
Alignment explanation
Indices: 18928416--18928588 Score: 172
Period size: 38 Copynumber: 4.5 Consensus size: 38
18928406 GGCTTAAAGA
*
18928416 CCCGCAGGCTAT-ATGCTGGAATTATATCTGGGTTAAAT
1 CCCGCAGGCT-TCATGCTGGAATTATATCCGGGTTAAAT
*
18928454 CCCGCAGGCTTCGTGCTGGTAA-TATATCCGGGTTAAAT
1 CCCGCAGGCTTCATGCTGG-AATTATATCCGGGTTAAAT
* * *
18928492 CCTGCAGGCTTCATGCTGGTATTATATCCGGGCTAAAT
1 CCCGCAGGCTTCATGCTGGAATTATATCCGGGTTAAAT
* * * * *
18928530 CTCGCAGGCCT-AGTGCTGGTATTATATCTGAGTTTAAAGT
1 CCCGCAGGCTTCA-TGCTGGAATTATATCCG-GGTTAAA-T
* *
18928570 CCCGTAGGCTTCGTGCTGG
1 CCCGCAGGCTTCATGCTGG
18928589 TGTTATGTTT
Statistics
Matches: 112, Mismatches: 16, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
37 3 0.03
38 87 0.78
39 7 0.06
40 15 0.13
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (38 bp):
CCCGCAGGCTTCATGCTGGAATTATATCCGGGTTAAAT
Found at i:18928546 original size:76 final size:78
Alignment explanation
Indices: 18928409--18928594 Score: 216
Period size: 76 Copynumber: 2.4 Consensus size: 78
18928399 GTATTCGGGC
* * * * * *
18928409 TTAAAGACCCGCAGGCTAT-ATGCTGGAATTATATCTGGGTTAAATCCCGCAGGCTTCGTGCTGG
1 TTAAAGTCCCGCAGGCT-TCATGCTGGTATTATATCCGGGCTAAATCCCGCAGGCCTAGTGCTGG
18928473 TAATATATCCG-GG
65 TAATATATCCGAGG
* *
18928486 TTAAA-TCCTGCAGGCTTCATGCTGGTATTATATCCGGGCTAAATCTCGCAGGCCTAGTGCTGGT
1 TTAAAGTCCCGCAGGCTTCATGCTGGTATTATATCCGGGCTAAATCCCGCAGGCCTAGTGCTGGT
* * *
18928550 ATTATATCTGAGT
66 AATATATCCGAGG
* * *
18928563 TTAAAGTCCCGTAGGCTTCGTGCTGGTGTTAT
1 TTAAAGTCCCGCAGGCTTCATGCTGGTATTAT
18928595 GTTTGGGTTT
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
75 1 0.01
76 57 0.63
77 11 0.12
78 22 0.24
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (78 bp):
TTAAAGTCCCGCAGGCTTCATGCTGGTATTATATCCGGGCTAAATCCCGCAGGCCTAGTGCTGGT
AATATATCCGAGG
Found at i:18934490 original size:75 final size:76
Alignment explanation
Indices: 18934312--18934491 Score: 231
Period size: 75 Copynumber: 2.4 Consensus size: 76
18934302 TGGGCACACA
* *
18934312 ACCGTCGGTTAATCCGACTAGCGCTGGGCGCAATTCACCGTTGGTTTATCCAACTAGAGCTGGGC
1 ACCGTCGGTTAATCCGACTAGCGCTGGGCACAAATCACCGTTGGTTTATCCAACTAGAGCTGGGC
18934377 TCACAATTCTT
66 TCACAATTCTT
* * * * * **
18934388 ATCGTAGGTTAA-CTCGGCTAGCACTGGGTACAAAT-ATTGTTGGTTTATCCAACTAGAGCTGGG
1 ACCGTCGGTTAATC-CGACTAGCGCTGGGCACAAATCACCGTTGGTTTATCCAACTAGAGCTGGG
18934451 CTCAC-ATTCATT
65 CTCACAATTC-TT
*
18934463 ACCGTCGGTTAATCCGACTAGTGCTGGGC
1 ACCGTCGGTTAATCCGACTAGCGCTGGGC
18934492 GCAACCTCTT
Statistics
Matches: 86, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
74 4 0.05
75 55 0.64
76 27 0.31
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (76 bp):
ACCGTCGGTTAATCCGACTAGCGCTGGGCACAAATCACCGTTGGTTTATCCAACTAGAGCTGGGC
TCACAATTCTT
Found at i:18936560 original size:22 final size:22
Alignment explanation
Indices: 18936534--18936575 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18936524 TTGTATTAGT
18936534 TTATTAAATTAAATTAAAAATA
1 TTATTAAATTAAATTAAAAATA
**
18936556 TTATTAAATTTCATTAAAAA
1 TTATTAAATTAAATTAAAAA
18936576 AATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATTAAATTAAATTAAAAATA
Found at i:18938743 original size:60 final size:62
Alignment explanation
Indices: 18938631--18938753 Score: 180
Period size: 61 Copynumber: 2.0 Consensus size: 62
18938621 TCAATTTGTA
* *
18938631 TTAGATATTATAATTATTTAAATTTATTTTTATCTAATTAATATTTAGATACTA-TTTATAT
1 TTAGATATTATAATTATTTAAATTTATTTTTATCCAAATAATATTTAGATACTATTTTATAT
* *
18938692 TTAGATATTGTAATTA-TTAAATTTTATTTTTA-CCAAATAATATTTATATACTATTTTATAT
1 TTAGATATTATAATTATTTAAA-TTTATTTTTATCCAAATAATATTTAGATACTATTTTATAT
18938753 T
1 T
18938754 ATTTGACTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
60 23 0.41
61 33 0.59
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (62 bp):
TTAGATATTATAATTATTTAAATTTATTTTTATCCAAATAATATTTAGATACTATTTTATAT
Found at i:18940591 original size:58 final size:60
Alignment explanation
Indices: 18940526--18940651 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 60
18940516 AATATAAATA
* * * *
18940526 AATTACCTTATTACAACCATACCTTTGGAAACAAATC-A-AAGGTTTCCTCGTCCTCACT
1 AATTACCTTATTACAACCACAACTTTGGAAACAAATCAATAAAGTTTCCTCGGCCTCACT
* *
18940584 AATTACCTTATTACACCCACAATTTTGGAAACAAATCAAATTAAAGTTTCCTCGGCCTCACT
1 AATTACCTTATTACAACCACAACTTTGGAAACAAATC-AA-TAAAGTTTCCTCGGCCTCACT
18940646 AATTAC
1 AATTAC
18940652 TCAGTAAGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 33 0.57
60 1 0.02
62 24 0.41
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (60 bp):
AATTACCTTATTACAACCACAACTTTGGAAACAAATCAATAAAGTTTCCTCGGCCTCACT
Found at i:18947177 original size:18 final size:17
Alignment explanation
Indices: 18947144--18947182 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
18947134 TTGTATAAAT
18947144 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
18947162 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
18947179 TGTG
1 TGTG
18947183 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:18947314 original size:8 final size:8
Alignment explanation
Indices: 18947301--18947329 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
18947291 CACTAGAGAC
18947301 CAGTGTTA
1 CAGTGTTA
18947309 CAGTGTTA
1 CAGTGTTA
18947317 CAGTGTTA
1 CAGTGTTA
18947325 CAGTG
1 CAGTG
18947330 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:18947443 original size:23 final size:23
Alignment explanation
Indices: 18947416--18947488 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
18947406 AGTGTTATTG
18947416 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
18947439 TTCAGTGGTAGCTAT-GGCTACAT
1 ATCAGTGGTAGCT-TCGGCTACAT
