Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 119 of 325
Found at i:38262835 original size:19 final size:19
Alignment explanation
Indices: 38262794--38262839 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
38262784 GTAAGTGATT
* *
38262794 AAAAAAATTAAAAAAATCG
1 AAAAAAATAAAAAAAATCA
38262813 AAAAAAATAAAAAAAAGT-A
1 AAAAAAATAAAAAAAA-TCA
38262832 AAAAAAAT
1 AAAAAAAT
38262840 TCGTGGATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (19 bp):
AAAAAAATAAAAAAAATCA
Found at i:38263829 original size:6 final size:6
Alignment explanation
Indices: 38263790--38263887 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
38263780 TAATGAATTC
** * *
38263790 GAAAAA GAAAGT GAAGAA G-AAAA GAAAACA -AAAAA GAAAAA GAAAAC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
** * * *
38263837 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
38263888 TATGAAAATG
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
5 5 0.07
6 51 0.75
7 8 0.12
8 4 0.06
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:38263883 original size:13 final size:12
Alignment explanation
Indices: 38263790--38263886 Score: 74
Period size: 12 Copynumber: 7.9 Consensus size: 12
38263780 TAATGAATTC
*
38263790 GAAAAAGAAAGT
1 GAAAAAGAAAAT
*
38263802 GAAGAAGAAAA-
1 GAAAAAGAAAAT
*
38263813 GAAAACA-AAAAA
1 GAAAA-AGAAAAT
*
38263825 GAAAAAGAAAAC
1 GAAAAAGAAAAT
* *
38263837 GAAAAAGTGAGA-
1 GAAAAAG-AAAAT
38263849 GAAAAAGAAAAT
1 GAAAAAGAAAAT
38263861 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAA-T
38263876 GAAAAAGAAAA
1 GAAAAAGAAAA
38263887 ATATGAAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
11 11 0.16
12 34 0.49
13 12 0.17
14 10 0.14
15 2 0.03
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (12 bp):
GAAAAAGAAAAT
Found at i:38263930 original size:17 final size:18
Alignment explanation
Indices: 38263905--38263944 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38263895 ATGAGATTTC
38263905 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
* *
38263922 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
38263940 AAAAA
1 AAAAA
38263945 GAAAGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:38263936 original size:18 final size:17
Alignment explanation
Indices: 38263905--38263954 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
38263895 ATGAGATTTC
38263905 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
* *
38263922 AAAAGCAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
38263940 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
38263955 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:38263960 original size:36 final size:34
Alignment explanation
Indices: 38263891--38263986 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 34
38263881 AGAAAAATAT
* *
38263891 GAAAATGAGATTTCAAAAACAAAAGAGAG-TGAAAA
1 GAAAATGAGA-TTGAAAAA-GAAAGAGAGTTGAAAA
38263926 GCAAAATGAGATTGAAAAAGAAAGAGAGTTTGAAAA
1 G-AAAATGAGATTGAAAAAGAAAGAGAG-TTGAAAA
* *
38263962 GAAAACGAG--TGAAGAAG-AAGAGAGT
1 GAAAATGAGATTGAAAAAGAAAGAGAGT
38263987 GCTCAAACAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.02
32 7 0.13
33 7 0.13
34 8 0.15
35 15 0.28
36 16 0.30
ACGTcount: A:0.56, C:0.04, G:0.26, T:0.14
Consensus pattern (34 bp):
GAAAATGAGATTGAAAAAGAAAGAGAGTTGAAAA
Found at i:38263963 original size:17 final size:16
Alignment explanation
Indices: 38263912--38263986 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 16
38263902 TTCAAAAACA
38263912 AAAGAGAG-TGAAAAG
1 AAAGAGAGTTGAAAAG
38263927 CAAA-ATGAGATTGAAAAAG
1 -AAAGA-GAG-TTG-AAAAG
38263946 AAAGAGAGTTTGAAAAG
1 AAAGAGAG-TTGAAAAG
38263963 AAA-ACGAG-TGAAGAAG
1 AAAGA-GAGTTGAA-AAG
38263979 -AAGAGAGT
1 AAAGAGAGT
38263987 GCTCAAACAC
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
15 10 0.20
16 11 0.22
17 11 0.22
18 11 0.22
19 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.12
Consensus pattern (16 bp):
AAAGAGAGTTGAAAAG
Found at i:38265254 original size:20 final size:21
Alignment explanation
Indices: 38265219--38265257 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38265209 CAGCTCGTTG
38265219 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
38265240 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
38265258 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:38265665 original size:13 final size:13
Alignment explanation
Indices: 38265647--38265672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38265637 TGTGTCCTAA
38265647 TATGAATTAAATT
1 TATGAATTAAATT
38265660 TATGAATTAAATT
1 TATGAATTAAATT
38265673 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:38278877 original size:459 final size:457
Alignment explanation
Indices: 38278218--38279049 Score: 1312
Period size: 459 Copynumber: 1.8 Consensus size: 457
38278208 AATTAGGTTT
** **
38278218 TTTTTTTAGTTTTCCTAATAGGGTTAGGAAAAAAGATAGAAGGCTATAATAAGGCTTGGCCGGCC
1 TTTTTTTAGTTTTCCTAATAGGACTAGGAAAAAAGATAGAAGGCTATAATAAGGCTTGGCCAACC
38278283 ACCTTATACATAATTACATTGAACAACACATTGAAATCAGATTTTTTATTCAGTGAAAAATTCTC
66 ACCTTATACATAATTACATTGAACAACACATTGAAATCAGATTTTTTATTCAGTGAAAAATTCTC
* * *
38278348 TTTGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTTTTTTAGAAGTAGTTTTAACAATCTTTTTTA
131 TTTGAG-TTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGAAGTTTTAACAATCTTTTTGA
* * *
38278413 TTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGTCCTACATTGGAGGGGAGATTAGAGCTGT
195 TTGTGGGAGCCATCTTCAGCCTTCTTCTTACCATTGTCCTACATTCGAGGGGAGATTAGAGCCGT
38278478 TTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGGACTTTTCTTTA-TTTTCTTA
260 TTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGGACTTTTCTTTATTTTTCTTA
* * *
38278542 CTGTTTATTCCTCTTTAATTTTTCTGCTTGTGCTGATTCATTGATTAAATTGTTTTAATCTCTCT
325 CTATTTATTACTCTTTAAATTTTCTGCTTGTGCTGATTCATTGATTAAATTGTTTTAATCTCTCT
38278607 TGTTGCGTTTCTAGTCACCCTTTAAAGTCCTTGGTCGAATTTCCCCTTTAAAGTAAAAAAAATTT
390 TGTTGCGTTTCTAGTCACCCTTTAAAGTCCTTGGTCGAATTTCCCCTTTAAAGTAAAAAAAATTT
38278672 AGG
455 AGG
* * * * *
38278675 TTTTTTTAGTTTTCCTATTAGGACTAGGAAAATAGTTAGAAGGCCTATATGTATGGCTTGGCCAA
1 TTTTTTTAGTTTTCCTAATAGGACTAGGAAAAAAGATAGAAGG-CTATA-ATAAGGCTTGGCCAA
* * * * *
38278740 CCACCCTTATACA-CATTACACTTGAAGAATACATTGAAATCAGATTTGTTTTGTTGAGTG-AAA
64 CCA-CCTTATACATAATTACA-TTGAACAACACATTGAAATCAGA-TT-TTTTATTCAGTGAAAA
*
38278803 ATTCTCTTTGAG-TTCTCCAAGAATTTTCTCTTGAGTTTTCTTTAGAAGAAGTTTTAACAATCTT
125 ATTCTCTTTGAGTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGAAGTTTTAACAATCTT
*
38278867 TTTGATTGTGGGAGTCATCTTCAGCCTTCTTCTTACCATTGTCCTACATTCGAGGGGAGATTAGA
190 TTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTACCATTGTCCTACATTCGAGGGGAGATTAGA
*
38278932 GCCGTTTGAAGGGAGTTGTGAAATCTTTTTCGATTTCAAGGCTTCTTAGGACTTTTCTTTATTTT
255 GCCGTTTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGGACTTTTCTTTATTTT
** *
38278997 TCTTGTTATTTATTACTCTTTAAATTTTCTGCTTGTGCTGATTCATTGTTTAA
320 TCTTACTATTTATTACTCTTTAAATTTTCTGCTTGTGCTGATTCATTGATTAA
38279050 TCTCTTTTGT
Statistics
Matches: 339, Mismatches: 29, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
457 38 0.11
458 5 0.01
459 189 0.56
460 80 0.24
461 17 0.05
462 10 0.03
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (457 bp):
TTTTTTTAGTTTTCCTAATAGGACTAGGAAAAAAGATAGAAGGCTATAATAAGGCTTGGCCAACC
ACCTTATACATAATTACATTGAACAACACATTGAAATCAGATTTTTTATTCAGTGAAAAATTCTC
TTTGAGTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGAAGTTTTAACAATCTTTTTGAT
TGTGGGAGCCATCTTCAGCCTTCTTCTTACCATTGTCCTACATTCGAGGGGAGATTAGAGCCGTT
TGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGGACTTTTCTTTATTTTTCTTAC
TATTTATTACTCTTTAAATTTTCTGCTTGTGCTGATTCATTGATTAAATTGTTTTAATCTCTCTT
GTTGCGTTTCTAGTCACCCTTTAAAGTCCTTGGTCGAATTTCCCCTTTAAAGTAAAAAAAATTTA
GG
Found at i:38279357 original size:78 final size:78
Alignment explanation
Indices: 38279235--38279383 Score: 228
Period size: 78 Copynumber: 1.9 Consensus size: 78
38279225 TTTTGATATG
* **
38279235 AGTCACAAAGGCCCAACTCAAGCTCAAGAATGTGATGGGCTCAAATTACCACAAGGCCCAATAAC
1 AGTCACAAAGGCCCAACTCAAGCTCAAAAACATGATGGGCTCAAATTACCACAAGGCCCAATAAC
38279300 GAGATCTGATACA
66 GAGATCTGATACA
* * *
38279313 AGTCATAAAGGCCCAA-TCCAAGTTCAAAAACATGATGGGCTCAAATTGCCACAAGGCCCAATAA
1 AGTCACAAAGGCCCAACT-CAAGCTCAAAAACATGATGGGCTCAAATTACCACAAGGCCCAATAA
38279377 CGAGATC
65 CGAGATC
38279384 AAAGGCCCGA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
77 1 0.02
78 63 0.98
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (78 bp):
AGTCACAAAGGCCCAACTCAAGCTCAAAAACATGATGGGCTCAAATTACCACAAGGCCCAATAAC
GAGATCTGATACA
Found at i:38287595 original size:19 final size:19
Alignment explanation
Indices: 38287571--38287607 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
38287561 AAAATGATAA
38287571 AAGAAAATGAGAAA-AAGAC
1 AAGAAAA-GAGAAAGAAGAC
38287590 AAGAAAAGAGAAAGAAGA
1 AAGAAAAGAGAAAGAAGA
38287608 AAAAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.70, C:0.03, G:0.24, T:0.03
Consensus pattern (19 bp):
AAGAAAAGAGAAAGAAGAC
Found at i:38287608 original size:33 final size:32
Alignment explanation
