Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 62 of 259
Found at i:19945205 original size:605 final size:605
Alignment explanation
Indices: 19944049--19945259 Score: 2244
Period size: 605 Copynumber: 2.0 Consensus size: 605
19944039 GAGGGGGGAA
19944049 TGATACGAGCACGCCCCGCGAACTTCATCGAACAAGTCTGTCAAGCCGAGCATTGACATGTTGGC
1 TGATACGAGCACGCCCCGCGAACTTCATCGAACAAGTCTGTCAAGCCGAGCATTGACATGTTGGC
*
19944114 AAGCTGATCCCAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAGC
66 AAGCTGATCCCAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCAAGC
*
19944179 TCAATCCAACTTGCCTGAGCTAAACCGATCTCACTCCTAGCTCATATTCAGCTCACGAGCTAAAC
131 TCAATCCAACTTGCCTGAGCTAAACCGAGCTCACTCCTAGCTCATATTCAGCTCACGAGCTAAAC
* *
19944244 CTTATCTCAACTTCAACTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTTAG
196 CTTAGCTCAACTTCAACTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAACTTAG
* *
19944309 CTCATTTTTAGTTTAACTCGGTTTTGTCTTTAATGCATTAAATAAAATTTGCACATATTTATTTA
261 CTCATTTTTAGTTTAACTCGGTTTTGTCTTTAATACATTAAATAAAATTTGCACATATTCATTTA
*
19944374 AGCATTAAACTTGTCTTATATTAATATTTGTTATTAATATGTCATAGTCATTACATAAATTGATT
326 AGCATTAAACTTGTCTTATATTAATATTTGTTATTAATATATCATAGTCATTACATAAATTGATT
19944439 ATGTTCACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCAAATTTATGAGTGT
391 ATGTTCACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCAAATTTATGAGTGT
*
19944504 TTATGAGATGTCTTAATGACTTGTTTATTTCATGTAGGTACATTCCTTTGGACGGTACAATGTAT
456 TCATGAGATGTCTTAATGACTTGTTTATTTCATGTAGGTACATTCCTTTGGACGGTACAATGTAT
*
19944569 GGATGAAGAAACATCTCTTTTGGGCATTCCACACTCATGAATGAAGAAGTATTAAATGCTGGTGC
521 GAATGAAGAAACATCTCTTTTGGGCATTCCACACTCATGAATGAAGAAGTATTAAATGCTGGTGC
19944634 ATGTACGGCTAGATGCAATG
586 ATGTACGGCTAGATGCAATG
*
19944654 TGATACGAGCACGCCCCGCGAACTTCATCGAGCAAGTCTGTCAAGCCGAGCATTGACATGTTGGC
1 TGATACGAGCACGCCCCGCGAACTTCATCGAACAAGTCTGTCAAGCCGAGCATTGACATGTTGGC
*
19944719 AAGCTGATCCCAGCTCGTTTCCAGCTCCACGAGCTCCGTCTAGCTCAAATCCAGCTTATTCAAGC
66 AAGCTGATCCCAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCAAGC
* *
19944784 TCGATCCAACTTGCCTGAGCTAAACCGAGCTCACTCCTAGCTCATATTTAGCTCACGAGCTAAAC
131 TCAATCCAACTTGCCTGAGCTAAACCGAGCTCACTCCTAGCTCATATTCAGCTCACGAGCTAAAC
*
19944849 CTTAGCTCAACTTCAGCTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAACTTAG
196 CTTAGCTCAACTTCAACTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAACTTAG
19944914 CTCA-TTTTAGTTTAAACTCGGTTTTGTCTTTAATACATTAAATAAAATTTGCACATATTCATTT
261 CTCATTTTTAGTTT-AACTCGGTTTTGTCTTTAATACATTAAATAAAATTTGCACATATTCATTT
* *
19944978 AAGCATTAAACTTGTCTTATATTAATATTTGTTATTAATATATCATTGTCATTATATAAATTGAT
325 AAGCATTAAACTTGTCTTATATTAATATTTGTTATTAATATATCATAGTCATTACATAAATTGAT
*
19945043 TATGTTCACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCGAATTTATGAGTG
390 TATGTTCACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCAAATTTATGAGTG
19945108 TTCATGAGATGTCTTAATGACTTGTTTATTTCATGTAGGTACATTCCTTTGGACGGTACAATGTA
455 TTCATGAGATGTCTTAATGACTTGTTTATTTCATGTAGGTACATTCCTTTGGACGGTACAATGTA
*
19945173 TGAATGAAGAAACATCTCTTTTGGGTATTCCACACTCATGAATGAAGAAGTATTAAATGCTGGTG
520 TGAATGAAGAAACATCTCTTTTGGGCATTCCACACTCATGAATGAAGAAGTATTAAATGCTGGTG
19945238 CATGTACGGCTAGATGCAATG
585 CATGTACGGCTAGATGCAATG
19945259 T
1 T
19945260 TTCTACAAAT
Statistics
Matches: 587, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
604 9 0.02
605 578 0.98
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (605 bp):
TGATACGAGCACGCCCCGCGAACTTCATCGAACAAGTCTGTCAAGCCGAGCATTGACATGTTGGC
AAGCTGATCCCAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCAAGC
TCAATCCAACTTGCCTGAGCTAAACCGAGCTCACTCCTAGCTCATATTCAGCTCACGAGCTAAAC
CTTAGCTCAACTTCAACTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAACTTAG
CTCATTTTTAGTTTAACTCGGTTTTGTCTTTAATACATTAAATAAAATTTGCACATATTCATTTA
AGCATTAAACTTGTCTTATATTAATATTTGTTATTAATATATCATAGTCATTACATAAATTGATT
ATGTTCACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCAAATTTATGAGTGT
TCATGAGATGTCTTAATGACTTGTTTATTTCATGTAGGTACATTCCTTTGGACGGTACAATGTAT
GAATGAAGAAACATCTCTTTTGGGCATTCCACACTCATGAATGAAGAAGTATTAAATGCTGGTGC
ATGTACGGCTAGATGCAATG
Found at i:19949248 original size:20 final size:20
Alignment explanation
Indices: 19949225--19949278 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
19949215 AGTTTTTCCC
*
19949225 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
19949245 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
19949265 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
19949279 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:19949260 original size:30 final size:30
Alignment explanation
Indices: 19949225--19949298 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
19949215 AGTTTTTCCC
19949225 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
19949255 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19949285 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
19949299 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:19949288 original size:20 final size:20
Alignment explanation
Indices: 19949225--19949289 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
19949215 AGTTTTTCCC
* * * *
19949225 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
19949245 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
19949264 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
19949285 AGCTC
1 AGCTC
19949290 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:19950907 original size:13 final size:13
Alignment explanation
Indices: 19950891--19950950 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 13
19950881 CAAAAAAATC
19950891 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
19950904 AAAAAAAATTTGA
1 AAAAAAAATTCGA
19950917 TTGAAAAAAAATTC-A
1 ---AAAAAAAATTCGA
*
19950932 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
19950944 AAAAAAA
1 AAAAAAA
19950951 TCAAGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 17 0.43
13 12 0.30
15 1 0.03
16 10 0.25
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:19950962 original size:23 final size:23
Alignment explanation
Indices: 19950882--19950951 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 23
19950872 TTGGAGTAAC
*
19950882 AAAAAAA-TCAAAAAAAATTCGAA
1 AAAAAAAGTGAAAAAAAATTC-AA
19950905 AAAAAAATTTGATTGAAAAAAAATTCAA
1 AAAAAAA---G--TGAAAAAAAATTCAA
19950933 AAAAAAAGTGAAAAAAAAT
1 AAAAAAAGTGAAAAAAAAT
19950952 CAAGCAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
23 18 0.45
25 1 0.03
28 9 0.22
29 12 0.30
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.17
Consensus pattern (23 bp):
AAAAAAAGTGAAAAAAAATTCAA
Found at i:19952027 original size:12 final size:12
Alignment explanation
Indices: 19952006--19952108 Score: 59
Period size: 12 Copynumber: 8.6 Consensus size: 12
19951996 AGAAAAGGAG
*
19952006 AAAGAGATTGAA
1 AAAGAAATTGAA
19952018 AAAGAAATTG--
1 AAAGAAATTGAA
**
19952028 AAAGAAA-ACAA
1 AAAGAAATTGAA
**
19952039 AAAGAAAACGAA
1 AAAGAAATTGAA
*
19952051 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
19952063 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
19952075 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
19952089 AAAGAAAATTGAA
1 AAAG-AAATTGAA
19952102 AAAGAAA
1 AAAGAAA
19952109 AAGCGAAAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
10 7 0.10
11 7 0.10
12 39 0.56
13 6 0.09
14 6 0.09
15 5 0.07
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:19952044 original size:11 final size:12
Alignment explanation
Indices: 19952028--19952123 Score: 70
Period size: 12 Copynumber: 7.6 Consensus size: 12
19952018 AAAGAAATTG
19952028 AAAGAAAAC-AA