18947462 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
18947485 ATCA
1 ATCA
18947489 ATGTGGCACT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.02
23 44 0.96
24 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:18953060 original size:69 final size:69
Alignment explanation
Indices: 18952949--18953078 Score: 251
Period size: 69 Copynumber: 1.9 Consensus size: 69
18952939 TGGGATGCTA
*
18952949 AAACTATGCTATGATCATGTAGAATAATGATTTCAAGCTATAACCAAAGTTTGCATGAAGCCGAG
1 AAACTATGCTATGATCATGTAGAATAATGATTCCAAGCTATAACCAAAGTTTGCATGAAGCCGAG
18953014 ATAG
66 ATAG
18953018 AAACTATGCTATGATCATGTAGAATAATGATTCCAAGCTATAACCAAAGTTTGCATGAAGC
1 AAACTATGCTATGATCATGTAGAATAATGATTCCAAGCTATAACCAAAGTTTGCATGAAGC
18953079 ATATCTGAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (69 bp):
AAACTATGCTATGATCATGTAGAATAATGATTCCAAGCTATAACCAAAGTTTGCATGAAGCCGAG
ATAG
Found at i:18958518 original size:15 final size:15
Alignment explanation
Indices: 18958498--18958527 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18958488 CATATTTTAT
*
18958498 TTAATATTATATAAA
1 TTAATATAATATAAA
18958513 TTAATATAATATAAA
1 TTAATATAATATAAA
18958528 AATTATTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAATATAATATAAA
Found at i:18967633 original size:46 final size:49
Alignment explanation
Indices: 18967577--18967668 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
18967567 AATATAATTG
* * *
18967577 TTTTATCTTTTAAC-TT-AATAA-GTAAATATTTATCAAAACAACGAAA
1 TTTTACCTTTTAACTTTAAAAAAGGTAAACATTTATCAAAACAACGAAA
*
18967623 TTTTACCTTTTAACTTTAAAAAAGGTAAACATTTATCGAAACAACG
1 TTTTACCTTTTAACTTTAAAAAAGGTAAACATTTATCAAAACAACG
18967669 TAGTTTTCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
46 13 0.33
47 2 0.05
48 4 0.10
49 20 0.51
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (49 bp):
TTTTACCTTTTAACTTTAAAAAAGGTAAACATTTATCAAAACAACGAAA
Found at i:18971476 original size:25 final size:25
Alignment explanation
Indices: 18971435--18971488 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
18971425 TTACATATAC
* * *
18971435 AAATAATTTTATTTATTTAATACAA
1 AAATAATTTGATGTATTTAATAAAA
18971460 AAATAATTTGATGTATTTAATAAAA
1 AAATAATTTGATGTATTTAATAAAA
18971485 AAAT
1 AAAT
18971489 TCATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (25 bp):
AAATAATTTGATGTATTTAATAAAA
Found at i:18971519 original size:31 final size:30
Alignment explanation
Indices: 18971484--18971547 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
18971474 ATTTAATAAA
18971484 AAAATTCATATATATATAATT-ATACTAAATT
1 AAAATTCATA-ATATA-AATTCATACTAAATT
* *
18971515 AAAATTTATAATATAAATTGCATATTAAATT
1 AAAATTCATAATATAAATT-CATACTAAATT
18971546 AA
1 AA
18971548 CACTCAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 5 0.17
31 20 0.69
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (30 bp):
AAAATTCATAATATAAATTCATACTAAATT
Found at i:18971929 original size:15 final size:15
Alignment explanation
Indices: 18971900--18971955 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
18971890 TGTTATAATT
**
18971900 AATTTTTTATTTTAA
1 AATTTTTTAAATTAA
18971915 AATTTTTTAAATTAA
1 AATTTTTTAAATTAA
* * *
18971930 TAAATATTTAAA-TAT
1 -AATTTTTTAAATTAA
18971945 AATTTTTTAAA
1 AATTTTTTAAA
18971956 AATTATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
14 9 0.27
15 15 0.45
16 9 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTTAAATTAA
Found at i:18981608 original size:14 final size:15
Alignment explanation
Indices: 18981560--18981614 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
18981550 ATTTTTTTAA
*
18981560 AAAAAATATTTGTTC-
1 AAAAATTATTT-TTCG
*
18981575 AAATAA-TATTTTTTG
1 AAA-AATTATTTTTCG
*
18981590 TAAAATTATTTTTCG
1 AAAAATTATTTTTCG
18981605 AAAAATTATT
1 AAAAATTATT
18981615 CAAATGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 4 0.12
15 27 0.82
16 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (15 bp):
AAAAATTATTTTTCG
Found at i:18988156 original size:6 final size:6
Alignment explanation
Indices: 18988145--18988174 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
18988135 TTATTCTTCC
18988145 CCATTT CCATTT CCATTT CCATTT CCATTT
1 CCATTT CCATTT CCATTT CCATTT CCATTT
18988175 ATATTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
CCATTT
Found at i:18988180 original size:18 final size:18
Alignment explanation
Indices: 18988145--18988180 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18988135 TTATTCTTCC
*
18988145 CCATTTCCATTTCCATTT
1 CCATTTCCATTTACATTT
*
18988163 CCATTTCCATTTATATTT
1 CCATTTCCATTTACATTT
18988181 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (18 bp):
CCATTTCCATTTACATTT
Found at i:19005497 original size:18 final size:18
Alignment explanation
Indices: 19005474--19005559 Score: 109
Period size: 18 Copynumber: 4.7 Consensus size: 18
19005464 GAACGATAAT
*
19005474 TTATTCAGTAACAATCAG
1 TTATTCAGTAACAATCAA
*
19005492 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
* * *
19005510 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATCAA
*
19005528 TTATTCAGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
19005547 TTATTCAGTAACA
1 TTATTCAGTAACA
19005560 GTCGATCTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
18 42 0.74
19 15 0.26
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:19005802 original size:45 final size:45
Alignment explanation
Indices: 19005739--19005848 Score: 148
Period size: 45 Copynumber: 2.4 Consensus size: 45
19005729 TCCGGAACAG
* * *
19005739 TAACAGCAACAATAACAGTATTCAACACACAAAGTGCTGAATCGA
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
* * **
19005784 TAACGGTTACAGTAACAGTATTTGACACACAAAGTGCCGAATCGA