Indices: 38287531--38287617 Score: 80
Period size: 32 Copynumber: 2.8 Consensus size: 32
38287521 ATGAAAATAC
**
38287531 AAAAGA-AAAG-A-AAAATGAGAAAAAGAGGG
1 AAAAGAGAAAGAAGAAAATGAGAAAAAGAAAG
38287560 AAAA-ATGATAA-AAGAAAATGAGAAAAAGACAAG
1 AAAAGA-GA-AAGAAGAAAATGAGAAAAAGA-AAG
38287593 AAAAGAGAAAGAAGAAAA--AGAAAAA
1 AAAAGAGAAAGAAGAAAATGAGAAAAA
38287618 TATTGTGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
28 1 0.02
29 4 0.08
30 1 0.02
31 10 0.21
32 17 0.35
33 14 0.29
34 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (32 bp):
AAAAGAGAAAGAAGAAAATGAGAAAAAGAAAG
Found at i:38288707 original size:13 final size:13
Alignment explanation
Indices: 38288681--38288730 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
38288671 ATAGAAGATA
*
38288681 TTATTTTATTTTAT
1 TTATTTT-TATTAT
*
38288695 TTAGTTTTATTAT
1 TTATTTTTATTAT
38288708 TTATTTTTATT-T
1 TTATTTTTATTAT
38288720 TTATTTTTATT
1 TTATTTTTATT
38288731 TTATTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 12 0.36
13 15 0.45
14 6 0.18
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (13 bp):
TTATTTTTATTAT
Found at i:38288708 original size:23 final size:22
Alignment explanation
Indices: 38288679--38288735 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
38288669 AAATAGAAGA
38288679 TATTATTTTATTTTATTTAGTT-T
1 TATTATTTTATTTTATTT--TTAT
38288702 TATTA-TTTATTTTTATTTTTAT
1 TATTATTTTA-TTTTATTTTTAT
*
38288724 TTTTATTTTATT
1 TATTATTTTATT
38288736 AATTTAGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 2 0.07
22 11 0.37
23 17 0.57
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (22 bp):
TATTATTTTATTTTATTTTTAT
Found at i:38288735 original size:5 final size:6
Alignment explanation
Indices: 38288694--38288732 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
38288684 TTTTATTTTA
*
38288694 TTTAGT TTTATT ATTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT -TTTATT TTTATT TTTATT TTTATT TT
38288733 ATTAATTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:38289163 original size:20 final size:20
Alignment explanation
Indices: 38289138--38289177 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38289128 ATCGGGATAG
38289138 ACCAATCATCCCTTAAGGTT
1 ACCAATCATCCCTTAAGGTT
38289158 ACCAATCATCCCTTAAGGTT
1 ACCAATCATCCCTTAAGGTT
38289178 GAATTCGATT
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:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (20 bp):
ACCAATCATCCCTTAAGGTT
Found at i:38291130 original size:49 final size:50
Alignment explanation
Indices: 38291063--38291309 Score: 309
Period size: 49 Copynumber: 5.0 Consensus size: 50
38291053 AGCTATTGTG
* *
38291063 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* * * * *
38291113 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-AGTT
* * * * *
38291163 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* * * *
38291213 AGGTCACGTGTGTAGTACTAAGAGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
* *
38291263 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAG
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
38291310 CTTCGGCTAC
Statistics
Matches: 168, Mismatches: 27, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
49 83 0.49
50 47 0.28
51 38 0.23
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
Found at i:38291200 original size:28 final size:28
Alignment explanation
Indices: 38291168--38291251 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
38291158 AACTTCGATC
38291168 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
38291196 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
*
38291218 ACGTGTGTAGTACTAAGAGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
38291246 ACGTGT
1 ACGTGT
38291252 ACCGGATAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 16
0.64 0.11 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.20
23 2 0.05
24 2 0.05
25 6 0.15
26 3 0.07
27 2 0.05
28 14 0.34
29 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:38299223 original size:30 final size:30
Alignment explanation
Indices: 38299189--38299285 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
38299179 TAAACTAAAA
*
38299189 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
38299219 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
38299249 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
38299279 TGAGCTA
1 TGAGCTA
38299286 GGAGTAAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
30 48 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:38302036 original size:14 final size:14
Alignment explanation
Indices: 38302014--38302061 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
38302004 ACCTAAACCG
* *
38302014 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
38302028 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
38302042 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
38302056 ACCATT
1 ACCATT
38302062 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:38303348 original size:6 final size:6
Alignment explanation
Indices: 38303334--38303378 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
38303324 TTTCTTGTTA
*
38303334 TTTCAT TTTCTT TTTC-- -TTCTT TTTCTT TTTCTT TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
38303378 T
1 T
38303379 GTTTTCTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
3 3 0.09
5 5 0.15
6 26 0.76
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:38303369 original size:21 final size:21
Alignment explanation
Indices: 38303323--38303389 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
38303313 CTTGCCTCTC
*
38303323 TTTTCTTGTTATTTCATTTTCT
1 TTTTCTT-TTATTTCTTTTTCT
38303345 TTTTCTTCTT-TTTCTTTTTCT
1 TTTTCTT-TTATTTCTTTTTCT
* *
38303366 TTTTCTTTTCTTTGTTTTCTCT
1 TTTTCTTTTATTTCTTTT-TCT
38303388 TT
1 TT
38303390 ACAAGAATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.05
21 24 0.60
22 14 0.35
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTATTTCTTTTTCT
Found at i:38303383 original size:15 final size:15
Alignment explanation
Indices: 38303321--38303389 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 15
38303311 CTCTTGCCTC
38303321 TCTTTTC-TTGTTATT
1 TCTTTTCTTTGTT-TT
*
38303336 TCATTTTCTTT-TTCT
1 TC-TTTTCTTTGTTTT
*
38303351 TCTTTTTCTTTTTCTTTT
1 TC-TTTTC--TTTGTTTT
38303369 TCTTTTCTTTGTTTT
1 TCTTTTCTTTGTTTT
38303384 CTCTTT
1 -TCTTT
38303390 ACAAGAATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
15 17 0.39
16 12 0.27
17 10 0.23
18 5 0.11
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (15 bp):
TCTTTTCTTTGTTTT
Found at i:38312300 original size:22 final size:22
Alignment explanation
Indices: 38312272--38312313 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
38312262 CCTTTTTGAA
38312272 CCATTACCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
38312294 CCATTACCATTTCGTACCAA
1 CCATTACCATTTCGTACCAA
38312314 TTCCCAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:38312807 original size:21 final size:19
Alignment explanation
Indices: 38312771--38312809 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
38312761 AAGAAATTCG
*
38312771 AAAAAAAAATTAAAAAAAT
1 AAAAAAAAATGAAAAAAAT
38312790 AAAAAAAAAGTGACAAAAAA
1 AAAAAAAAA-TGA-AAAAAA
38312810 ATCGAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (19 bp):
AAAAAAAAATGAAAAAAAT
Found at i:38321512 original size:20 final size:20
Alignment explanation
Indices: 38321487--38321536 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
38321477 AGCTAATTTC
38321487 AGCTCAATTCCAGCTCCCTT
1 AGCTCAATTCCAGCTCCCTT
38321507 AGCTCAATTCCAGCTCCCTT
1 AGCTCAATTCCAGCTCCCTT
38321527 AGCTCAATTC
1 AGCTCAATTC
38321537 GACTTCAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.38, G:0.10, T:0.30
Consensus pattern (20 bp):
AGCTCAATTCCAGCTCCCTT
Found at i:38324598 original size:10 final size:10
Alignment explanation
Indices: 38324583--38324644 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
38324573 TTTGAACCAT
*
38324583 TACCAATTCG
1 TACCAATTCA
*
38324593 TACCAAATACCA
1 TACC-AAT-TCA
*
38324605 TACCATTTCA
1 TACCAATTCA
38324615 TACCAATTCCA
1 TACCAATT-CA
* *
38324626 TACCATTTCG
1 TACCAATTCA
38324636 TACCAATTC
1 TACCAATTC
38324645 CCAATTCCCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:38324628 original size:21 final size:21
Alignment explanation
Indices: 38324583--38324645 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38324573 TTTGAACCAT
* *
38324583 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
38324605 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
38324626 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
38324646 CAATTCCCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38326904 original size:30 final size:30
Alignment explanation
Indices: 38326870--38326966 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
38326860 TAAACTAAAA
*
38326870 TGAGCTAAGCTTTAGCTCGTGAGATAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGATAAAGT
* * * * * * * *
38326900 TGAGCTGAGATTAAACTCCTAAGCTGAATT