1 AAAGAAAACGAA
19952039 AAAGAAAACGAA
1 AAAGAAAACGAA
*
19952051 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
19952063 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
19952075 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
19952089 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
19952102 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
19952117 AAAGAAA
1 AAAGAAA
19952124 TTGAAAGAGA
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
11 11 0.16
12 25 0.36
13 7 0.10
14 18 0.26
15 8 0.12
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.05
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:19952080 original size:6 final size:6
Alignment explanation
Indices: 19952028--19952111 Score: 53
Period size: 6 Copynumber: 13.7 Consensus size: 6
19952018 AAAGAAATTG
* * ** ** *
19952028 AAAG-A AAACAA AAAGAA AACGAA AAAGAA ATCGAA AAAGTG AGAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* *
19952075 AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
19952112 CGAAAAAAGA
Statistics
Matches: 57, Mismatches: 18, Indels: 7
0.70 0.22 0.09
Matches are distributed among these distances:
5 3 0.05
6 43 0.75
7 7 0.12
8 4 0.07
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:19952093 original size:14 final size:13
Alignment explanation
Indices: 19952072--19952109 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
19952062 AAAAGTGAGA
19952072 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
19952084 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
19952099 GAAAAAGAAAA
1 GAAAAAGAAAA
19952110 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:19952123 original size:21 final size:21
Alignment explanation
Indices: 19952073--19952123 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
19952063 AAAGTGAGAG
*
19952073 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
19952094 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
19952115 AAAAAGAAA
1 AAAAAGAAA
19952124 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:19952163 original size:33 final size:33
Alignment explanation
Indices: 19952126--19952188 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
19952116 AAAAGAAATT
19952126 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
19952159 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
19952189 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:19953987 original size:20 final size:20
Alignment explanation
Indices: 19953964--19954017 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
19953954 AGTTTTTCCC
*
19953964 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
19953984 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
19954004 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
19954018 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:19953999 original size:30 final size:30
Alignment explanation
Indices: 19953964--19954035 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
19953954 AGTTTTTCCC
19953964 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
19953994 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19954024 AGCTCGTTTGAG
1 AGCTCGTTTGAG
19954036 TTTGGCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:19954027 original size:20 final size:20
Alignment explanation
Indices: 19953964--19954028 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
19953954 AGTTTTTCCC
* * * *
19953964 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
19953984 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
19954003 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
19954024 AGCTC
1 AGCTC
19954029 GTTTGAGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:19957615 original size:20 final size:20
Alignment explanation
Indices: 19957592--19957656 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
19957582 AGTTTTTCCC
* *
19957592 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACTTG
* **
19957612 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACTTG
* *
19957632 AGCTCAATTTAGCTTACTTT
1 AGCTCAATTTAGCTCACTTG
19957652 AGCTC
1 AGCTC
19957657 GTTTGAGCTC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACTTG
Found at i:19957627 original size:30 final size:30
Alignment explanation
Indices: 19957592--19957687 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19957582 AGTTTTTCCC
19957592 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
19957622 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
** *
19957652 AGCTCGTTTGAGCTCAACCGAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19957682 CAGCTC
1 -AGCTC
19957688 CTTCTTTCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
29 4 0.07
30 49 0.84
31 5 0.09
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:19959195 original size:15 final size:14
Alignment explanation
Indices: 19959175--19959234 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 14
19959165 AAAAAATAAG
*
19959175 AAAATTTCGAAAAA
1 AAAAATTCGAAAAA
19959189 AAAAATT-GATTGAAAA
1 AAAAATTCGA---AAAA
19959205 AAAAATTC-AAAAA
1 AAAAATTCGAAAAA
*
19959218 AAAAAGT-GAAAAA
1 AAAAATTCGAAAAA
19959231 AAAA
1 AAAA
19959235 TCGAGCAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
13 21 0.54
14 6 0.15
16 12 0.31
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (14 bp):
AAAAATTCGAAAAA
Found at i:19959244 original size:15 final size:15
Alignment explanation
Indices: 19959226--19959267 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
19959216 AAAAAAAGTG
*
19959226 AAAAAAAAATCGAGC
1 AAAAAAAAATCGACC
19959241 AAAAAAAAAGGT-GACC
1 AAAAAAAAA--TCGACC
19959257 AAAAAAAAATC
1 AAAAAAAAATC
19959268 AAGTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 1 0.04
15 9 0.39
16 12 0.52
17 1 0.04
ACGTcount: A:0.69, C:0.12, G:0.12, T:0.07
Consensus pattern (15 bp):
AAAAAAAAATCGACC
Found at i:19960215 original size:15 final size:16
Alignment explanation
Indices: 19960195--19960226 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
19960185 AGAAAATGAA
19960195 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
19960210 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
19960226 A
1 A
19960227 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:19960341 original size:17 final size:18
Alignment explanation
Indices: 19960309--19960342 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19960299 AAAAGAGAGT
*
19960309 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
19960327 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
19960343 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:19961631 original size:20 final size:20
Alignment explanation
Indices: 19961608--19961672 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
19961598 AGTTTTTCCC
* *
19961608 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACTTG
* **
19961628 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACTTG
* *
19961648 AGCTCAATTTAGCTTACTTT
1 AGCTCAATTTAGCTCACTTG
19961668 AGCTC
1 AGCTC
19961673 GTTTGAGCTC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACTTG
Found at i:19961643 original size:30 final size:30
Alignment explanation
Indices: 19961608--19961703 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19961598 AGTTTTTCCC
19961608 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
19961638 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
** *
19961668 AGCTCGTTTGAGCTCAACCGAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19961698 CAGCTC
1 -AGCTC
19961704 CTTCTTTCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