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
*
19005829 TAACAGTAACGGTAACAGTA
1 TAACAGTAACAGTAACAGTA
19005849 ACGGTAGTCG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (45 bp):
TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
Found at i:19005846 original size:12 final size:12
Alignment explanation
Indices: 19005829--19005854 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19005819 GCCGAATCGA
19005829 TAACAGTAACGG
1 TAACAGTAACGG
19005841 TAACAGTAACGG
1 TAACAGTAACGG
19005853 TA
1 TA
19005855 GTCGGCACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (12 bp):
TAACAGTAACGG
Found at i:19006622 original size:15 final size:15
Alignment explanation
Indices: 19006599--19006652 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
19006589 TTGCTCTCTG
*
19006599 TTTCGTTTCATTCTT
1 TTTCTTTTCATTCTT
19006614 TTTCTTTTC-TATCTT
1 TTTCTTTTCAT-TCTT
*
19006629 TTTTTTTTCATTTCTT
1 TTTCTTTTCA-TTCTT
19006645 TTTCTTTT
1 TTTCTTTT
19006653 GTTTTACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 1 0.03
15 20 0.61
16 11 0.33
17 1 0.03
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTCTTTTCATTCTT
Found at i:19006814 original size:31 final size:32
Alignment explanation
Indices: 19006758--19006820 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
19006748 CACACTTGTC
*
19006758 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
19006790 ATAATATAAT-TATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
19006821 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:19009506 original size:21 final size:21
Alignment explanation
Indices: 19009481--19009549 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
19009471 TATAATGATT
19009481 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
19009502 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
19009522 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
19009542 ATTATTAT
1 ATTATTAT
19009550 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:19009562 original size:15 final size:14
Alignment explanation
Indices: 19009536--19009566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
19009526 TATGGTTTTA
19009536 TATTAGATTATTAT
1 TATTAGATTATTAT
19009550 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
19009565 TA
1 TA
19009567 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:19014707 original size:49 final size:49
Alignment explanation
Indices: 19014635--19014822 Score: 223
Period size: 49 Copynumber: 3.8 Consensus size: 49
19014625 TAGCCGAATC
* *
19014635 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTATACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * *
19014684 AATCTGGTACACTTAGTAGCCTGCACTTAGTACTACATATGTGATCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* * * * *
19014735 TTTCAGGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACTAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
** *
19014784 TATCTGGTACATGTAGTAGCCTGCACTTAATACTACACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
19014823 CGTGACCTCA
Statistics
Matches: 113, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 72 0.64
50 2 0.02
51 39 0.35
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:19014754 original size:100 final size:100
Alignment explanation
Indices: 19014640--19014820 Score: 301
Period size: 100 Copynumber: 1.8 Consensus size: 100
19014630 GAATCTATCT
*
19014640 GGTACGCATAGTAGCCTGCACTTAGTACTATACATGCGACCAATAATCTGGTACACT-TAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACA-TGTAGTAGC
*
19014704 CTGCACTTAGTACTACATATGTGATCACAGTTTTCA
65 CTGCACTTAATACTACATATGTGATCACAGTTTTCA
* * *
19014740 GGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACTAATTATCTGGTACATGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACATGTAGTAGCC
19014805 TGCACTTAATACTACA
66 TGCACTTAATACTACA
19014821 CACGTGACCT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
99 1 0.01
100 74 0.99
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACATGTAGTAGCC
TGCACTTAATACTACATATGTGATCACAGTTTTCA
Found at i:19020687 original size:11 final size:11
Alignment explanation
Indices: 19020673--19020705 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
19020663 ATATTATTCA
19020673 ACATTCAGTGG
1 ACATTCAGTGG
19020684 ACATTCAGTGG
1 ACATTCAGTGG
*
19020695 ACACTCAGTGG
1 ACATTCAGTGG
19020706 TTAATTACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (11 bp):
ACATTCAGTGG
Found at i:19021625 original size:18 final size:18
Alignment explanation
Indices: 19021602--19021687 Score: 100
Period size: 18 Copynumber: 4.7 Consensus size: 18
19021592 GAACGATTAT
* *
19021602 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAATCAA
*
19021620 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
* * *
19021638 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATCAA
*
19021656 TTATTCAGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
19021675 TTATTCAGTAACA
1 TTATTCAGTAACA
19021688 GCCGATCTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
18 41 0.73
19 15 0.27
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:19021656 original size:36 final size:37
Alignment explanation
Indices: 19021568--19021687 Score: 120
Period size: 36 Copynumber: 3.3 Consensus size: 37
19021558 CAATCAGTAA
* * * * *
19021568 TATTCATTAACAATCAGTCAATCAG-AACGATT-ATT
1 TATTCAATAACAATCAGTTATTCAGTAACAATTAAAT
* * * *
19021603 TATTCAGTAACAGTCAGTTATTCGGTAACAA-TCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATTAAAT
*
19021639 TATTCAATAATAATCAGTTATTCAGTAACAATTAAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATTAAAT
*