1 TGAGCTAAGATTTAGCTCGTGAGATAAAGT
* *
38326930 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGAT-AAAGT
38326960 TGAGCTA
1 TGAGCTA
38326967 GGAGTAAGCT
Statistics
Matches: 48, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
30 46 0.96
31 2 0.04
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGATAAAGT
Found at i:38328286 original size:9 final size:9
Alignment explanation
Indices: 38328272--38328299 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
38328262 TTTCCCAATT
38328272 TCTTCTCCA
1 TCTTCTCCA
38328281 TCTTCTCCA
1 TCTTCTCCA
38328290 TCTTCTCCA
1 TCTTCTCCA
38328299 T
1 T
38328300 AAATAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.43, G:0.00, T:0.46
Consensus pattern (9 bp):
TCTTCTCCA
Found at i:38331473 original size:20 final size:19
Alignment explanation
Indices: 38331440--38331490 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
38331430 ATAGAAGATA
*
38331440 TTATTTTATTTTATTTAGTT
1 TTATTTT-TATTATTTAGTT
*
38331460 TTATTATTTATTATTTATTT
1 TTATT-TTTATTATTTAGTT
38331480 TTATTTTTATT
1 TTATTTTTATT
38331491 TTATTAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 20 0.71
21 2 0.07
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTATTTTTATTATTTAGTT
Found at i:38331484 original size:6 final size:6
Alignment explanation
Indices: 38331453--38331492 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
38331443 TTTTATTTTA
*
38331453 TTTAGT TTTATT ATTTATT ATTTATT TTTATT TTTATT TT
1 TTTATT TTTATT -TTTATT -TTTATT TTTATT TTTATT TT
38331493 ATTAATTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 19 0.59
7 13 0.41
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:38333354 original size:20 final size:19
Alignment explanation
Indices: 38333326--38333367 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
38333316 GTTTCAAGGA
* *
38333326 TTTTTTTTAATTTAATATAG
1 TTTTATTTAAATTAATA-AG
38333346 TTTTATTTAAATTAATAAG
1 TTTTATTTAAATTAATAAG
38333365 TTT
1 TTT
38333368 GTATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTATTTAAATTAATAAG
Found at i:38335600 original size:20 final size:19
Alignment explanation
Indices: 38335577--38335641 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
38335567 AAGCTCAAAC
38335577 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
38335597 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
38335617 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
38335637 GAGCT
1 GAGCT
38335642 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:38339224 original size:15 final size:15
Alignment explanation
Indices: 38339204--38339251 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
38339194 TCAAAGATGG
38339204 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
38339219 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
38339233 GTTTATGGATATAAA
1 GTTTATGGATATGAA
38339248 GTTT
1 GTTT
38339252 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:38339238 original size:14 final size:14
Alignment explanation
Indices: 38339198--38339241 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38339188 AAGGATTCAA
38339198 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
38339212 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
38339227 AGATGGGTTTATGG
1 AGATGGGTTTATGG
38339241 A
1 A
38339242 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:38339267 original size:29 final size:29
Alignment explanation
Indices: 38339198--38339257 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
38339188 AAGGATTCAA
*
38339198 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
38339227 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
38339256 AG
1 AG
38339258 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:38340275 original size:14 final size:14
Alignment explanation
Indices: 38340233--38340277 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
38340223 TTAAAGAAGC
38340233 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
38340247 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
38340260 AACTCATTTAATTA
1 AACTCATTAAATTA
38340274 AACT
1 AACT
38340278 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:38351006 original size:12 final size:12
Alignment explanation
Indices: 38350964--38351005 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
38350954 AGATTTTGTT
*
38350964 TTTTTTTTCAAA
1 TTTTTTTTCGAA
38350976 TTTTTTTT-GAA
1 TTTTTTTTCGAA
*
38350987 CTTTTTTTCG-A
1 TTTTTTTTCGAA
38350998 TTTTTTTT
1 TTTTTTTT
38351006 TTGAAACTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:38351248 original size:15 final size:15
Alignment explanation
Indices: 38351228--38351275 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
38351218 TCAAAGATGG
38351228 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
38351243 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
38351257 GTTTATGGATATAAA
1 GTTTATGGATATGAA
38351272 GTTT
1 GTTT
38351276 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:38351262 original size:14 final size:14
Alignment explanation
Indices: 38351222--38351265 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38351212 AAGGATTCAA
38351222 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
38351236 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
38351251 AGATGGGTTTATGG
1 AGATGGGTTTATGG
38351265 A
1 A
38351266 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:38351291 original size:29 final size:29
Alignment explanation
Indices: 38351222--38351281 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
38351212 AAGGATTCAA
*
38351222 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
38351251 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
38351280 AG
1 AG
38351282 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:38352298 original size:14 final size:14
Alignment explanation
Indices: 38352256--38352300 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
38352246 TTAAAGAAGC
38352256 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
38352270 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
38352283 AACTCATTTAATTA
1 AACTCATTAAATTA
38352297 AACT
1 AACT
38352301 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:38353858 original size:100 final size:100
Alignment explanation
Indices: 38353685--38353864 Score: 290
Period size: 100 Copynumber: 1.8 Consensus size: 100
38353675 TATCTGGTAC
* * *
38353685 GCATAGTAGCCTGTACTTAGTACTACACATGCGACCAATAATCTGGTACATGTAGTAGCTTGAAC
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCCTGAAC
*
38353750 TTAGTACTATACACGCAATCACAGTTTTCGAGTAT
66 TTAGTACTACACACGCAATCACAGTTTTCGAGTAT
* *
38353785 GCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCTGGTACACGTAGTAGCCT-ACA
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCCTGA-A
38353849 CTTAGTACTACACACG
65 CTTAGTACTACACACG
38353865 TGACCTCACA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
99 1 0.01
100 72 0.99
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (100 bp):
GCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCCTGAAC
TTAGTACTACACACGCAATCACAGTTTTCGAGTAT
Found at i:38353868 original size:49 final size:49
Alignment explanation
Indices: 38353675--38353869 Score: 169
Period size: 49 Copynumber: 3.9 Consensus size: 49
38353665 TAGCCAAAGC
* ** *
38353675 TATCTGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCAAT
* ** * * * *
38353724 AATCTGGTACATGTAGTAGCTTGA-ACTTAGTACTATACACGCAATCACAGT
1 TATCTGGTACACATAGTAGCCT-ACACTTAGTACTACACACGCGA-C-CAAT
* ** * * *
38353775 TTTC-GAGTATGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
1 TATCTG-GTACACATAGTAGCCTACACTTAGTACTACACACGCGACCAAT
* *
38353824 TATCTGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACC
1 TATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGCGACC
38353870 TCACAATAGT
Statistics
Matches: 111, Mismatches: 29, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
49 75 0.68
50 4 0.04
51 32 0.29
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCAAT
Found at i:38360243 original size:30 final size:31
Alignment explanation
Indices: 38360209--38360303 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 31
38360199 AGCTCACTCC
*
38360209 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
38360239 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
38360269 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
38360299 TAGCT
1 TAGCT
38360304 AATTTTAGTT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
30 45 0.92
31 4 0.08
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:38364380 original size:43 final size:42
Alignment explanation
Indices: 38364326--38364482 Score: 149
Period size: 44 Copynumber: 3.7 Consensus size: 42
38364316 AACATATACA
*
38364326 ATGCCAATGTCCCAGACGTGGTCTTACATGTAACCAAACATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAAACAAA-ATCG
* * * *
38364369 ATGCCACTGTCCTAGACAG-GGCCTTACATG-AAATC-AGATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAAA-CAAAAT-CG