29 4 0.07
30 49 0.84
31 5 0.09
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:19963915 original size:29 final size:29
Alignment explanation
Indices: 19963882--19963941 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
19963872 ATAACCAAAC
*
19963882 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
19963911 CTACATAAACTTCATATCCATAAACCTAT
1 CTACAAAAACTTCATATCCATAAACCCAT
19963940 CT
1 CT
19963942 TTGAATCCTT
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:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:19963934 original size:15 final size:15
Alignment explanation
Indices: 19963888--19963935 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
19963878 AAACCTACAA
*
19963888 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
19963903 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
19963917 AAACTTCATATCCAT
1 AAACTTCATATCCAT
19963932 AAAC
1 AAAC
19963936 CTATCTTTGA
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:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:19964173 original size:11 final size:11
Alignment explanation
Indices: 19964159--19964201 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
19964149 TAAGTTTCAA
19964159 AAAAAAAATTG
1 AAAAAAAATTG
*
19964170 AAAAAAAATTC
1 AAAAAAAATTG
19964181 AAAAAAAATTTGG
1 AAAAAAAA-TT-G
19964194 AAAAAAAA
1 AAAAAAAA
19964202 ACAAAATCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 2 0.07
13 8 0.29
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:19964206 original size:23 final size:23
Alignment explanation
Indices: 19964158--19964207 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
19964148 GTAAGTTTCA
*
19964158 AAAAAAAAATTGAAAAAAAATTC
1 AAAAAAAAATTGAAAAAAAATAC
*
19964181 AAAAAAAATTTGGAAAAAAAA-AC
1 AAAAAAAAATT-GAAAAAAAATAC
19964204 AAAA
1 AAAA
19964208 TCTGAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAAAAAAATTGAAAAAAAATAC
Found at i:19965281 original size:18 final size:19
Alignment explanation
Indices: 19965238--19965283 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
19965228 TGAGAGAAGC
*
19965238 GAAAAAG-AGAAAGAATGT
1 GAAAAAGAAAAAAGAATGT
* *
19965256 GAACAAGAAAAAAGAGTG-
1 GAAAAAGAAAAAAGAATGT
19965274 GAAAAAGAAA
1 GAAAAAGAAA
19965284 TTGAGATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAAAGAATGT
Found at i:19966180 original size:29 final size:29
Alignment explanation
Indices: 19966147--19966206 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
19966137 ATAACCAAAC
*
19966147 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
19966176 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
19966205 CT
1 CT
19966207 TTGAATCCTT
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:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:19966199 original size:15 final size:15
Alignment explanation
Indices: 19966153--19966200 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
19966143 AAACCTACAA
*
19966153 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
19966168 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
19966182 AAACTTCATATCCAT
1 AAACTTCATATCCAT
19966197 AAAC
1 AAAC
19966201 CCATCTTTGA
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:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:19966678 original size:10 final size:10
Alignment explanation
Indices: 19966665--19966710 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
19966655 AGCTCACTTG
19966665 AGCTCGTTTT
1 AGCTCGTTTT
*
19966675 AGCTCGTTTG
1 AGCTCGTTTT
*
19966685 AGCTCGAATTT
1 AGCTCG-TTTT
19966696 AGCTCGTTTT
1 AGCTCGTTTT
19966706 AGCTC
1 AGCTC
19966711 ATTCCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:19966698 original size:21 final size:20
Alignment explanation
Indices: 19966662--19966710 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
19966652 ATCAGCTCAC
*
19966662 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
19966682 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
19966703 TTTAGCTC
1 TTGAGCTC
19966711 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:19972683 original size:20 final size:20
Alignment explanation
Indices: 19972627--19972683 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
19972617 AGCTCCGTTT
*
19972627 AGCTCATTTCCAGCTCACTCA
1 AGCTCAATT-CAGCTCACTCA
* *
19972648 AGCTCAAGTCAACTCACTCA
1 AGCTCAATTCAGCTCACTCA
19972668 AGCTCAATTCAGCTCA
1 AGCTCAATTCAGCTCA
19972684 ATCTTAACCC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 24 0.77
21 7 0.23
ACGTcount: A:0.30, C:0.35, G:0.11, T:0.25
Consensus pattern (20 bp):
AGCTCAATTCAGCTCACTCA
Found at i:19977706 original size:18 final size:17
Alignment explanation
Indices: 19977685--19977767 Score: 58
Period size: 18 Copynumber: 4.5 Consensus size: 17
19977675 TTTCACATCC
19977685 TTTTCAATCTCAATTTCT
1 TTTTCAATCTC-ATTTCT
*
19977703 TTTTCCATGACACTCATTTCT
1 TTTT-CA--A-TCTCATTTCT
* * *
19977724 TTTACACTCTCGTTTCT
1 TTTTCAATCTCATTTCT
*
19977741 TTCTTCAATCTCACTCTCT
1 TT-TTCAATCTCA-TTTCT
19977760 TTTTCAAT
1 TTTTCAAT
19977768 TTCTTGTTCT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
17 10 0.20
18 17 0.34
19 8 0.16
20 2 0.04
21 10 0.20
22 3 0.06
ACGTcount: A:0.18, C:0.28, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTTCAATCTCATTTCT
Found at i:19980323 original size:20 final size:20
Alignment explanation
Indices: 19980300--19980346 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
19980290 GGGTTAAGAT
*
19980300 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
19980320 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
19980340 TGAGCTG
1 TGAGCTG
19980347 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:19983990 original size:20 final size:20
Alignment explanation
Indices: 19983953--19983991 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19983943 AATCAGCTCA
*
19983953 TTTGAGCTTGTTTCAGCTTG
1 TTTGAGCTTATTTCAGCTTG
19983973 TTTGAGCTTAATTT-AGCTT
1 TTTGAGCTT-ATTTCAGCTT
19983992 CTTTCCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTGAGCTTATTTCAGCTTG
Found at i:19987728 original size:30 final size:30
Alignment explanation
Indices: 19987694--19987790 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19987684 AGCTCACTCC
19987694 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
19987724 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
19987754 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
19987784 TAGCTCA
1 TAGCTCA
19987791 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:19991686 original size:33 final size:33
Alignment explanation
Indices: 19991648--19991710 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
19991638 GATTACTCAC
19991648 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
19991681 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
19991711 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:19991737 original size:21 final size:21
Alignment explanation
Indices: 19991708--19991763 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
19991698 CAAGCTCTCT
*
19991708 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
19991729 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
19991750 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
19991764 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:19991756 original size:14 final size:14
Alignment explanation
Indices: 19991707--19991763 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
19991697 TCAAGCTCTC
19991707 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