19021676 TATTCAGTAACA
1 TATTCAATAACA
19021688 GCCGATCTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
35 21 0.31
36 33 0.49
37 14 0.21
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (37 bp):
TATTCAATAACAATCAGTTATTCAGTAACAATTAAAT
Found at i:19021972 original size:45 final size:45
Alignment explanation
Indices: 19021864--19021973 Score: 141
Period size: 45 Copynumber: 2.4 Consensus size: 45
19021854 AAATCCGGAA
* *
19021864 CAGTAACAGTAACAATAACAGTATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
* * **
19021909 C-GATAACGGTTACAGTAACAGTATTTGACACACAAAGTGCCGAAT
1 CAG-TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
*
19021954 CAGTAACAGTAACGGTAACA
1 CAGTAACAGTAACAGTAACA
19021974 ATAACGGTAG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 1 0.02
45 52 0.96
46 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT
Found at i:19022933 original size:31 final size:32
Alignment explanation
Indices: 19022877--19022939 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
19022867 CACACTTGTC
*
19022877 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
19022909 ATAATATAAT-TATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
19022940 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:19024285 original size:96 final size:96
Alignment explanation
Indices: 19024116--19024305 Score: 256
Period size: 96 Copynumber: 2.0 Consensus size: 96
19024106 GTGTTCGAGG
* *
19024116 AAGTTTGTCATCGAAGGGAACGATGGAACAGACAAGGAGCCCAAGAAGCTTAGTTCGAACAAGGG
1 AAGTCTGTCATCGAAGGGAACGATGGAACAGACAAGGAGCCCAAGAAGCCTAGTTCGAACAAGGG
* * *
19024181 AAGAGCCGAAGCTAAGGGGGCAAAGAGGAAC
66 AAAAGCCGAAGCCAAGAGGGCAAAGAGGAAC
* ** * * **
19024212 AAGTCTGTCATTGAAGGGAACGATGGAGTAGACGAA-GAGCCTAAGAAGCCTGGTTCGAGTAAGG
1 AAGTCTGTCATCGAAGGGAACGATGGAACAGAC-AAGGAGCCCAAGAAGCCTAGTTCGAACAAGG
19024276 GAAAAGCCGAAGCCAAGAGGGCAAAGAGGA
65 GAAAAGCCGAAGCCAAGAGGGCAAAGAGGA
19024306 GCAAAAAGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 79 0.98
97 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.34, T:0.12
Consensus pattern (96 bp):
AAGTCTGTCATCGAAGGGAACGATGGAACAGACAAGGAGCCCAAGAAGCCTAGTTCGAACAAGGG
AAAAGCCGAAGCCAAGAGGGCAAAGAGGAAC
Found at i:19025859 original size:10 final size:11
Alignment explanation
Indices: 19025820--19025861 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
19025810 TATTTACAAA
*
19025820 GTTAATTGAGTG
1 GTTAATT-AGAG
19025832 GTTAATTAGAG
1 GTTAATTAGAG
*
19025843 TTTAATTA-AG
1 GTTAATTAGAG
19025853 GTTAATTAG
1 GTTAATTAG
19025862 GTATAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 9 0.35
11 10 0.38
12 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (11 bp):
GTTAATTAGAG
Found at i:19026304 original size:24 final size:23
Alignment explanation
Indices: 19026277--19026329 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 23
19026267 TATGTATTTG
19026277 TTATTAAATAGATATT-TATTATAA
1 TTATTAAATAG-TATTATATTA-AA
*
19026301 TTATT--ATAGTTTTATATTAAA
1 TTATTAAATAGTATTATATTAAA
19026322 TTATTAAA
1 TTATTAAA
19026330 ATGAATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 10 0.40
22 9 0.36
23 1 0.04
24 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
TTATTAAATAGTATTATATTAAA
Found at i:19026451 original size:3 final size:3
Alignment explanation
Indices: 19026443--19026485 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
19026433 ATGAATTAAA
*
19026443 TAT TAT TA- TAT TA- TAT TAT TAT GTAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
19026486 ACTAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:19026460 original size:13 final size:13
Alignment explanation
Indices: 19026442--19026483 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
19026432 TATGAATTAA
19026442 ATATTATTATATT
1 ATATTATTATATT
*
19026455 ATATTATTAT-GT
1 ATATTATTATATT
19026467 ATTATTATTAATATT
1 A-TATTATT-ATATT
19026482 AT
1 AT
19026484 TAACTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 2 0.08
13 17 0.71
14 3 0.12
15 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
ATATTATTATATT
Found at i:19035996 original size:26 final size:26
Alignment explanation
Indices: 19035960--19036015 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
19035950 CCTTCTTAAA
19035960 ACAACAAGGACTTAGTTAATGACATC
1 ACAACAAGGACTTAGTTAATGACATC
19035986 ACAACAAGGACTTAGTTAATGACATC
1 ACAACAAGGACTTAGTTAATGACATC
19036012 ACAA
1 ACAA
19036016 GCTTTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (26 bp):
ACAACAAGGACTTAGTTAATGACATC
Found at i:19039870 original size:51 final size:51
Alignment explanation
Indices: 19039794--19039956 Score: 238
Period size: 51 Copynumber: 3.2 Consensus size: 51
19039784 TATCCTGATA
* *
19039794 AAATATGAAGCTCTTGTTGAAGCTAGAGTAATAAAGTAATTATTCTGGATG
1 AAATATGAAGCTCTTGTTGAAGCTAGAGTAACAAAGTAATTATTCCGGATG
* *
19039845 AAATATGAAGCTCTTGTTGAAGCTAGA-TCAACAAAGTAATTAATCCAGATG
1 AAATATGAAGCTCTTGTTGAAGCTAGAGT-AACAAAGTAATTATTCCGGATG
* * * *
19039896 AAATATGAAGCTCTTGTTGAAGTTAGAGCAACAAGGTAATAATTCCGGATG
1 AAATATGAAGCTCTTGTTGAAGCTAGAGTAACAAAGTAATTATTCCGGATG
19039947 AAATATGAAG
1 AAATATGAAG
19039957 TAAGTTTGAG
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
50 1 0.01
51 99 0.99
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (51 bp):
AAATATGAAGCTCTTGTTGAAGCTAGAGTAACAAAGTAATTATTCCGGATG
Found at i:19041688 original size:40 final size:40
Alignment explanation
Indices: 19041600--19041695 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
19041590 TCCAATTTCT
* *
19041600 AGCACAAAACCTGCGGGATTTAACCCGGATATCTATTACC
1 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACC
19041640 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACC
1 AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACC
*
19041680 AGCACAAAGCTTGCGG
1 AGCACAAAGCCTGCGG
19041696 ACTATAAGTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (40 bp):
AGCACAAAGCCTGCGGGATTTAACCCGAATATCTATTACC
Found at i:19050109 original size:21 final size:19
Alignment explanation
Indices: 19050070--19050109 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
19050060 TGAACATGTG
*
19050070 TTTATTGTGAAATTGAATA
1 TTTATTGTGAAAGTGAATA
19050089 TTTATTAGTGAAAAGTGAATA
1 TTTATT-GTG-AAAGTGAATA
19050110 GAATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
TTTATTGTGAAAGTGAATA
Found at i:19050318 original size:12 final size:12
Alignment explanation
Indices: 19050301--19050325 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19050291 GCCGACTACT
19050301 GTTACTGTTACC
1 GTTACTGTTACC
19050313 GTTACTGTTACC
1 GTTACTGTTACC
19050325 G
1 G
19050326 ATTCGGCACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:19050679 original size:72 final size:72
Alignment explanation
Indices: 19050541--19050732 Score: 176
Period size: 72 Copynumber: 2.7 Consensus size: 72
19050531 TAAATGTATA
* * * * * * * *
19050541 AAATAACTGATTATTACTGAATAATTGA-CTGTTACCGGATAATTGACTATTACTGGATATTAGA
1 AAATAACTGAATATTACTGAATAATTGATC-ATTACTGAATAACTGACTATCACTGAATAATAGA
*
19050605 CTGTTACT
65 CTGCTACT
* * *
19050613 GAATAACTGAATATTACTGAATAATTGATCATTACTGAATAACTGATTGTCACTGAATGAAT-GA
1 AAATAACTGAATATTACTGAATAATTGATCATTACTGAATAACTGACTATCACTGAAT-AATAGA
19050677 CTGCTACT
65 CTGCTACT
* * * *
19050685 AAATAACTTAATTGTTACTGAAT-ATCTGAT-TTTACTGAATAATTGACT
1 AAATAACTGAA-TATTACTGAATAAT-TGATCATTACTGAATAACTGACT
19050733 GTTACTGGAT
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
72 81 0.83
73 17 0.17
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (72 bp):
AAATAACTGAATATTACTGAATAATTGATCATTACTGAATAACTGACTATCACTGAATAATAGAC
TGCTACT
Found at i:19050745 original size:54 final size:55
Alignment explanation
Indices: 19050542--19050824 Score: 209
Period size: 54 Copynumber: 5.1 Consensus size: 55
19050532 AAATGTATAA
* * * *
19050542 AATAACTGATTATTACTGAATAATTGACTGTTACCGGATAA-TTGACTATTACTG
1 AATAACTGATTATTACTGAATAATTGACTGTTACTGAATAACTTGATTGTTACTG
* * * * * * * **
19050596 GAT-ATTAGACTGTTACTGAATAACTGAATATTACTGAATAA-TTGATCATTACTG
1 AATAACT-GATTATTACTGAATAATTGACTGTTACTGAATAACTTGATTGTTACTG
* * * * *
19050650 AATAACTGATTGTCACTGAATGAA-TGACTGCTACTAAATAACTTAATTGTTACTG
1 AATAACTGATTATTACTGAAT-AATTGACTGTTACTGAATAACTTGATTGTTACTG
* * *
19050705 AATATCTGATT-TTACTGAATAATTGACTGTTACTGGATAACCGATTAATTGATCGATACTG
1 AATAACTGATTATTACTGAATAATTGACTGTTACTGAATAA-C--TTGATTG-T---TACTG
* * * * *
19050766 AATAACTGGTTATTATTGAATAATTGATTGTTACCGAATAAC-TGACTGTTACTG
1 AATAACTGATTATTACTGAATAATTGACTGTTACTGAATAACTTGATTGTTACTG
19050820 AATAA
1 AATAA
19050825 ATAATTGTTC
Statistics
Matches: 181, Mismatches: 35, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
53 4 0.02
54 99 0.55
55 25 0.14
57 8 0.04
58 5 0.03
61 15 0.08
62 25 0.14
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (55 bp):
AATAACTGATTATTACTGAATAATTGACTGTTACTGAATAACTTGATTGTTACTG
Found at i:19050833 original size:18 final size:18
Alignment explanation
Indices: 19050542--19050837 Score: 159
Period size: 18 Copynumber: 16.1 Consensus size: 18
19050532 AAATGTATAA
*
19050542 AATAACTGATTATTACTG
1 AATAACTGATTGTTACTG
* * *
19050560 AATAATTGACTGTTACCG
1 AATAACTGATTGTTACTG
* * * *
19050578 GATAATTGACTATTACTG
1 AATAACTGATTGTTACTG
* * *
19050596 GAT-ATTAGACTGTTACTG
1 AATAACT-GATTGTTACTG
* *
19050614 AATAACTGAATATTACTG
1 AATAACTGATTGTTACTG
* **
19050632 AATAATTGATCATTACTG
1 AATAACTGATTGTTACTG
*
19050650 AATAACTGATTGTCACTG
1 AATAACTGATTGTTACTG
* * *
19050668 AATGAA-TGACTGCTACTA
1 AAT-AACTGATTGTTACTG
*
19050686 AATAACTTAATTGTTACTG
1 AATAAC-TGATTGTTACTG
*
19050705 AATATCTGATT-TTACTG
1 AATAACTGATTGTTACTG
* *
19050722 AATAATTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
19050740 GATAACCGATTAATTGATCGATACTG
1 AATAA-C---TGATTG-T---TACTG
* * *
19050766 AATAACTGGTTATTATTG
1 AATAACTGATTGTTACTG
* *
19050784 AATAATTGATTGTTACCG
1 AATAACTGATTGTTACTG
*
19050802 AATAACTGACTGTTACTG
1 AATAACTGATTGTTACTG
* *
19050820 AATAAATAATTGTT-CTG
1 AATAACTGATTGTTACTG
19050837 A
1 A
19050838 GAGTTAATGA
Statistics
Matches: 212, Mismatches: 52, Indels: 29
0.72 0.18 0.10
Matches are distributed among these distances:
17 23 0.11
18 153 0.72
19 17 0.08
21 1 0.00
22 7 0.03
23 1 0.00
25 1 0.00
26 9 0.04
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
AATAACTGATTGTTACTG
Found at i:19051981 original size:21 final size:21
Alignment explanation
Indices: 19051955--19052037 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
19051945 TGATCAGTAT
*
19051955 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
19051976 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* * *
19051997 ACGACACACGAGGTGCTTGAAA
1 ACGACACACAAAGTGCCT-AAA
*
19052019 TACGACACATAAAGTGCCT
1 -ACGACACACAAAGTGCCT
19052038 GACAGATAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
21 33 0.69
22 1 0.02
23 14 0.29
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:19052005 original size:23 final size:22
Alignment explanation
Indices: 19051953--19052027 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 22
19051943 CCTGATCAGT
** *
19051953 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
19051974 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
*
19051995 ATACGACACACGAGGTGCTTGAA
1 ATACGACACACGAGGTGCCTG-A
19052018 ATACGACACA
1 ATACGACACA
19052028 TAAAGTGCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 35 0.78