* * * *
38364411 ATGCCGATGTCCCAGACATGGTCTTACAAGTAAAACAGAAGTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGT-AAACA-AAATCG
*
38364455 ATGCCAATGTCCCAGATGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
38364483 CGATAACACA
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
41 2 0.02
42 28 0.31
43 27 0.30
44 31 0.34
45 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAAACAAAATCG
Found at i:38364428 original size:42 final size:43
Alignment explanation
Indices: 38364326--38364496 Score: 143
Period size: 43 Copynumber: 4.0 Consensus size: 43
38364316 AACATATACA
* * * *
38364326 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAACCAAACATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGAAAACAGATATCG
* * * *
38364369 ATGCCACTGTCCTAGACAGGGCCTTACATGAAATCAGATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGAAAACAGATATCG
* * *
38364411 ATGCCGATGTCCCAGACATGGTCTTACAAGTAAAACAGA-AGTCG
1 ATGCCAATGTCCCAGACAGGGTCTTACATG-AAAACAGATA-TCG
* * * *
38364455 ATGCCAATGTCCCAGA-TGTGGTCTTACACGATAACACATATC
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGAAAACAGATATC
38364497 AGAATCCTAT
Statistics
Matches: 102, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
42 27 0.26
43 46 0.45
44 29 0.28
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGAAAACAGATATCG
Found at i:38369224 original size:27 final size:27
Alignment explanation
Indices: 38369194--38369245 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
38369184 ACAAGTGAGG
38369194 AAAAAGAAAAGGAGAATGAAAAAGAGC
1 AAAAAGAAAAGGAGAATGAAAAAGAGC
* ** *
38369221 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAGGAGAATGAAAAAGA
38369246 AATTGAAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAGGAGAATGAAAAAGAGC
Found at i:38369244 original size:18 final size:16
Alignment explanation
Indices: 38369221--38369263 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
38369211 GAAAAAGAGC
38369221 AAAAAGAGATTGAGAGTG
1 AAAAAGAGATTGA-AG-G
*
38369239 AAAAAGAAATTGAAGG
1 AAAAAGAGATTGAAGG
*
38369255 AAGAAGAGA
1 AAAAAGAGA
38369264 AAATGACTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (16 bp):
AAAAAGAGATTGAAGG
Found at i:38383243 original size:30 final size:30
Alignment explanation
Indices: 38383158--38383254 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
38383148 TAAACTAAAA
* *
38383158 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
38383188 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
38383218 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
38383247 ATGAGCTA
1 -TGAGCTA
38383255 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:38384588 original size:30 final size:30
Alignment explanation
Indices: 38384552--38384612 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
38384542 CATTTAATAC
*
38384552 AAACTTTGGAAAAATTACATTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
38384582 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
38384612 A
1 A
38384613 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:38387760 original size:18 final size:18
Alignment explanation
Indices: 38387739--38387774 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38387729 AGTTATCTAA
38387739 TTTTAAAAGTATATAAAAT
1 TTTTAAAAG-ATATAAAAT
*
38387758 TTTTGAAAGATATAAAA
1 TTTTAAAAGATATAAAA
38387775 CCCTTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TTTTAAAAGATATAAAAT
Found at i:38389869 original size:28 final size:28
Alignment explanation
Indices: 38389837--38389920 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
38389827 AACTTCGATC
38389837 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
38389865 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
38389887 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
38389915 ACGTGT
1 ACGTGT
38389921 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:38389910 original size:50 final size:51
Alignment explanation
Indices: 38389789--38389979 Score: 208
Period size: 50 Copynumber: 3.8 Consensus size: 51
38389779 TGAGGTCGCA
* * * *
38389789 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTAGATCACG
* ** *
38389840 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT-GGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTAGATCACG
* * * *
38389890 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTAGATCACG
** * * *
38389939 CATGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAAC
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAC
38389980 CTTGTCTACA
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
49 39 0.33
50 46 0.39
51 34 0.29
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (51 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTTAGATCACG
Found at i:38406762 original size:31 final size:31
Alignment explanation
Indices: 38406724--38406787 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
38406714 ACAAAAATGA
38406724 TCATCTTCTCCATAAGTTGCTGCTGAATTTT
1 TCATCTTCTCCATAAGTTGCTGCTGAATTTT
38406755 TCATCTTCTCCATAAGTTGCTGCTGAATTTT
1 TCATCTTCTCCATAAGTTGCTGCTGAATTTT
38406786 TC
1 TC
38406788 TCTCCACCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.45
Consensus pattern (31 bp):
TCATCTTCTCCATAAGTTGCTGCTGAATTTT
Found at i:38407689 original size:46 final size:46
Alignment explanation
Indices: 38407639--38407806 Score: 153
Period size: 46 Copynumber: 3.6 Consensus size: 46
38407629 TATTTGGGCA
* *
38407639 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * * * *
38407685 TCCGAACTCGTTAAGTTGAGTTCGAGTTC-GTGA--AATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
38407732 TCCAAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
38407778 CCCGAGCTCGTTGAGTTGAGTCCGTGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
38407807 GCTAATGGGC
Statistics
Matches: 92, Mismatches: 23, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
43 4 0.04
45 3 0.03
46 51 0.55
47 26 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:38407795 original size:93 final size:93
Alignment explanation
Indices: 38407635--38407807 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
38407625 CAGATATTTG
* * * * *
38407635 GGCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTAAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGCCCGAACTCGTTAAG
*
38407700 TTGAGTTCGAGTTCGTGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
* *
38407728 GGCATCCAAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGCCCGAACTCGTTAAG
*
38407793 TTGAGTCCGTGTTCG
66 TTGAGTCCGAGTTCG
38407808 CTAATGGGCG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (93 bp):
GGCATCCAAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGCCCGAACTCGTTAAG
TTGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:38410577 original size:30 final size:30
Alignment explanation
Indices: 38410543--38410639 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
38410533 TAAACTAAAA
38410543 TGAGCTAAGCTTTAGCTCGTGAGCT-AAGGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTGAA-GT
* * * * *
38410573 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTGAAGT
* *
38410603 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCTG-AAGT
38410633 TGAGCTA
1 TGAGCTA
38410640 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
29 2 0.04
30 41 0.80
31 8 0.16
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTGAAGT
Found at i:38411826 original size:15 final size:15
Alignment explanation
Indices: 38411806--38411853 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
38411796 TCAAAGATGG
38411806 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
38411821 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
38411836 -TTTATGGATATAAA
1 GTTTATGGATATGAA
38411850 GTTT
1 GTTT
38411854 TTGTAAGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:38411833 original size:29 final size:29
Alignment explanation
Indices: 38411800--38411858 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
38411790 AAGGATTCAA
* *
38411800 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
38411829 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
38411858 A
1 A
38411859 AGTTTGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:38412576 original size:14 final size:14
Alignment explanation
Indices: 38412554--38412598 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
38412544 TTAAAGAAGC
38412554 AACTCATTAAATTA
1 AACTCATTAAATTA
*
38412568 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
38412581 AACTCATTTAATTA
1 AACTCATTAAATTA
38412595 AACT
1 AACT
38412599 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:38412636 original size:22 final size:22
Alignment explanation
Indices: 38412610--38412679 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
38412600 AGATGAGTTG
38412610 TATTAATGACCAGCAACTCATT
1 TATTAATGACCAGCAACTCATT
* *
38412632 TATTAA--ACTA--AGA-TGAGTT
1 TATTAATGACCAGCA-ACTCA-TT
38412651 GTATTAATGACCAGCAACTCATT
1 -TATTAATGACCAGCAACTCATT
38412674 TATTAA
1 TATTAA
38412680 ACTAAGAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 9 0.25