19991720 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
19991734 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
19991748 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
19991762 TT
1 TT
19991764 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:19991823 original size:18 final size:18
Alignment explanation
Indices: 19991725--19991828 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
19991715 TCTTTTTTCG
19991725 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
19991744 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
19991764 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
19991782 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
19991800 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
19991818 CTTTTTGTTTT
1 CTTTTTCTTTT
19991829 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:19991845 original size:6 final size:6
Alignment explanation
Indices: 19991725--19991832 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
19991715 TCTTTTTTCG
* * * **
19991725 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
19991776 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
19991824 -GTTTT CTTT
1 CTTTTT CTTT
19991833 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:19992894 original size:10 final size:10
Alignment explanation
Indices: 19992879--19992921 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
19992869 TTTTGCTCAC
19992879 CTTTTTTTTT
1 CTTTTTTTTT
19992889 CTTTTTTTTT
1 CTTTTTTTTT
*
19992899 CGATTTTTTTTCA
1 C--TTTTTTTT-T
19992912 CTTTTTTTTT
1 CTTTTTTTTT
19992922 GAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 11 0.39
11 8 0.29
12 8 0.29
13 1 0.04
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:19992905 original size:12 final size:12
Alignment explanation
Indices: 19992880--19992969 Score: 66
Period size: 12 Copynumber: 7.6 Consensus size: 12
19992870 TTTGCTCACC
19992880 TTTTTTTTTC--
1 TTTTTTTTTCGA
19992890 TTTTTTTTTCGA
1 TTTTTTTTTCGA
19992902 -TTTTTTTTC-A
1 TTTTTTTTTCGA
19992912 CTTTTTTTTT-GAA
1 -TTTTTTTTTCG-A
*
19992925 TTTTTTTTCAATCAA
1 TTTTTTTT---TCGA
*
19992940 ATTTTTTTTCGA
1 TTTTTTTTTCGA
*
19992952 ATTTTTTTT-GA
1 TTTTTTTTTCGA
19992963 TTTTTTT
1 TTTTTTT
19992970 GTTACTCCAA
Statistics
Matches: 66, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
10 11 0.17
11 17 0.26
12 28 0.42
13 1 0.02
15 9 0.14
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTCGA
Found at i:19992906 original size:23 final size:22
Alignment explanation
Indices: 19992880--19992932 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
19992870 TTTGCTCACC
*
19992880 TTTTTTTTTCTTTTTTTTTCG-A
1 TTTTTTTTACTTTTTTTTT-GAA
19992902 TTTTTTTTCACTTTTTTTTTGAA
1 TTTTTTTT-ACTTTTTTTTTGAA
19992925 TTTTTTTT
1 TTTTTTTT
19992933 CAATCAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTTTTTACTTTTTTTTTGAA
Found at i:19996609 original size:5 final size:5
Alignment explanation
Indices: 19996599--19996660 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
19996589 AAGAGAAAAC
* *
19996599 AAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAGA AAAGA AAA-GA
19996646 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
19996661 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.04
5 35 0.73
6 10 0.21
7 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:19996629 original size:26 final size:26
Alignment explanation
Indices: 19996599--19996660 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
19996589 AAGAGAAAAC
19996599 AAAGAAAAGAAAAGAAAAAGAAA-AA
1 AAAGAAAAGAAAAGAAAAAGAAATAA
* * *
19996624 GCAAGAGAAGAAAAGAAAATGAAATAA
1 -AAAGAAAAGAAAAGAAAAAGAAATAA
19996651 AAAGAAAAGA
1 AAAGAAAAGA
19996661 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (26 bp):
AAAGAAAAGAAAAGAAAAAGAAATAA
Found at i:19996661 original size:31 final size:30
Alignment explanation
Indices: 19996587--19996662 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
19996577 TACATTCTTG
* *
19996587 TAAAGAGAAAACA-AAGAAAAGAAAAGAAA
1 TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
19996616 -AAGAAA-AAGCAAGAGAAGAAAAGAAAATGAAA
1 TAA-AAAGAA--AAGAGAAGAAAAGAAAA-GAAA
19996648 TAAAAAGAAAAGAGA
1 TAAAAAGAAAAGAGA
19996663 GGCAAGAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
28 4 0.11
29 2 0.05
30 3 0.08
31 18 0.47
32 7 0.18
33 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.04
Consensus pattern (30 bp):
TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
Found at i:19996739 original size:11 final size:12
Alignment explanation
Indices: 19996708--19996738 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
19996698 TTGAGAGAAC
19996708 TTGAAAAAGCCT
1 TTGAAAAAGCCT
19996720 TTGAAAAAGCCT
1 TTGAAAAAGCCT
19996732 TTGAAAA
1 TTGAAAA
19996739 GTAAAAAGAA
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:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:19998953 original size:30 final size:30
Alignment explanation
Indices: 19998919--19999015 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19998909 AGCTCACTCC
19998919 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
19998949 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
19998979 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
19999009 TAGCTCA
1 TAGCTCA
19999016 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:20001565 original size:20 final size:20
Alignment explanation
Indices: 20001540--20001631 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 20
20001530 GAAAGGAAAT
20001540 GAAAAAGAAAAGAAAAATGA
1 GAAAAAGAAAAGAAAAATGA
* *
20001560 GAAAAAGAACACAAAAAT-A
1 GAAAAAGAAAAGAAAAATGA
*
20001579 GCAAAAGAGAGAAA-AAAAGTGA
1 G-AAAA-AGA-AAAGAAAAATGA
* **
20001601 G-AAAAGAAAAAGAAGAACAA
1 GAAAAAG-AAAAGAAAAATGA
20001621 GAAAAAGAAAA
1 GAAAAAGAAAA
20001632 TAGGAAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
19 7 0.12
20 33 0.58
21 13 0.23
22 4 0.07
ACGTcount: A:0.73, C:0.04, G:0.20, T:0.03
Consensus pattern (20 bp):
GAAAAAGAAAAGAAAAATGA
Found at i:20001612 original size:15 final size:15
Alignment explanation
Indices: 20001600--20001629 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20001590 AAAAAAAGTG
20001600 AGAA-AAGAAAAAGA
1 AGAACAAGAAAAAGA
20001614 AGAACAAGAAAAAGA
1 AGAACAAGAAAAAGA
20001629 A
1 A
20001630 AATAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAACAAGAAAAAGA
Found at i:20002407 original size:14 final size:14
Alignment explanation
Indices: 20002388--20002432 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
20002378 AACTCATCTT
*
20002388 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
20002402 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
20002415 AATTTAATTTAATG
1 AGTTTAATTTAATG
20002429 AGTT
1 AGTT
20002433 GCTTCTTTAA
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:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:20003439 original size:29 final size:29
Alignment explanation
Indices: 20003406--20003465 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
20003396 ATAACCAAAC
*
20003406 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
20003435 CTACATAAACTTCATATCCATAAACCTAT
1 CTACAAAAACTTCATATCCATAAACCCAT
20003464 CT
1 CT
20003466 TTGAATCCTT
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:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:20003458 original size:15 final size:15
Alignment explanation
Indices: 20003412--20003459 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
20003402 AAACCTACAA
*
20003412 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