23 10 0.22
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:19052436 original size:15 final size:15
Alignment explanation
Indices: 19052411--19052468 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
19052401 TCATATATAT
19052411 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
19052427 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
19052442 AATAATTTCAATCAA
1 TATAAATTCAATCAA
19052457 TATAAATTCAAT
1 TATAAATTCAAT
19052469 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:19058848 original size:29 final size:29
Alignment explanation
Indices: 19058814--19058877 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
19058804 TATAATTTTT
19058814 ATTTTTATTTTT-TTTATCAATATTTTATA
1 ATTTTTATTTTTATTTAT-AATATTTTATA
* *
19058843 ATTTTTATTTTTATTTATATTTTTTTATA
1 ATTTTTATTTTTATTTATAATATTTTATA
*
19058872 CTTTTT
1 ATTTTT
19058878 CAAAATTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (29 bp):
ATTTTTATTTTTATTTATAATATTTTATA
Found at i:19058867 original size:20 final size:20
Alignment explanation
Indices: 19058798--19058870 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
19058788 AAGAGAAGCA
* *
19058798 ATATTTTATAATTTTTATTT
1 ATATTTTTTTATTTTTATTT
* ***
19058818 TTATTTTTTTTATCAATATTT
1 ATA-TTTTTTTATTTTTATTT
*
19058839 -TATAATTTTTATTTTTATTT
1 ATAT-TTTTTTATTTTTATTT
19058859 ATATTTTTTTAT
1 ATATTTTTTTAT
19058871 ACTTTTTCAA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
19 1 0.03
20 23 0.59
21 15 0.38
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (20 bp):
ATATTTTTTTATTTTTATTT
Found at i:19058876 original size:11 final size:10
Alignment explanation
Indices: 19058815--19058877 Score: 51
Period size: 11 Copynumber: 6.3 Consensus size: 10
19058805 ATAATTTTTA
19058815 TTTTTAT-TT
1 TTTTTATATT
*
19058824 TTTTTATCAAT
1 TTTTTAT-ATT
* *
19058835 ATTTTATA-A
1 TTTTTATATT
19058844 TTTTTAT-TT
1 TTTTTATATT
19058853 TTATTTATATT
1 TT-TTTATATT
19058864 TTTTTATACTT
1 TTTTTATA-TT
19058875 TTT
1 TTT
19058878 CAAAATTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
9 15 0.35
10 12 0.28
11 16 0.37
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTATATT
Found at i:19077635 original size:7 final size:7
Alignment explanation
Indices: 19077623--19077669 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
19077613 AAACGGAATT
19077623 TTTTTAA
1 TTTTTAA
19077630 TTTTTAA
1 TTTTTAA
19077637 TTTTTAA
1 TTTTTAA
19077644 TTTTTAA
1 TTTTTAA
19077651 TTTTTAA
1 TTTTTAA
19077658 TTTTTAA
1 TTTTTAA
19077665 TTTTT
1 TTTTT
19077670 TTTGTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:19080748 original size:23 final size:22
Alignment explanation
Indices: 19080715--19080763 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
19080705 ACAGATACGC
19080715 GAATTCCACCCAAACACACC-A
1 GAATTCCACCCAAACACACCTA
19080736 GAATGTCCAACCCAAACACACCTA
1 GAAT-TCC-ACCCAAACACACCTA
19080760 GAAT
1 GAAT
19080764 ATTATAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.16
22 3 0.12
23 13 0.52
24 5 0.20
ACGTcount: A:0.43, C:0.37, G:0.08, T:0.12
Consensus pattern (22 bp):
GAATTCCACCCAAACACACCTA
Found at i:19081694 original size:3 final size:3
Alignment explanation
Indices: 19081686--19081747 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
19081676 ATCTTTAACT
** *
19081686 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA -AA CCA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
19081732 TTAA TAT TAA TAA TAA
1 -TAA TAA TAA TAA TAA
19081748 AATCTTAGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19083665 original size:17 final size:18
Alignment explanation
Indices: 19083645--19083678 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
19083635 AATGAATTGT
19083645 TTTATTGAAT-AAATTAA
1 TTTATTGAATGAAATTAA
19083662 TTTATTGAATGAAATTA
1 TTTATTGAATGAAATTA
19083679 TTAATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (18 bp):
TTTATTGAATGAAATTAA
Found at i:19084758 original size:39 final size:39
Alignment explanation
Indices: 19084713--19084833 Score: 215
Period size: 39 Copynumber: 3.1 Consensus size: 39
19084703 ATGCAAGGCA
19084713 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
19084752 CTGGAAATGTATCCGGGCTAAAGTTCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
19084791 CTGGAAATGTGTCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
19084830 CTGG
1 CTGG
19084834 TGCTGGTAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:19087672 original size:17 final size:19
Alignment explanation
Indices: 19087652--19087686 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
19087642 GGTTGAAGTC
19087652 GATAAAAT-T-TTAATTAT
1 GATAAAATATATTAATTAT
19087669 GATAAAATATATTAATTA
1 GATAAAATATATTAATTA
19087687 AAGGAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (19 bp):
GATAAAATATATTAATTAT
Found at i:19088799 original size:33 final size:33
Alignment explanation
Indices: 19088738--19088802 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
19088728 ACTTTACCCT
**
19088738 TCCATTTCTTTCTCAGGTCTAGACCTTTCTTCA
1 TCCATTTCTTTCTCACCTCTAGACCTTTCTTCA
* * *
19088771 TCCATTTCTTTCTCACCTTTGGAGCTTTCTTC
1 TCCATTTCTTTCTCACCTCTAGACCTTTCTTC
19088803 TTTTTTTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.12, C:0.31, G:0.09, T:0.48
Consensus pattern (33 bp):
TCCATTTCTTTCTCACCTCTAGACCTTTCTTCA
Found at i:19090260 original size:57 final size:57
Alignment explanation
Indices: 19090196--19090303 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
19090186 GATCCGATTG
* *
19090196 AAAAATGAAAACTTTTTTTT-AAGACACGAGAATTTTGAAGCACGAAAATTTTTTTTA