22 15 0.42
23 3 0.08
24 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
TATTAATGACCAGCAACTCATT
Found at i:38412642 original size:42 final size:42
Alignment explanation
Indices: 38412581--38412686 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
38412571 TCATTAAATA
38412581 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
38412624 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
38412666 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
38412687 GGCTTAAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 54 0.86
43 9 0.14
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:38417320 original size:21 final size:21
Alignment explanation
Indices: 38417271--38417321 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
38417261 TTGCATTCGA
* *
38417271 ATCTTGACCACTTTCAAGATC
1 ATCTTGATCACTTTCAACATC
38417292 A-CTATGATCA-TTTACAACATC
1 ATCT-TGATCACTTT-CAACATC
38417313 ATCTTGATC
1 ATCTTGATC
38417322 TCTTCGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 5 0.20
21 18 0.72
22 2 0.08
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (21 bp):
ATCTTGATCACTTTCAACATC
Found at i:38418203 original size:15 final size:15
Alignment explanation
Indices: 38418183--38418230 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
38418173 TCAAAGATGG
38418183 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
38418198 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
38418213 -TTTATGGATATAAA
1 GTTTATGGATATGAA
38418227 GTTT
1 GTTT
38418231 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:38418210 original size:29 final size:29
Alignment explanation
Indices: 38418177--38418236 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
38418167 AAGGATTCAA
* *
38418177 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
38418206 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
38418235 AG
1 AG
38418237 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:38418953 original size:14 final size:13
Alignment explanation
Indices: 38418931--38418975 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
38418921 TTAAAGAAGC
38418931 AACTCATTAAATTA
1 AACTCATT-AATTA
* *
38418945 AATTCATTAAGTA
1 AACTCATTAATTA
38418958 AACTCATTTAATTA
1 AACTCA-TTAATTA
38418972 AACT
1 AACT
38418976 AAGATGAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (13 bp):
AACTCATTAATTA
Found at i:38419019 original size:42 final size:42
Alignment explanation
Indices: 38418958--38419063 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
38418948 TCATTAAGTA
38418958 AACTCATTTAATTAAACTAAGATGAGTTGTATTAACGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAACGACCAGC
*
38419001 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAACGACCAGC
38419043 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
38419064 GGCTTAAATG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 53 0.85
43 9 0.15
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAACGACCAGC
Found at i:38422083 original size:23 final size:22
Alignment explanation
Indices: 38422031--38422083 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
38422021 TCCACGTCTT
*
38422031 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
38422053 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
38422076 TTTCTTTT
1 TTTCTTTT
38422084 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:38428169 original size:21 final size:20
Alignment explanation
Indices: 38428141--38428180 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
38428131 AGATATAATA
38428141 GCCAAGCTTA-ATCATATTCG
1 GCCAAGCTTATAT-ATATTCG
38428161 GCCATAGCTTATATATATTC
1 GCCA-AGCTTATATATATTC
38428181 ACACATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 12 0.67
22 2 0.11
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
GCCAAGCTTATATATATTCG
Found at i:38432105 original size:30 final size:30
Alignment explanation
Indices: 38432034--38432116 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
38432024 CTTTTGTTTC
* *
38432034 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
38432065 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
38432094 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
38432117 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:38432116 original size:18 final size:18
Alignment explanation
Indices: 38432067--38432122 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
38432057 CACTCTCAAA
* *
38432067 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
38432084 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
38432102 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
38432121 TT
1 TT
38432123 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:38432123 original size:12 final size:12
Alignment explanation
Indices: 38432092--38432116 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38432082 TTTTTCAATC
38432092 TCATTTTCTTTT
1 TCATTTTCTTTT
38432104 TCATTTTCTTTT
1 TCATTTTCTTTT
38432116 T
1 T
38432117 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:38432134 original size:12 final size:12
Alignment explanation
Indices: 38432119--38432149 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38432109 TTCTTTTTGC
38432119 TTTTCAAAGGCT
1 TTTTCAAAGGCT
38432131 TTTTCAAAGGCT
1 TTTTCAAAGGCT
38432143 TTTTCAA
1 TTTTCAA
38432150 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:38432207 original size:5 final size:5
Alignment explanation
Indices: 38432197--38432253 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
38432187 CTCTTGCCTC
*
38432197 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
38432244 TCTTT TCTTT
1 TCTTT TCTTT
38432254 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:38432237 original size:15 final size:14
Alignment explanation
Indices: 38432197--38432253 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
38432187 CTCTTGCCTC
*
38432197 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
38432212 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
38432227 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
38432244 TCTTTTCTTT
1 TCTTTTCTTT
38432254 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:38432263 original size:21 final size:20
Alignment explanation
Indices: 38432195--38432264 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
38432185 GCCTCTTGCC
38432195 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
38432218 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
38432238 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
38432258 TCTCTTT
1 TCTCTTT
38432265 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:38433204 original size:13 final size:13
Alignment explanation
Indices: 38433183--38433226 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
38433173 TTCAGATTTT
38433183 TTTTCTTTTCGAAA
1 TTTT-TTTTCGAAA
*
38433197 TTTTTTTT-GAAT
1 TTTTTTTTCGAAA
38433209 TTTTTTTTCG-AA
1 TTTTTTTTCGAAA
38433221 TTTTTT
1 TTTTTT
38433227 GTTTGACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 18 0.67
13 5 0.19
14 4 0.15
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTTTTTCGAAA
Found at i:38433217 original size:25 final size:27
Alignment explanation
Indices: 38433182--38433232 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
38433172 TTTCAGATTT
38433182 TTTTTCTTTTCGAAATTTTT-TTTGAA
1 TTTTTCTTTTCGAAATTTTTGTTTGAA
*
38433208 TTTTT-TTTTCGAATTTTTTGTTTGA
1 TTTTTCTTTTCGAAATTTTTGTTTGA
38433233 CTTGTATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.16, C:0.06, G:0.10, T:0.69
Consensus pattern (27 bp):
TTTTTCTTTTCGAAATTTTTGTTTGAA
Found at i:38435014 original size:30 final size:30
Alignment explanation
Indices: 38434980--38435062 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
38434970 TAAACTAAAA
38434980 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
38435010 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
38435040 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGCTTTAGCTCGTGAG
38435063 TTGAAAGTGA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:38435429 original size:15 final size:15
Alignment explanation
Indices: 38435409--38435456 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
38435399 TCAAACATGG
38435409 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
38435424 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
38435438 GTTTATGGATATAAA
1 GTTTATGGATATGAA
38435453 GTTT
1 GTTT
38435457 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:38435472 original size:29 final size:29
Alignment explanation
Indices: 38435405--38435462 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
38435395 GGATTCAAAC
*
38435405 ATGGGTTTATGGATATGAAGTTTATGTAG
1 ATGGGTTTATGGATATAAAGTTTATGTAG
*
38435434 ATGGGTTTATGGATATAAAGTTTTTGTAG
1 ATGGGTTTATGGATATAAAGTTTATGTAG
38435463 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.29, T:0.43
Consensus pattern (29 bp):
ATGGGTTTATGGATATAAAGTTTATGTAG
Found at i:38441390 original size:53 final size:53