20003427 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
20003441 AAACTTCATATCCAT
1 AAACTTCATATCCAT
20003456 AAAC
1 AAAC
20003460 CTATCTTTGA
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:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:20003720 original size:13 final size:12
Alignment explanation
Indices: 20003681--20003724 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
20003671 AGTAAGTTTC
20003681 AAAAAAAA-TCG
1 AAAAAAAATTCG
*
20003692 AAAAAAAATTCA
1 AAAAAAAATTCG
*
20003704 AAAAAAAATTTGG
1 AAAAAAAA-TTCG
20003717 AAAAAAAA
1 AAAAAAAA
20003725 CAAAATCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 8 0.29
12 10 0.36
13 10 0.36
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:20006080 original size:20 final size:20
Alignment explanation
Indices: 20006057--20006103 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20006047 GGGTTAAGAT
*
20006057 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
20006077 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
20006097 TGAGCTG
1 TGAGCTG
20006104 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:20007825 original size:48 final size:48
Alignment explanation
Indices: 20007769--20007874 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
20007759 TTGTCTTTTC
*
20007769 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
20007817 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
20007865 TTTCTTTTTC
1 TTTCTTTTTC
20007875 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:20008983 original size:13 final size:13
Alignment explanation
Indices: 20008967--20009014 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
20008957 TTTTTTTCAC
20008967 TTTTTTTTGAATT
1 TTTTTTTTGAATT
*
20008980 TTTTTTTTCAATCAAT
1 TTTTTTTTGAAT---T
20008996 TTTTTTTTCGAATT
1 TTTTTTTT-GAATT
20009010 TTTTT
1 TTTTT
20009015 GATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 11 0.38
14 6 0.21
16 9 0.31
17 3 0.10
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:20011295 original size:13 final size:13
Alignment explanation
Indices: 20011279--20011355 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 13
20011269 AAAAAAAATC
20011279 AAAAAAATTCGAA
1 AAAAAAATTCGAA
*
20011292 AAAAAAATTTGATTGAAA
1 AAAAAAA--T--TCG-AA
20011310 AAAAAAATTC-AA
1 AAAAAAATTCGAA
*
20011322 AAAAAAAGT-GAA
1 AAAAAAATTCGAA
*
20011334 AAAAAAATCTAGCAA
1 AAAAAAAT-TCG-AA
20011349 AAAAAAA
1 AAAAAAA
20011356 AGGTGACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
12 19 0.37
13 8 0.16
14 2 0.04
15 10 0.20
16 1 0.02
17 2 0.04
18 9 0.18
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:20011323 original size:12 final size:12
Alignment explanation
Indices: 20011308--20011355 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
20011298 ATTTGATTGA
20011308 AAAAAAAAATTC
1 AAAAAAAAATTC
* *
20011320 AAAAAAAAAGTG
1 AAAAAAAAATTC
20011332 AAAAAAAAATCTAGC
1 AAAAAAAAAT-T--C
20011347 AAAAAAAAA
1 AAAAAAAAA
20011356 AGGTGACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 19 0.66
13 1 0.03
15 9 0.31
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:20011381 original size:29 final size:29
Alignment explanation
Indices: 20011320--20011384 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
20011310 AAAAAAATTC
*
20011320 AAAAAAAAAGTGAAAAAAAAATCTAGCAA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCAA
* **
20011349 AAAAAAAAGGTGACAAAAAAAATCAAGTTA
1 AAAAAAAAAGTGA-AAAAAAAATCAAGCAA
20011379 AAAAAA
1 AAAAAA
20011385 GTGAAAAGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.72, C:0.06, G:0.11, T:0.11
Consensus pattern (29 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCAA
Found at i:20011382 original size:30 final size:28
Alignment explanation
Indices: 20011320--20011391 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
20011310 AAAAAAATTC
*
20011320 AAAAAAAAAGTGAAAAAAAAATCTAGCA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCA
20011348 AAAAAAAAAGGTGACAAAAAAAATCAAG--
1 AAAAAAAAA-GTGA-AAAAAAAATCAAGCA
**
20011376 TTAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
20011392 GTCTTGCGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 3 0.08
27 4 0.10
28 16 0.41
29 4 0.10
30 12 0.31
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.11
Consensus pattern (28 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCA
Found at i:20012320 original size:15 final size:16
Alignment explanation
Indices: 20012300--20012331 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
20012290 AGAAAATGAA
20012300 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
20012315 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
20012331 A
1 A
20012332 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:20012445 original size:17 final size:18
Alignment explanation
Indices: 20012413--20012446 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20012403 AAAAGAGAGT
*
20012413 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
20012431 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
20012447 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:20017597 original size:30 final size:28
Alignment explanation
Indices: 20017561--20017616 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
20017551 AAGCGAAAAA
* *
20017561 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
20017591 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
20017617 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:20023704 original size:10 final size:10
Alignment explanation
Indices: 20023688--20023745 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
20023678 CAACTCCGGC
20023688 CAGCTCAATT
1 CAGCTCAATT
* *
20023698 GAGCTCATTT
1 CAGCTCAATT
20023708 CAGCTCAA-T
1 CAGCTCAATT
20023717 CGAGCTCAATT
1 C-AGCTCAATT
*
20023728 TAGCTACAATT
1 CAGCT-CAATT
20023739 CAGCTCA
1 CAGCTCA
20023746 TTTATTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:20023711 original size:20 final size:20
Alignment explanation
Indices: 20023688--20023748 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
20023678 CAACTCCGGC
20023688 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
20023708 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
20023729 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
20023749 ATTTAATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:20025124 original size:21 final size:21
Alignment explanation
Indices: 20025087--20025144 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
20025077 TATTGGATTT
* * *
20025087 AAAAAAAGAGAAGAAATTC-A
1 AAAAAAAGAAAAAAAAATCGA
**
20025107 AAAAAAATTAAAAAAAATCGA
1 AAAAAAAGAAAAAAAAATCGA
20025128 AAAAAAAGAAAAAAAAA
1 AAAAAAAGAAAAAAAAA
20025145 GAAGTGACAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAATCGA
Found at i:20025138 original size:9 final size:10
Alignment explanation
Indices: 20025106--20025143 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
20025096 GAAGAAATTC
*
20025106 AAAAAAAATT
1 AAAAAAAATG
20025116 AAAAAAAATCG
1 AAAAAAAAT-G
20025127 AAAAAAAA-G
1 AAAAAAAATG
20025136 AAAAAAAA
1 AAAAAAAA
20025144 AGAAGTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 9 0.35
10 9 0.35
11 8 0.31
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:20025171 original size:39 final size:36
Alignment explanation
Indices: 20025117--20025190 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 36
20025107 AAAAAAATTA
20025117 AAAAAAATCG-AAAAAAAAGAAAAAAAAAGAAGTGAC
1 AAAAAAATCGAAAAAAAAAGAAAAAAAAA-AAGTGAC
*
20025153 AAAAAAATCGAGTTAAAAAAAAGAAGAAAAAAAAGTGA