1 AAAAATG-AAACTTTTTTTTAAAAACACGAGAATTTTGAAACACGAAAATTTTTTTTA
* * *
19090253 AAAAATGAAAGTTTTTTTTAAAAACACGAGAATTTTTAAACACGGAAATTT
1 AAAAATGAAACTTTTTTTTAAAAACACGAGAATTTTGAAACACGAAAATTT
19090304 CAGAAACACG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
56 11 0.24
57 34 0.76
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (57 bp):
AAAAATGAAACTTTTTTTTAAAAACACGAGAATTTTGAAACACGAAAATTTTTTTTA
Found at i:19090262 original size:20 final size:20
Alignment explanation
Indices: 19090239--19090276 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19090229 TTTGAAGCAC
19090239 GAAAATTTTTTTTAAAAAAT
1 GAAAATTTTTTTTAAAAAAT
*
19090259 GAAAGTTTTTTTTAAAAA
1 GAAAATTTTTTTTAAAAA
19090277 CACGAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (20 bp):
GAAAATTTTTTTTAAAAAAT
Found at i:19090320 original size:33 final size:32
Alignment explanation
Indices: 19090274--19090358 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 32
19090264 TTTTTTTTAA
19090274 AAACACGAGAATTTTTAAACACGGAAATTTCAG
1 AAACACGAGAATTTTTAAACAC-GAAATTTCAG
* * **
19090307 AAACACGAAAATTTTTAAAACACGACATTTTTG
1 AAACACGAGAATTTTT-AAACACGAAATTTCAG
19090340 AAACACGAGAATTTTTAAA
1 AAACACGAGAATTTTTAAA
19090359 ACAAGACATT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.07
33 37 0.80
34 6 0.13
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (32 bp):
AAACACGAGAATTTTTAAACACGAAATTTCAG
Found at i:19090452 original size:18 final size:17
Alignment explanation
Indices: 19090267--19090785 Score: 220
Period size: 17 Copynumber: 29.8 Consensus size: 17
19090257 ATGAAAGTTT
*
19090267 TTTTTAAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
*
19090285 TTTTT-AAACACGGAAA
1 TTTTTAAAACACGAAAA
*
19090301 -TTTCAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
*
19090318 TTTTTAAAACACG-ACA
1 TTTTTAAAACACGAAAA
* *
19090334 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAAAA
* * *
19090351 TTTTTAAAACAAGACAT
1 TTTTTAAAACACGAAAA
* **
19090368 TTTTTGAAACAC-AATT
1 TTTTTAAAACACGAAAA
**
19090384 TTTTTCTTAA-A--AAAA
1 TTTTT-AAAACACGAAAA
* *
19090399 --TTTAAAATACGAGAA
1 TTTTTAAAACACGAAAA
19090414 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
19090431 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* * *
19090448 TTTTTGAAACAGGGAAAT
1 TTTTTAAAACA-CGAAAA
**
19090466 TTTTTAGAAA-ACG-ATT
1 TTTTTA-AAACACGAAAA
* * *
19090482 TTTTTAAATCACCG-GAG
1 TTTTTAAAACA-CGAAAA
19090499 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* *
19090517 TCTTTGAAACACCG-AAA
1 TTTTTAAAACA-CGAAAA
*
19090534 TTTTTGAAAACACGAAGA
1 TTTTT-AAAACACGAAAA
* *
19090552 TTTTTGAAACACGAAATT
1 TTTTTAAAACACGAAA-A
* *
19090570 TTTTTGAAAATACGAAGAT
1 TTTTT-AAAACACGAA-AA
** **
19090589 TTTTTTTAACACGGGAA
1 TTTTTAAAACACGAAAA
* ***
19090606 TTTTTGAAACACGGTCATTTTT
1 TTTTTAAAACAC-G--A--AAA
19090628 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* **
19090646 TTTTTGAAAGACATG-ATT
1 TTTTT-AAA-ACACGAAAA
* *
19090664 TTTTTGAAAATACGGAAA
1 TTTTT-AAAACACGAAAA
* *
19090682 TTTATAAAACACGAAATTT
1 TTTTTAAAACACGAAA--A
*
19090701 TTTTCTAAAAACAAGAAAA
1 TTTT-T-AAAACACGAAAA
* * *
19090720 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAAAA
*
19090737 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* * *
19090754 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAAAA
19090771 TTTTTAAAAGCACGA
1 TTTTTAAAA-CACGA
19090786 GGATTATTGA
Statistics
Matches: 373, Mismatches: 93, Indels: 70
0.70 0.17 0.13
Matches are distributed among these distances:
12 2 0.01
13 4 0.01
15 10 0.03
16 40 0.11
17 181 0.49
18 83 0.22
19 28 0.08
20 3 0.01
21 10 0.03
22 6 0.02
23 6 0.02
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:19090574 original size:19 final size:20
Alignment explanation
Indices: 19090499--19090594 Score: 86
Period size: 18 Copynumber: 5.2 Consensus size: 20
19090489 ATCACCGGAG
*
19090499 TTTTTGAAAACACGAA-A-A
1 TTTTTGAAAACACGAAGATT
*
19090517 TCTTTG-AAACACCGAA-A--
1 TTTTTGAAAACA-CGAAGATT
19090534 TTTTTGAAAACACGAAGA--
1 TTTTTGAAAACACGAAGATT
19090552 TTTTTG-AAACACGAA-ATT
1 TTTTTGAAAACACGAAGATT
*
19090570 TTTTTGAAAATACGAAGATT
1 TTTTTGAAAACACGAAGATT
19090590 TTTTT
1 TTTTT
19090595 TAACACGGGA
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.01
17 23 0.34
18 28 0.41
19 8 0.12
20 8 0.12
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (20 bp):
TTTTTGAAAACACGAAGATT
Found at i:19090704 original size:94 final size:94
Alignment explanation
Indices: 19090534--19090702 Score: 229
Period size: 94 Copynumber: 1.8 Consensus size: 94
19090524 AACACCGAAA
* * **
19090534 TTTTTGAAAACACGAAGATTTTTGAAACACGAAATTTTTTTGAAAATACGAAGATTTTTTTTAAC
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAATTTTTTTGAAAATACGAAGATTTTATAAAAC
*
19090599 ACGGGAATTTTTGAAACACGGTCATTTTT
66 ACGGAAATTTTTGAAACACGGTCATTTTT
* *
19090628 TTTTTGAAAACACGAAAATTTTTGAAAGAC-ATGATTTTTTTGAAAATACGGAA-A-TTTATAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGA-AATTTTTTTGAAAATAC-GAAGATTTTATAAA
19090690 ACAC-GAAATTTTT
64 ACACGGAAATTTTT
19090703 TTCTAAAAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
92 8 0.12
93 10 0.15
94 45 0.68
95 3 0.05
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (94 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACGAAATTTTTTTGAAAATACGAAGATTTTATAAAAC
ACGGAAATTTTTGAAACACGGTCATTTTT
Found at i:19090972 original size:17 final size:16
Alignment explanation
Indices: 19090938--19090988 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
19090928 AAAATTATTT
19090938 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
* *
19090954 AAAATCAAATTAAATTA
1 AAAAT-AAAATAAAATA