Alignment explanation
Indices: 38441328--38441534 Score: 177
Period size: 53 Copynumber: 3.8 Consensus size: 53
38441318 TTCCTTTTTA
* *
38441328 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
1 AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
* * * * * *
38441381 AACTCACCATTGCCATGCCTTTG-CATAGTTTTACATGGGATCTTTTCCTTATAG
1 AACTTACCATTGCCATGCC-TTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
** * * * * *
38441435 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAT-
1 -AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCC-T-TATG
* * *
38441490 AACTTACCAATT-CCACGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACC-ATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
38441535 AAACCCTAAT
Statistics
Matches: 116, Mismatches: 31, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
53 40 0.34
54 39 0.34
55 33 0.28
56 1 0.01
57 3 0.03
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.39
Consensus pattern (53 bp):
AACTTACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
Found at i:38443322 original size:27 final size:27
Alignment explanation
Indices: 38443285--38443431 Score: 181
Period size: 27 Copynumber: 5.4 Consensus size: 27
38443275 AGCATGGCTG
* *
38443285 CCAGAACAGATA-ATGTGACAGAGTCA
1 CCAGAACAGATATATGTGGCAGAGCCA
*
38443311 CCAGATACAGATA-ATCATGGCAGAGCCA
1 CCAGA-ACAGATATAT-GTGGCAGAGCCA
*
38443339 CCAGAACAGATATATATGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* * * *
38443366 CCAGATCAAATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
38443393 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
*
38443420 CCAGATCAGATA
1 CCAGAACAGATA
38443432 ATTCTGACCT
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.05
27 84 0.80
28 16 0.15
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATATATGTGGCAGAGCCA
Found at i:38443445 original size:27 final size:27
Alignment explanation
Indices: 38443285--38443450 Score: 131
Period size: 27 Copynumber: 6.1 Consensus size: 27
38443275 AGCATGGCTG
* * * *
38443285 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGATCAGATAATTGTGGCATAGCCA
** *
38443311 CCAGATACAGATAATCATGGCAGAGCCA
1 CCAGAT-CAGATAATTGTGGCATAGCCA
* * *
38443339 CCAGAACAGAT-ATATATGGCAGAGCCA
1 CCAGATCAGATAAT-TGTGGCATAGCCA
* *
38443366 CCAGATCAAATATTTGTGGCATAGCCA
1 CCAGATCAGATAATTGTGGCATAGCCA
* *
38443393 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGATCAGATAAT-TGTGGCATAGCCA
* * *
38443420 CCAGATCAGATAATTCTGACCTAGCCA
1 CCAGATCAGATAATTGTGGCATAGCCA
38443447 CCAG
1 CCAG
38443451 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 21, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
26 8 0.07
27 88 0.78
28 17 0.15
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (27 bp):
CCAGATCAGATAATTGTGGCATAGCCA
Found at i:38443445 original size:54 final size:54
Alignment explanation
Indices: 38443285--38443450 Score: 219
Period size: 54 Copynumber: 3.1 Consensus size: 54
38443275 AGCATGGCTG
* * *
38443285 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAA-TCATGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTC-TGGCATAGCCA
* * * *
38443339 CCAGAACAGATATATATGGCAGAGCCACCAGATCAAATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTCTGGCATAGCCA
* *
38443393 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTCTGACCTAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTCTGGCATAGCCA
38443447 CCAG
1 CCAG
38443451 GACGCTTCCT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
54 79 0.81
55 18 0.19
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTCTGGCATAGCCA
Found at i:38445112 original size:26 final size:26
Alignment explanation
Indices: 38445066--38445199 Score: 209
Period size: 26 Copynumber: 5.2 Consensus size: 26
38445056 ACATGAATTC
38445066 TTATCATG-AA-ATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
38445090 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
38445116 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
38445142 TTATCATGAAACATTTATCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
38445168 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
38445194 TTATCA
1 TTATCA
38445200 ATTTGTATCA
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
24 8 0.08
25 2 0.02
26 90 0.90
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:38445135 original size:52 final size:52
Alignment explanation
Indices: 38445066--38445199 Score: 236
Period size: 52 Copynumber: 2.6 Consensus size: 52
38445056 ACATGAATTC
*
38445066 TTATCAT-GAA-ATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
*
38445116 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTATCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
38445168 TTATCATGGAACATTTACCTAACCTATTATCA
1 TTATCATGGAACATTTACCTAACCTATTATCA
38445200 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
50 7 0.09
51 3 0.04
52 70 0.88
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (52 bp):
TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
Found at i:38449118 original size:19 final size:22
Alignment explanation
Indices: 38449079--38449118 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
38449069 AGAAACCCAA
38449079 CCATATCCAACCGTATACACCC
1 CCATATCCAACCGTATACACCC
38449101 CCATA-CCAACC-T-TACACC
1 CCATATCCAACCGTATACACC
38449119 GTGTGGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.47, G:0.03, T:0.17
Consensus pattern (22 bp):
CCATATCCAACCGTATACACCC
Found at i:38449217 original size:27 final size:28
Alignment explanation
Indices: 38449180--38449518 Score: 290
Period size: 27 Copynumber: 12.1 Consensus size: 28
38449170 AGCATGGCTG
* *
38449180 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
38449206 CCAGATACAGATA-ATCATGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
38449234 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
38449261 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
38449288 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* ***
38449315 CCAGAT-CAGATATATGTGATCCCAAGAATAGA
1 CCAGATACAGATATATGTG---GC-AG-AGCCA
*** * * * *
38449347 TTGGATCCAGAACAGATAATGTGACAGAGTCA
1 CCAGATACAG---ATAT-ATGTGGCAGAGCCA
*
38449379 CCAGATACAGATA-ATCATGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
38449407 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* * *
38449434 CCAGAT-CAGATATTTGGGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
38449461 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
38449488 CCAGAT-CAGATA-ATTGTGGCATAGCCA
1 CCAGATACAGATATA-TGTGGCAGAGCCA
38449515 CCAG
1 CCAG
38449519 GACGCTTCCT
Statistics
Matches: 255, Mismatches: 36, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
26 6 0.02
27 185 0.73
28 32 0.13
29 2 0.01
30 1 0.00
31 2 0.01
32 13 0.05
33 5 0.02
34 1 0.00
36 3 0.01
37 5 0.02
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:38449469 original size:173 final size:173
Alignment explanation
Indices: 38449180--38449499 Score: 631
Period size: 173 Copynumber: 1.8 Consensus size: 173
38449170 AGCATGGCTG
38449180 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCATGGCAGAGCCACCAGAACAGAT
1 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCATGGCAGAGCCACCAGAACAGAT
*
38449245 ATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCACCAGAACAGATATATGTGGCAG
66 ATATGTGGCAGAGCCACCAGATCAGATATTTGGGGCATAGCCACCAGAACAGATATATGTGGCAG
38449310 AGCCACCAGATCAGATATATGTGATCCCAAGAATAGATTGGAT
131 AGCCACCAGATCAGATATATGTGATCCCAAGAATAGATTGGAT
38449353 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCATGGCAGAGCCACCAGAACAGAT
1 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCATGGCAGAGCCACCAGAACAGAT
38449418 ATATGTGGCAGAGCCACCAGATCAGATATTTGGGGCATAGCCACCAGAACAGATATATGTGGCAG
66 ATATGTGGCAGAGCCACCAGATCAGATATTTGGGGCATAGCCACCAGAACAGATATATGTGGCAG
38449483 AGCCACCAGATCAGATA
131 AGCCACCAGATCAGATA
38449500 ATTGTGGCAT
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 146 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (173 bp):
CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCATGGCAGAGCCACCAGAACAGAT
ATATGTGGCAGAGCCACCAGATCAGATATTTGGGGCATAGCCACCAGAACAGATATATGTGGCAG
AGCCACCAGATCAGATATATGTGATCCCAAGAATAGATTGGAT
Found at i:38451176 original size:26 final size:26
Alignment explanation
Indices: 38451140--38451275 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
38451130 CATGATATTC
38451140 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
38451166 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
38451192 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
38451218 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
38451244 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
38451270 TTATCA
1 TTATCA
38451276 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:38464749 original size:32 final size:32
Alignment explanation
Indices: 38464713--38464776 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
38464703 ACACATCTCC
38464713 ACATACTTGAATCGATTATTCATTCATTCAAT