1 AAAAAAATCGA---AAAAAAAAGAAAAAAAAAAAGTGA
20025191 AAAGTCTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 10 0.30
39 6 0.18
40 17 0.52
ACGTcount: A:0.73, C:0.04, G:0.15, T:0.08
Consensus pattern (36 bp):
AAAAAAATCGAAAAAAAAAGAAAAAAAAAAAGTGAC
Found at i:20025431 original size:30 final size:30
Alignment explanation
Indices: 20025397--20025493 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
20025387 AGCTCACTCC
20025397 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
20025427 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
20025457 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
20025487 TAGCTCA
1 TAGCTCA
20025494 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:20026223 original size:30 final size:30
Alignment explanation
Indices: 20026189--20026285 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
20026179 TAAACTAAAA
*
20026189 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
20026219 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
20026249 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
20026278 ATGAGCTA
1 -TGAGCTA
20026286 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:20026826 original size:11 final size:10
Alignment explanation
Indices: 20026802--20026850 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
20026792 AAGAAATTCA
*
20026802 AAAAAAAATA
1 AAAAAAAATG
20026812 AAAAAAAATCG
1 AAAAAAAAT-G
*
20026823 -AAAAAAAGG
1 AAAAAAAATG
20026832 AAAAAAAAGTG
1 AAAAAAAA-TG
20026843 AAAAAAAA
1 AAAAAAAA
20026851 AATCGAGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 1 0.03
10 23 0.70
11 9 0.27
ACGTcount: A:0.82, C:0.02, G:0.10, T:0.06
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:20026826 original size:20 final size:20
Alignment explanation
Indices: 20026811--20026849 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
20026801 AAAAAAAAAT
20026811 AAAAAAAAATCGAAAAAAAGG
1 AAAAAAAAAT-GAAAAAAAGG
*
20026832 AAAAAAAAGTGAAAAAAA
1 AAAAAAAAATGAAAAAAA
20026850 AAATCGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (20 bp):
AAAAAAAAATGAAAAAAAGG
Found at i:20026851 original size:14 final size:14
Alignment explanation
Indices: 20026832--20026890 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
20026822 GAAAAAAAGG
20026832 AAAAAAAAGTGAAA
1 AAAAAAAAGTGAAA
*
20026846 AAAAAAATCGAGTTAAA
1 AAAAAAA---AGTGAAA
20026863 AAAAAAGAA--GAAA
1 AAAAAA-AAGTGAAA
*
20026876 AAACAAAAGTGAAA
1 AAAAAAAAGTGAAA
20026890 A
1 A
20026891 GTCTTGTGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
12 2 0.06
13 8 0.22
14 12 0.33
15 1 0.03
17 12 0.33
18 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.08
Consensus pattern (14 bp):
AAAAAAAAGTGAAA
Found at i:20027798 original size:6 final size:6
Alignment explanation
Indices: 20027778--20027827 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
20027768 AAGAGAAAAC
*
20027778 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
20027827 A
1 A
20027828 TAAAAGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:20027808 original size:21 final size:21
Alignment explanation
Indices: 20027778--20027837 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
20027768 AAGAGAAAAC
20027778 AAAGAAAAGAAAAGAAAAAGAA
1 AAAG-AAAGAAAAGAAAAAGAA
* *
20027800 AAAGCAAGAGAAGAAAAAGAA
1 AAAGAAAGAAAAGAAAAAGAA
* *
20027821 AATGAAATAAAAGAAAA
1 AAAGAAAGAAAAGAAAA
20027838 GAGAGGCAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAGAAAGAAAAGAAAAAGAA
Found at i:20027808 original size:26 final size:25
Alignment explanation
Indices: 20027778--20027839 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
20027768 AAGAGAAAAC
20027778 AAAGAAAAGAAAAGAAAAAGAAA-A
1 AAAGAAAAGAAAAGAAAAAGAAATA
* *
20027802 AGCAAGAGAAGAAAAAGAAAATGAAATA
1 A--AAGAAAAG-AAAAGAAAAAGAAATA
20027830 AAAGAAAAGA
1 AAAGAAAAGA
20027840 GAGGCAAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.03
25 1 0.03
26 14 0.45
27 13 0.42
28 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (25 bp):
AAAGAAAAGAAAAGAAAAAGAAATA
Found at i:20027919 original size:11 final size:12
Alignment explanation
Indices: 20027887--20027917 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
20027877 TTGAGAGAAC
20027887 TTGAAAAAGCCT
1 TTGAAAAAGCCT
20027899 TTGAAAAAGCCT
1 TTGAAAAAGCCT
20027911 TTGAAAA
1 TTGAAAA
20027918 GCAAAAAGAA
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:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:20030131 original size:30 final size:30
Alignment explanation
Indices: 20030097--20030193 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
20030087 AGCTCACTCC
20030097 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
20030127 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
20030157 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
20030187 TAGCTCA
1 TAGCTCA
20030194 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:20031146 original size:13 final size:13
Alignment explanation
Indices: 20031128--20031152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20031118 GTATTGATCC
20031128 TGTGTTCACACCT
1 TGTGTTCACACCT
20031141 TGTGTTCACACC
1 TGTGTTCACACC
20031153 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:20033652 original size:13 final size:13
Alignment explanation
Indices: 20033618--20033651 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
20033608 ATAGGTACGT
*
20033618 AAAAAAAAGTTCG
1 AAAAAAAAATTCG
20033631 AAAAAAAAATT-G
1 AAAAAAAAATTCG
20033643 AAAAAAAAA
1 AAAAAAAAA
20033652 AATTGCATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:20034858 original size:17 final size:18
Alignment explanation
Indices: 20034826--20034859 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20034816 AAAAGAGAGT
*
20034826 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
20034844 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
20034860 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:20036973 original size:10 final size:10
Alignment explanation
Indices: 20036960--20036997 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
20036950 TTGTAGCTAA
20036960 ATTGAGCTCG
1 ATTGAGCTCG
20036970 ATTGAGCT-G
1 ATTGAGCTCG
20036979 ACTTGAGCTCG
1 A-TTGAGCTCG
*
20036990 AGTGAGCT
1 ATTGAGCT
20036998 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:20036977 original size:20 final size:20
Alignment explanation
Indices: 20036937--20036997 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
20036927 ACCAATAAAA
20036937 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
20036957 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
20036977 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
20036997 T
1 T
20036998 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:20036998 original size:20 final size:20
Alignment explanation
Indices: 20036961--20036998 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20036951 TGTAGCTAAA
*
20036961 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
20036981 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
20036999 GAAACGAGCT
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:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:20039703 original size:15 final size:15
Alignment explanation
Indices: 20039670--20039707 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
20039660 TTTAACTTGA
20039670 TTTTTTTTGCTCACCT
1 TTTTTTTTGCTCA-CT
20039686 TTTTTTTTGCTCGA-T
1 TTTTTTTTGCTC-ACT
20039701 TTTTTTT
1 TTTTTTT
20039708 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 12 0.57