19090971 AAAATATAAATATAAATA
1 AAAATA-AAATA-AAATA
19090989 TGCATAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 18 0.64
18 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:19091141 original size:11 final size:11
Alignment explanation
Indices: 19091115--19091187 Score: 66
Period size: 11 Copynumber: 6.8 Consensus size: 11
19091105 GAACTGAACC
19091115 TCTTTTTT--T
1 TCTTTTTTCCT
19091124 TCTTTTTTTCCT
1 TC-TTTTTTCCT
19091136 TCTTTTTTCCT
1 TCTTTTTTCCT
19091147 TCTCTTTTT-CT
1 TCT-TTTTTCCT
*
19091158 TC-TTTTTCTTT
1 TCTTTTTTC-CT
*
19091169 TCTTTTTTTCT
1 TCTTTTTTCCT
19091180 T-TTTTTTC
1 TCTTTTTTC
19091188 TCTGCTGGGC
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
9 7 0.13
10 12 0.23
11 21 0.40
12 13 0.25
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTTTTTCCT
Found at i:19091154 original size:22 final size:20
Alignment explanation
Indices: 19091115--19091190 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 20
19091105 GAACTGAACC
19091115 TCTT-TTTTTTCTT-T-TTT
1 TCTTCTTTTTTCTTCTCTTT
19091132 TCCTTCTTTTTTCCTTCTCTTTT
1 T-CTTCTTTTTT-CTTCTC-TTT
*
19091155 TCTTC-TTTTTCTTTTCTTT
1 TCTTCTTTTTTCTTCTCTTT
*
19091174 TTTTCTTTTTT-TTCTCT
1 TCTTCTTTTTTCTTCTCT
19091191 GCTGGGCCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
17 1 0.02
18 3 0.06
19 18 0.37
20 13 0.27
21 6 0.12
22 4 0.08
23 4 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTCTTTTTTCTTCTCTTT
Found at i:19091483 original size:24 final size:24
Alignment explanation
Indices: 19091463--19091522 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
19091453 CTTTTCTTTT
*
19091463 TCTTTT-TTCTTTCTTTCTTCTTCC
1 TCTTTTCTTC-TTCCTTCTTCTTCC
19091487 TCTTTTCTTCTTCCTTCTTCTTCC
1 TCTTTTCTTCTTCCTTCTTCTTCC
*
19091511 T-TCTTCTTCTTC
1 TCTTTTCTTCTTC
19091523 AAAGTCTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 10 0.30
24 20 0.61
25 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
TCTTTTCTTCTTCCTTCTTCTTCC
Found at i:19091485 original size:3 final size:3
Alignment explanation
Indices: 19091451--19091522 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
19091441 TTTTTATTAT
* *
19091451 TTC TT- TTC TTT TTC TT- TT- TTC TTTC TTTC TTC TTC CTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC
19091494 TTC TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TTC TT-C TTC TTC TT-C TTC TTC TTC TTC
19091523 AAAGTCTAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:19091490 original size:13 final size:13
Alignment explanation
Indices: 19091474--19091522 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
19091464 CTTTTTTCTT
19091474 TCTTTCTTCTTCC
1 TCTTTCTTCTTCC
19091487 TCTTTTCTTCTT-C
1 TC-TTTCTTCTTCC
19091500 -C-TTCTTCTTCC
1 TCTTTCTTCTTCC
19091511 T-TCTTCTTCTTC
1 TCT-TTCTTCTTC
19091523 AAAGTCTAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
12 1 0.03
13 12 0.39
14 9 0.29
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTTCTTCTTCC
Found at i:19091506 original size:10 final size:10
Alignment explanation
Indices: 19091491--19091519 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19091481 TCTTCCTCTT
19091491 TTCTTCTTCC
1 TTCTTCTTCC
19091501 TTCTTCTTCC
1 TTCTTCTTCC
19091511 TTCTTCTTC
1 TTCTTCTTC
19091520 TTCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:19091633 original size:9 final size:9
Alignment explanation
Indices: 19091594--19091634 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
19091584 CGCCGTCGAC
*
19091594 TCCTCCTCT
1 TCCTCTTCT
19091603 T-CTCTTCT
1 TCCTCTTCT
19091611 TCCT-TTCT
1 TCCTCTTCT
19091619 TCCTCTTCT
1 TCCTCTTCT
*
19091628 TTCTCTT
1 TCCTCTT
19091635 TTCTTCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 15 0.54
9 13 0.46
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (9 bp):
TCCTCTTCT
Found at i:19091637 original size:20 final size:22
Alignment explanation
Indices: 19091597--19091640 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
19091587 CGTCGACTCC
19091597 TCCTCTTCTCTTCTTCCTTTCT
1 TCCTCTTCTCTTCTTCCTTTCT
*
19091619 TCCTCTTCT-TTC-TCTTTTCT
1 TCCTCTTCTCTTCTTCCTTTCT
19091639 TC
1 TC
19091641 TTTTCGAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 3 0.14
22 9 0.43
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (22 bp):
TCCTCTTCTCTTCTTCCTTTCT
Found at i:19091927 original size:29 final size:29
Alignment explanation
Indices: 19091894--19092010 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
19091884 TGTAATTTTT
*
19091894 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
19091923 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
19091953 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
19091982 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
19092011 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:19091949 original size:30 final size:30
Alignment explanation
Indices: 19091909--19092010 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
19091899 ATTTAGGATT
*
19091909 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
19091939 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
19091969 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
19091999 AAAATGCAATTT
1 AAAATGAAATTT
19092011 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:19092031 original size:14 final size:15
Alignment explanation
Indices: 19092006--19092040 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
19091996 GTCAAAATGC
*
19092006 AATTTTTATTTTTTA
1 AATTTTTATTTTTGA
19092021 AATTTTT-TTTTTGA
1 AATTTTTATTTTTGA
19092035 AATTTT
1 AATTTT
19092041 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
AATTTTTATTTTTGA
Done.