1 ACATACTTGAATCGATTATTCATTCATTCAAT
*
38464745 ACATACTTGAATCGGTTATTCATTCATTCAAT
1 ACATACTTGAATCGATTATTCATTCATTCAAT
38464777 CATGTATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.41
Consensus pattern (32 bp):
ACATACTTGAATCGATTATTCATTCATTCAAT
Found at i:38465687 original size:38 final size:38
Alignment explanation
Indices: 38465644--38465720 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
38465634 AAACATCTTA
38465644 AAATTATAATAAAATTAAGAAATTGAGGCATGGGCTTG
1 AAATTATAATAAAATTAAGAAATTGAGGCATGGGCTTG
38465682 AAATTATAATAAAATTAAGAAATTGAGGCATGGGCTTG
1 AAATTATAATAAAATTAAGAAATTGAGGCATGGGCTTG
38465720 A
1 A
38465721 TAAAACACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (38 bp):
AAATTATAATAAAATTAAGAAATTGAGGCATGGGCTTG
Found at i:38467515 original size:28 final size:28
Alignment explanation
Indices: 38467465--38467521 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
38467455 TAGTTGGGCC
* *
38467465 TGATAGGCCATATGAATGTGATTAGGCT
1 TGATAGGCCATATGAACGAGATTAGGCT
* * *
38467493 TGATGGGCCATGTGAACGAGATTGGGCT
1 TGATAGGCCATATGAACGAGATTAGGCT
38467521 T
1 T
38467522 AAAGGGGCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.33, T:0.30
Consensus pattern (28 bp):
TGATAGGCCATATGAACGAGATTAGGCT
Found at i:38467866 original size:27 final size:27
Alignment explanation
Indices: 38467836--38468228 Score: 392
Period size: 27 Copynumber: 14.7 Consensus size: 27
38467826 TAATAAAGAG
38467836 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* * *
38467863 AAATTA-TCGAAATACCCCCGATTTATA
1 AAATTACT-AAAATACCCTCGATTTGTA
** *
38467890 AAATTACCGAAATACCCTCGATTT-TG
1 AAATTACTAAAATACCCTCGATTTGTA
38467916 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* * *
38467943 AAATTATTGAAATACCCTCGATTTGTG
1 AAATTACTAAAATACCCTCGATTTGTA
* * *
38467970 AAATTACCAAAACACGCC-CAATTTGTA
1 AAATTACTAAAATAC-CCTCGATTTGTA
*
38467997 AAATTA-TCAAAATA-CCTCGA-TTGTG
1 AAATTACT-AAAATACCCTCGATTTGTA
*
38468022 AAATTACTAAAATACCCTCGACTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* * *
38468049 AAATTA-TCGAAATACCCTTGATTTGTG
1 AAATTACT-AAAATACCCTCGATTTGTA
* *
38468076 AAATTA-TCGAAACACCCTCGATTTGTA
1 AAATTACT-AAAATACCCTCGATTTGTA
*
38468103 AAATTACCAAAATACCCTCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
**
38468130 AAATTACCGAAATACCCTCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* ** * *
38468157 ATATTACCGAAACACCCCCGATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* *
38468184 AAATTA-TCAAAATACCCT-TATAGTGTA
1 AAATTACT-AAAATACCCTCGAT-TTGTA
38468211 AAATTACTAAAATACCCT
1 AAATTACTAAAATACCCT
38468229 TGTAGTGTAA
Statistics
Matches: 308, Mismatches: 44, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
25 18 0.06
26 36 0.12
27 251 0.81
28 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGATTTGTA
Found at i:38467996 original size:54 final size:54
Alignment explanation
Indices: 38467836--38468228 Score: 436
Period size: 54 Copynumber: 7.3 Consensus size: 54
38467826 TAATAAAGAG
** * * * * *
38467836 AAATTACTAAAATACCCTCGATTTGTAAAATTATCGAAATACCCCCGATTTATA
1 AAATTACCGAAATACCCTCGATTTGTGAAATTACCAAAATACCCTCGATTTGTA
*
38467890 AAATTACCGAAATACCCTCGATTT-TGAAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTGAAATTACCAAAATACCCTCGATTTGTA
** * *
38467943 AAATTATTGAAATACCCTCGATTTGTGAAATTACCAAAACACGCC-CAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTGAAATTACCAAAATAC-CCTCGATTTGTA
* * * *
38467997 AAATTATCAAAATA-CCTCGA-TTGTGAAATTACTAAAATACCCTCGACTTGTA
1 AAATTACCGAAATACCCTCGATTTGTGAAATTACCAAAATACCCTCGATTTGTA
* * * * *
38468049 AAATTATCGAAATACCCTTGATTTGTGAAATTATCGAAACACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTGAAATTACCAAAATACCCTCGATTTGTA
* * *
38468103 AAATTACCAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTGAAATTACCAAAATACCCTCGATTTGTA
* * * * * * *
38468157 ATATTACCGAAACACCCCCGATTTGTAAAATTATCAAAATACCCT-TATAGTGTA
1 AAATTACCGAAATACCCTCGATTTGTGAAATTACCAAAATACCCTCGAT-TTGTA
**
38468211 AAATTACTAAAATACCCT
1 AAATTACCGAAATACCCT
38468229 TGTAGTGTAA
Statistics
Matches: 288, Mismatches: 45, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
51 2 0.01
52 38 0.13
53 58 0.20
54 188 0.65
55 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
AAATTACCGAAATACCCTCGATTTGTGAAATTACCAAAATACCCTCGATTTGTA
Found at i:38468055 original size:106 final size:106
Alignment explanation
Indices: 38467836--38468228 Score: 475
Period size: 106 Copynumber: 3.7 Consensus size: 106
38467826 TAATAAAGAG
** * *
38467836 AAATTACTAAAATACCCTCGATTTGTAAAATTATCGAAATAC-CCCCGATTTATAAAATTACCGA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTATC-AAA-ACACCCCGATTTGTAAAATTACCAA
*
38467900 AATACCCTCGATTTTGAAATTACTAAAATACCCTCGATTTGTA
64 AATACCCTCGATTGTGAAATTACTAAAATACCCTCGATTTGTA
** * * * *
38467943 AAATTATTGAAATACCCTCGATTTGTGAAATTACCAAAACACGCCCAATTTGTAAAATTATCAAA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTATCAAAACAC-CCCGATTTGTAAAATTACCAAA
*
38468008 ATA-CCTCGATTGTGAAATTACTAAAATACCCTCGACTTGTA
65 ATACCCTCGATTGTGAAATTACTAAAATACCCTCGATTTGTA
* * * *
38468049 AAATTATCGAAATACCCTTGATTTGTGAAATTATCGAAACACCCTCGATTTGTAAAATTACCAAA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTATCAAAACACCC-CGATTTGTAAAATTACCAAA
* **
38468114 ATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTA
65 ATACCCTCGA-TTGTGAAATTACTAAAATACCCTCGATTTGTA
* * * * ** * *
38468157 ATATTACCGAAACACCCCCGATTTGTAAAATTATCAAAATACCCTTATAGTGTAAAATTACTAAA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTATCAAAACACCCCGAT-TTGTAAAATTACCAAA
38468222 ATACCCT
65 ATACCCT
38468229 TGTAGTGTAA
Statistics
Matches: 248, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
105 4 0.02
106 99 0.40
107 60 0.24
108 85 0.34
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (106 bp):
AAATTACCGAAATACCCTCGATTTGTAAAATTATCAAAACACCCCGATTTGTAAAATTACCAAAA
TACCCTCGATTGTGAAATTACTAAAATACCCTCGATTTGTA
Found at i:38468123 original size:81 final size:81
Alignment explanation
Indices: 38467835--38468228 Score: 437
Period size: 81 Copynumber: 4.9 Consensus size: 81
38467825 ATAATAAAGA
* * * *
38467835 GAAATTA-CTAAAATACCCTCGATTTGTAAAATTATCGAAATACCCCCGATTTATAAAATTACCG
1 GAAATTATC-AAAACACCCTCGATTTGTAAAATTATCAAAATACCCTCGATTTGTAAAATTACCG
38467899 AAATACCCTCGATTT-T
65 AAATACCCTCGATTTGT
* ** * *
38467915 GAAATTA-CTAAAATACCCTCGATTTGTAAAATTATTGAAATACCCTCGATTTGTGAAATTACCA
1 GAAATTATC-AAAACACCCTCGATTTGTAAAATTATCAAAATACCCTCGATTTGTAAAATTACCG
* *
38467979 AAACACGCC-CAATTTGT
65 AAATAC-CCTCGATTTGT
* * * * *
38467996 AAAATTATCAAAATA-CCTCGA-TTGTGAAATTA-CTAAAATACCCTCGACTTGTAAAATTATCG
1 GAAATTATCAAAACACCCTCGATTTGTAAAATTATC-AAAATACCCTCGATTTGTAAAATTACCG
*
38468058 AAATACCCTTGATTTGT
65 AAATACCCTCGATTTGT
* *
38468075 GAAATTATCGAAACACCCTCGATTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCGA
1 GAAATTATCAAAACACCCTCGATTTGTAAAATTATCAAAATACCCTCGATTTGTAAAATTACCGA
38468140 AATACCCTCGATTTGT
66 AATACCCTCGATTTGT
* * * * * *
38468156 -AATATTACCGAAACACCCCCGATTTGTAAAATTATCAAAATACCCT-TATAGTGTAAAATTACT
1 GAA-ATTATCAAAACACCCTCGATTTGTAAAATTATCAAAATACCCTCGAT-TTGTAAAATTACC
*
38468219 AAAATACCCT
64 GAAATACCCT
38468229 TGTAGTGTAA
Statistics
Matches: 272, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
78 2 0.01
79 56 0.21
80 85 0.31
81 127 0.47
82 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (81 bp):
GAAATTATCAAAACACCCTCGATTTGTAAAATTATCAAAATACCCTCGATTTGTAAAATTACCGA
AATACCCTCGATTTGT
Found at i:38468229 original size:27 final size:27
Alignment explanation
Indices: 38468192--38468273 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
38468182 TAAAATTATC
*
38468192 AAAATACCCTTATAGTGTAAAATTACT
1 AAAATACCCTTATAGTGTAAAATGACT
*
38468219 AAAATACCCTTGTAGTGTAAAATGACT
1 AAAATACCCTTATAGTGTAAAATGACT
* * * * *
38468246 GACATACCCCTAGAGGGTAAAATGACT
1 AAAATACCCTTATAGTGTAAAATGACT
38468273 A
1 A
38468274 TTTTGCCCTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (27 bp):
AAAATACCCTTATAGTGTAAAATGACT
Found at i:38474471 original size:39 final size:39
Alignment explanation
Indices: 38474428--38474526 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
38474418 CATTTTCACT
* * *
38474428 TTTAAGCATATATCACATTACACATATAATCATACAACA
1 TTTAAGCATATATCACAATACACATATAATAACACAACA
* *
38474467 TTTAAGCATATATCACAATACTCATATAATAACATAACA
1 TTTAAGCATATATCACAATACACATATAATAACACAACA
* *
38474506 TTCAAACATATATCACAATAC
1 TTTAAGCATATATCACAATAC
38474527 TAAAAAACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATAACACAACA
Found at i:38475112 original size:7 final size:7
Alignment explanation
Indices: 38475100--38475147 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
38475090 CACATATTCA
38475100 TAAACCC
1 TAAACCC
*
38475107 TAAACCT
1 TAAACCC
38475114 TAAAACCC
1 T-AAACCC
38475122 TAAACCC
1 TAAACCC
*
38475129 TAAATCC
1 TAAACCC
38475136 TAAAACCC
1 T-AAACCC
38475144 TAAA
1 TAAA
38475148 TTTAGGACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
7 23 0.66
8 12 0.34
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:38475121 original size:15 final size:15
Alignment explanation