17 1 0.05
ACGTcount: A:0.05, C:0.16, G:0.08, T:0.71
Consensus pattern (15 bp):
TTTTTTTTGCTCACT
Found at i:20039715 original size:12 final size:12
Alignment explanation
Indices: 20039700--20039758 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 12
20039690 TTTTGCTCGA
*
20039700 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
20039712 TTTTTTTTGAATT
1 TTTTTTTTCAA-T
20039725 TTTTTTTCAATCAAT
1 TTTTTTT---TCAAT
*
20039740 TTTTTTTTGAAT
1 TTTTTTTTCAAT
20039752 TTTTTTT
1 TTTTTTT
20039759 GATTTTTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 20 0.51
13 8 0.21
15 8 0.21
16 3 0.08
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:20041285 original size:113 final size:113
Alignment explanation
Indices: 20041087--20041313 Score: 454
Period size: 113 Copynumber: 2.0 Consensus size: 113
20041077 ATAAATTAAG
20041087 TAATTTATTAATTTAGCTTAAATTACTACAGCTCATAATTATGTTTTGACTTATTACATGTTTTA
1 TAATTTATTAATTTAGCTTAAATTACTACAGCTCATAATTATGTTTTGACTTATTACATGTTTTA
20041152 AATGTGTCTTGGCCGAATTTAATATGTCTTGTTAAGACTTTATTAAAT
66 AATGTGTCTTGGCCGAATTTAATATGTCTTGTTAAGACTTTATTAAAT
20041200 TAATTTATTAATTTAGCTTAAATTACTACAGCTCATAATTATGTTTTGACTTATTACATGTTTTA
1 TAATTTATTAATTTAGCTTAAATTACTACAGCTCATAATTATGTTTTGACTTATTACATGTTTTA
20041265 AATGTGTCTTGGCCGAATTTAATATGTCTTGTTAAGACTTTATTAAAT
66 AATGTGTCTTGGCCGAATTTAATATGTCTTGTTAAGACTTTATTAAAT
20041313 T
1 T
20041314 TGTCTAATTT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (113 bp):
TAATTTATTAATTTAGCTTAAATTACTACAGCTCATAATTATGTTTTGACTTATTACATGTTTTA
AATGTGTCTTGGCCGAATTTAATATGTCTTGTTAAGACTTTATTAAAT
Found at i:20042634 original size:11 final size:13
Alignment explanation
Indices: 20042618--20042691 Score: 55
Period size: 17 Copynumber: 5.5 Consensus size: 13
20042608 TTGGAGTAAC
20042618 AAAAAAAA-TC-A
1 AAAAAAAATTCGA
20042629 AAAAAAAATTCGAA
1 AAAAAAAATTCG-A
*
20042643 AAAAAAAATTGATTGAA
1 AAAAAAAA-T--TCG-A
*
20042660 AAAAAAAATTCAA
1 AAAAAAAATTCGA
*
20042673 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
20042685 AAAAAAA
1 AAAAAAA
20042692 TCGAGCAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
11 8 0.15
12 10 0.19
13 10 0.19
14 10 0.19
15 1 0.02
16 1 0.02
17 12 0.23
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:20042635 original size:12 final size:13
Alignment explanation
Indices: 20042618--20042691 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 13
20042608 TTGGAGTAAC
20042618 AAAAAAAATC-AA
1 AAAAAAAATCGAA
*
20042630 AAAAAAATTCGAAA
1 AAAAAAAATCG-AA
*
20042644 AAAAAAATTGATTGAA
1 AAAAAAA---ATCGAA
20042660 AAAAAAAATTC-AA
1 AAAAAAAA-TCGAA
20042673 AAAAAAAAGT-GAA
1 AAAAAAAA-TCGAA
20042686 AAAAAA
1 AAAAAA
20042692 TCGAGCAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 9 0.18
13 20 0.40
14 10 0.20
16 9 0.18
17 2 0.04
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:20042645 original size:14 final size:14
Alignment explanation
Indices: 20042628--20042691 Score: 69
Period size: 13 Copynumber: 4.5 Consensus size: 14
20042618 AAAAAAAATC
20042628 AAAAAAAAATTCGA
1 AAAAAAAAATTCGA
*
20042642 AAAAAAAAATTGATTGA
1 AAAAAAAAA-T--TCGA
20042659 AAAAAAAAATTC-A
1 AAAAAAAAATTCGA
*
20042672 AAAAAAAAAGT-GA
1 AAAAAAAAATTCGA
20042685 AAAAAAA
1 AAAAAAA
20042692 TCGAGCAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 19 0.44
14 10 0.23
15 1 0.02
16 1 0.02
17 12 0.28
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (14 bp):
AAAAAAAAATTCGA
Found at i:20042703 original size:16 final size:16
Alignment explanation
Indices: 20042684--20042725 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
20042674 AAAAAAAGTG
20042684 AAAAAAAATCGAGCAA
1 AAAAAAAATCGAGCAA
*
20042700 AAAAAAAGGT-GAGCAA
1 AAAAAAA-ATCGAGCAA
20042716 AAAAAAAATC
1 AAAAAAAATC
20042726 AAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.69, C:0.10, G:0.14, T:0.07
Consensus pattern (16 bp):
AAAAAAAATCGAGCAA
Found at i:20046748 original size:10 final size:10
Alignment explanation
Indices: 20046735--20046772 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
20046725 TTGTAGCTAA
20046735 ATTGAGCTCG
1 ATTGAGCTCG
20046745 ATTGAGCT-G
1 ATTGAGCTCG
20046754 ACTTGAGCTCG
1 A-TTGAGCTCG
*
20046765 AGTGAGCT
1 ATTGAGCT
20046773 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:20046752 original size:20 final size:20
Alignment explanation
Indices: 20046712--20046772 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
20046702 ACCAATAAAA
20046712 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
20046732 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
20046752 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
20046772 T
1 T
20046773 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:20046773 original size:20 final size:20
Alignment explanation
Indices: 20046736--20046773 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20046726 TGTAGCTAAA
*
20046736 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
20046756 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
20046774 GAAACGAGCT
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:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:20047905 original size:13 final size:13
Alignment explanation
Indices: 20047887--20047911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20047877 GTATTGATCC
20047887 TGTGTTCACACCT
1 TGTGTTCACACCT
20047900 TGTGTTCACACC
1 TGTGTTCACACC
20047912 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:20051161 original size:18 final size:18
Alignment explanation
Indices: 20051135--20051184 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
20051125 AAATTGAAAG
*
20051135 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
20051153 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
20051171 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
20051185 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:20051163 original size:6 final size:6
Alignment explanation
Indices: 20051131--20051184 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
20051121 AAAGAAATTG
* * ** *
20051131 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
20051178 AAAGAA A
1 AAAGAA A
20051185 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:20051244 original size:18 final size:18
Alignment explanation
Indices: 20051223--20051257 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20051213 AGAAAAGAAA
20051223 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
20051241 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
20051258 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:20054896 original size:10 final size:10
Alignment explanation
Indices: 20054880--20054937 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
20054870 CAACTCCGAC
20054880 CAGCTCAATT
1 CAGCTCAATT
* *
20054890 GAGCTCATTT
1 CAGCTCAATT
20054900 CAGCTCAA-T
1 CAGCTCAATT
20054909 CGAGCTCAATT
1 C-AGCTCAATT
*
20054920 TAGCTACAATT
1 CAGCT-CAATT
20054931 CAGCTCA
1 CAGCTCA
20054938 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:20054903 original size:20 final size:20
Alignment explanation
Indices: 20054880--20054940 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
20054870 CAACTCCGAC
20054880 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
20054900 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
20054921 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
20054941 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:20058214 original size:6 final size:6
Alignment explanation
Indices: 20058203--20058236 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