Indices: 38475101--38475147 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
38475091 ACATATTCAT
*
38475101 AAACCCTAAACCTTA
1 AAACCCTAAACCCTA
38475116 AAACCCTAAACCCT-
1 AAACCCTAAACCCTA
*
38475130 AAATCCTAAAACCCTA
1 AAACCCT-AAACCCTA
38475146 AA
1 AA
38475148 TTTAGGACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 6 0.21
15 20 0.71
16 2 0.07
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACCCTAAACCCTA
Found at i:38475128 original size:22 final size:22
Alignment explanation
Indices: 38475100--38475147 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
38475090 CACATATTCA
38475100 TAAACCCTAAA-CCTTAAAACCC
1 TAAACCCTAAATCC-TAAAACCC
38475122 TAAACCCTAAATCCTAAAACCC
1 TAAACCCTAAATCCTAAAACCC
38475144 TAAA
1 TAAA
38475148 TTTAGGACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAACCCTAAATCCTAAAACCC
Found at i:38476231 original size:19 final size:22
Alignment explanation
Indices: 38476207--38476246 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
38476197 TATGCTTCAA
38476207 TCGTTT-TTA-AGAG-AAGTTG
1 TCGTTTATTATAGAGTAAGTTG
38476226 TCGTTTATTATAGAGTAAGTT
1 TCGTTTATTATAGAGTAAGTT
38476247 ATAACTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 4 0.22
22 5 0.28
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.45
Consensus pattern (22 bp):
TCGTTTATTATAGAGTAAGTTG
Found at i:38476937 original size:27 final size:28
Alignment explanation
Indices: 38476899--38476974 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
38476889 CAATTTGATG
*
38476899 AAATGACTATTTTGCCCTTATGA-GGTA
1 AAATGACTATTTTGCCCTTATGATAGTA
38476926 AAATGACTATTTTGCCCTTAT-ATAGTA
1 AAATGACTATTTTGCCCTTATGATAGTA
* * *
38476953 AGATGACTGTTTTGCCCCTATG
1 AAATGACTATTTTGCCCTTATG
38476975 TGATGTGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.02
27 42 0.98
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (28 bp):
AAATGACTATTTTGCCCTTATGATAGTA
Found at i:38479050 original size:23 final size:24
Alignment explanation
Indices: 38479000--38479056 Score: 98
Period size: 23 Copynumber: 2.4 Consensus size: 24
38478990 AATTAAAGCT
38479000 TAATCAAAATAGGGGATACTTTTAA
1 TAAT-AAAATAGGGGATACTTTTAA
38479025 TAATAAAATAGGGGATAC-TTTAA
1 TAATAAAATAGGGGATACTTTTAA
38479048 TAATAAAAT
1 TAATAAAAT
38479057 GTACTTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 14 0.44
24 14 0.44
25 4 0.12
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (24 bp):
TAATAAAATAGGGGATACTTTTAA
Found at i:38482388 original size:40 final size:40
Alignment explanation
Indices: 38482328--38482535 Score: 303
Period size: 40 Copynumber: 5.2 Consensus size: 40
38482318 CCTTTGGGGT
*
38482328 TTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
* * *
38482367 TTAGCCCGGTTATAGTAACTCGCACAATTTCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
38482407 TTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* * *
38482447 TTAGCCCGAATATAGTAACTCACACAAATGCCCTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
*
38482487 TTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
38482527 TTAGCCCGG
1 TTAGCCCGG
38482536 TTATCAATTC
Statistics
Matches: 153, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 5 0.03
40 148 0.97
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:38489176 original size:27 final size:27
Alignment explanation
Indices: 38489137--38489209 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
38489127 CAGTTTGATG
* *
38489137 AAATGACTGTTTTGCCGTTATGA-GGTA
1 AAATGACTATTTTGCCCTTAT-ATGGTA
38489164 AAATGACTATTTTGCCCTTATATGGTA
1 AAATGACTATTTTGCCCTTATATGGTA
*
38489191 AGATGACTATTTTGTCCCT
1 AAATGACTATTTTG-CCCT
38489210 ATGTGATGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 1 0.02
27 36 0.88
28 4 0.10
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (27 bp):
AAATGACTATTTTGCCCTTATATGGTA
Found at i:38494101 original size:25 final size:25
Alignment explanation
Indices: 38494054--38494101 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
38494044 TAATAATATG
* * * *
38494054 AAAATGACCGTTTTGCCCTTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38494079 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
38494102 GTTTAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:38494143 original size:17 final size:18
Alignment explanation
Indices: 38494121--38494154 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38494111 TAAATTTAAT
38494121 ACATGGGAT-TTTGATAA
1 ACATGGGATGTTTGATAA
*
38494138 ACATGGTATGTTTGATA
1 ACATGGGATGTTTGATA
38494155 TGCACATGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (18 bp):
ACATGGGATGTTTGATAA
Found at i:38494185 original size:11 final size:11
Alignment explanation
Indices: 38494150--38494204 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
38494140 ATGGTATGTT
38494150 TGATATGCACA
1 TGATATGCACA
* *
38494161 TGACATG--TA
1 TGATATGCACA
38494170 TGATATGCACA
1 TGATATGCACA
*
38494181 TGATATG--TA
1 TGATATGCACA
38494190 TGATATGCACA
1 TGATATGCACA
38494201 TGAT
1 TGAT
38494205 GTATTCATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (11 bp):
TGATATGCACA
Found at i:38494204 original size:20 final size:20
Alignment explanation
Indices: 38494138--38494204 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
38494128 ATTTTGATAA
* *
38494138 ACATGGTATGTTTGATATGC
1 ACATGATATGTATGATATGC
*
38494158 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
38494178 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
38494198 ACATGAT
1 ACATGAT
38494205 GTATTCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:38494281 original size:24 final size:24
Alignment explanation
Indices: 38494254--38494423 Score: 272
Period size: 24 Copynumber: 7.1 Consensus size: 24
38494244 GAGAAAGTGC
*
38494254 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
38494278 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
38494302 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38494326 AAAAAGGGCTTATGCCCCGGTTATT
1 -AAAAGGGCTTATGCCCCAGTTATT
38494351 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
38494375 AAAAGGGATT-TTCCCCATTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
38494398 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
38494421 AAA
1 AAA
38494424 GAGGCTAGGC
Statistics
Matches: 136, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
23 34 0.25
24 79 0.58
25 23 0.17
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:38494350 original size:49 final size:48
Alignment explanation
Indices: 38494254--38494423 Score: 272
Period size: 49 Copynumber: 3.6 Consensus size: 48
38494244 GAGAAAGTGC
*
38494254 AAAAGGGCTTATGCCCTAGTTATTAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
*
38494302 AAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTTATGCCCCGGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT-AAAAGGGCTTATGCCCCAGTTATT
* * *
38494351 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGATT-TTCCCCATTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
38494398 AAAAGGGCTT-TGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
38494424 GAGGCTAGGC
Statistics
Matches: 115, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
46 16 0.14
47 20 0.17
48 32 0.28
49 47 0.41
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
Found at i:38494373 original size:73 final size:71
Alignment explanation
Indices: 38494254--38494423 Score: 270
Period size: 73 Copynumber: 2.4 Consensus size: 71
38494244 GAGAAAGTGC
* *
38494254 AAAAGGGCTTATGCCCTAGTTATTAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCC
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTAAAAGGGATT-TGCCCC
38494319 AGTTATT
65 AGTTATT
* *
38494326 AAAAAGGGCTTATGCCCCGGTTATTAAAAGGGCTTATGCCCCAGTTATTAAAAGGGATTTTCCCC
1 -AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTAAAAGGGATTTGCCCC
*
38494391 ATTTATT
65 AGTTATT
38494398 AAAAGGGCTT-TGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
38494424 GAGGCTAGGC
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
70 15 0.16
71 10 0.11
72 11 0.12
73 55 0.60
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATTAAAAGGGATTTGCCCCA
GTTATT
Found at i:38501656 original size:25 final size:25
Alignment explanation
Indices: 38501627--38501674 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38501617 TAATAATATG
* * *
38501627 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38501652 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
38501675 GTTTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:38501736 original size:20 final size:20
Alignment explanation
Indices: 38501711--38501775 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
38501701 ATTTTGATAA
38501711 ACATGGTATGTATGATATGC
1 ACATGGTATGTATGATATGC
*
38501731 ACATGGCATGTATGATATGC
1 ACATGGTATGTATGATATGC
*
38501751 ACATGATATGTATGATATGC
1 ACATGGTATGTATGATATGC
38501771 ACATG
1 ACATG
38501776 ATGTATTCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.32
Consensus pattern (20 bp):
ACATGGTATGTATGATATGC
Done.