20058193 AATTTTTTTC
* *
20058203 TCAATA TCAATA TCAATA TCAATC TCAATC TCAA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAA
20058237 ATTTTTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (6 bp):
TCAATA
Found at i:20058265 original size:20 final size:22
Alignment explanation
Indices: 20058242--20058287 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
20058232 CTCAAATTTT
20058242 TTTTCTTTTTCTC-TCTCTC-A
1 TTTTCTTTTTCTCTTCTCTCAA
*
20058262 TTTTCTTTTTTTCTTCTCTCAA
1 TTTTCTTTTTCTCTTCTCTCAA
20058284 TTTT
1 TTTT
20058288 ATTCAAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.52
21 6 0.26
22 5 0.22
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCTTTTTCTCTTCTCTCAA
Found at i:20058273 original size:23 final size:23
Alignment explanation
Indices: 20058239--20058287 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
20058229 AATCTCAAAT
*
20058239 TTTTTTTCTTTTTCTCTCTCTC-A
1 TTTTCTTCTTTTTCT-TCTCTCAA
20058262 TTTTCTT-TTTTTCTTCTCTCAA
1 TTTTCTTCTTTTTCTTCTCTCAA
20058284 TTTT
1 TTTT
20058288 ATTCAAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 12 0.50
23 6 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCTTCTTTTTCTTCTCTCAA
Found at i:20059130 original size:32 final size:33
Alignment explanation
Indices: 20059094--20059174 Score: 121
Period size: 32 Copynumber: 2.5 Consensus size: 33
20059084 TTTCAATCAC
* *
20059094 TCTTTTTTTTTTCAATTTTG-ATTTTTTTTTCT
1 TCTTTTTTTTTTCAATTTCGAAATTTTTTTTCT
20059126 TCTTTTTTTTTT-AATTTCGAAATTTTTTTTCT
1 TCTTTTTTTTTTCAATTTCGAAATTTTTTTTCT
20059158 TCTTTTTTTTCTTCAAT
1 TCTTTTTTTT-TTCAAT
20059175 ACTAAATACA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 6 0.14
32 33 0.75
33 2 0.05
34 3 0.07
ACGTcount: A:0.12, C:0.11, G:0.02, T:0.74
Consensus pattern (33 bp):
TCTTTTTTTTTTCAATTTCGAAATTTTTTTTCT
Found at i:20059246 original size:25 final size:26
Alignment explanation
Indices: 20059207--20059255 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
20059197 AAATTGAATA
20059207 CAAACTTTTTTTTTGAATTTTTTTTT
1 CAAACTTTTTTTTTGAATTTTTTTTT
20059233 CAAA-TTTTTTTTTGAATTTTTTT
1 CAAACTTTTTTTTTGAATTTTTTT
20059256 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (26 bp):
CAAACTTTTTTTTTGAATTTTTTTTT
Found at i:20059265 original size:13 final size:12
Alignment explanation
Indices: 20059212--20059255 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
20059202 GAATACAAAC
20059212 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
20059224 TTTTTTTTTCAAA
1 TTTTTTTTT-GAA
20059237 TTTTTTTTTGAA
1 TTTTTTTTTGAA
20059249 TTTTTTT
1 TTTTTTT
20059256 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:20067295 original size:15 final size:15
Alignment explanation
Indices: 20067275--20067321 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
20067265 TCAAAGATGG
20067275 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
20067290 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
20067304 GTTTATGGATAT-AA
1 GTTTATGGATATGAA
20067318 GTTT
1 GTTT
20067322 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:20067309 original size:14 final size:14
Alignment explanation
Indices: 20067269--20067312 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20067259 AAGGATTCAA
20067269 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
20067283 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
20067298 AGATGGGTTTATGG
1 AGATGGGTTTATGG
20067312 A
1 A
20067313 TATAAGTTTT
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:20067337 original size:28 final size:29
Alignment explanation
Indices: 20067269--20067327 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
20067259 AAGGATTCAA
20067269 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATGAAGTTTATGT
*
20067298 AGATGGGTTTATGGATAT-AAGTTTTTGT
1 AGATGGGTTTATGGATATGAAGTTTATGT
20067326 AG
1 AG
20067328 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATGAAGTTTATGT
Found at i:20067955 original size:20 final size:20
Alignment explanation
Indices: 20067909--20067955 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20067899 AGCTCGTTTC
*
20067909 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
20067929 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
20067949 CAGCTCA
1 CAGCTCA
20067956 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:20069471 original size:26 final size:25
Alignment explanation
Indices: 20069416--20069472 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
20069406 ATTGTAATTG
* *
20069416 AAAAAAAAATCAAAAAAAATTGATTG
1 AAAAAAAAATCAAAAAAAAGTGA-TA
*
20069442 AAAAAAAATTCAAAAAAAAAGTGA-A
1 AAAAAAAAATC-AAAAAAAAGTGATA
20069467 AAAAAA
1 AAAAAA
20069473 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 10 0.37
27 11 0.41
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (25 bp):
AAAAAAAAATCAAAAAAAAGTGATA
Found at i:20069482 original size:25 final size:25
Alignment explanation
Indices: 20069452--20069512 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
20069442 AAAAAAAATT
*
20069452 CAAAAAAAAAGTGAAAAAAA-ATCGAG
1 CAAAAAAAAA-AGAAAAAAAGAT-GAG
*
20069478 CAAAAAAAAAAGAAAAAAAGGTGAG
1 CAAAAAAAAAAGAAAAAAAGATGAG
20069503 CAAAAAAAAA
1 CAAAAAAAAA
20069513 TCAAGTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 21 0.66
26 11 0.34
ACGTcount: A:0.74, C:0.07, G:0.15, T:0.05
Consensus pattern (25 bp):
CAAAAAAAAAAGAAAAAAAGATGAG
Found at i:20069483 original size:37 final size:36
Alignment explanation
Indices: 20069411--20069486 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
20069401 AGCATATTGT
* *
20069411 AATTGAAAAAAAAATCAAAAAAAATTGATTGAAAAAA
1 AATTCAAAAAAAAATCAAAAAAAATCGA-TGAAAAAA
*
20069448 AATTCAAAAAAAAAGTGAAAAAAAATCGA-GCAAAAAA
1 AATTCAAAAAAAAA-TCAAAAAAAATCGATG-AAAAAA
20069485 AA
1 AA
20069487 AAGAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 1 0.03
37 21 0.62
38 12 0.35
ACGTcount: A:0.71, C:0.05, G:0.09, T:0.14
Consensus pattern (36 bp):
AATTCAAAAAAAAATCAAAAAAAATCGATGAAAAAA
Found at i:20073814 original size:13 final size:13
Alignment explanation
Indices: 20073796--20073820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20073786 TGGTCATCAT
20073796 GGTGTGAACACAA
1 GGTGTGAACACAA
20073809 GGTGTGAACACA
1 GGTGTGAACACA
20073821 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:20074339 original size:10 final size:10
Alignment explanation
Indices: 20074326--20074363 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
20074316 TTGTAGCTAA
20074326 ATTGAGCTCG
1 ATTGAGCTCG
20074336 ATTGAGCT-G
1 ATTGAGCTCG
20074345 ACTTGAGCTCG
1 A-TTGAGCTCG
*
20074356 AGTGAGCT
1 ATTGAGCT
20074364 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:20074343 original size:20 final size:20
Alignment explanation
Indices: 20074303--20074363 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
20074293 ACCAATAAAA
20074303 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
20074323 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
20074343 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
20074363 T
1 T
20074364 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:20074364 original size:20 final size:20
Alignment explanation
Indices: 20074327--20074364 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20074317 TGTAGCTAAA
*
20074327 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
20074347 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
20074365 GAAACGAGCT
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:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Done.