Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007726.1 Hibiscus syriacus cultivar Beakdansim tig00109973_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 404270
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:323 original size:19 final size:19
Alignment explanation
Indices: 299--349 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
289 GAACATATTC
299 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
318 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
337 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
350 TTCAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:328 original size:62 final size:62
Alignment explanation
Indices: 194--351 Score: 158
Period size: 62 Copynumber: 2.5 Consensus size: 62
184 TGCACCAAGT
* ***
194 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGC---AAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
258 GTGCCATCGATGCAAATGCATTCGATGTTTTG-AACATATTCAGAGTGCATCGATGCATGGAGA
1 GTG-CATCGATGCAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAGA
*
321 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCA---AATGCATTCGATGTT
352 CAATTTAATC
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
62 31 0.39
63 22 0.28
64 3 0.04
65 24 0.30
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (62 bp):
GTGCATCGATGCAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:6389 original size:2 final size:2
Alignment explanation
Indices: 6382--6430 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
6372 TTTTTAAAAC
6382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6424 AT AT AT A
1 AT AT AT A
6431 CCCCCATCCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6614 original size:12 final size:12
Alignment explanation
Indices: 6589--6658 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
6579 TAACGAAGAT
* *
6589 CAGAAATCAAAA
1 CAGAATTCAGAA
6601 CAGAATTCAGAA
1 CAGAATTCAGAA
6613 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
6625 CAGAATCCAGAT
1 CAGAATTCAGAA
*
6637 CAGAAATCAGAA
1 CAGAATTCAGAA
6649 CAGAATTCAG
1 CAGAATTCAG
6659 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:6621 original size:24 final size:24
Alignment explanation
Indices: 6585--6681 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
6575 TCATTAACGA
*
6585 AGATCAGAAATCAAAACAGAATTC
1 AGATCAGAAATCAGAACAGAATTC
* * *
6609 AGAACAGATATCAGAACAGAATCC
1 AGATCAGAAATCAGAACAGAATTC
6633 AGATCAGAAATCAGAACAGAATTC
1 AGATCAGAAATCAGAACAGAATTC
* ***
6657 AGGTCATTTATCAGAACAGAATTC
1 AGATCAGAAATCAGAACAGAATTC
6681 A
1 A
6682 AGTTGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (24 bp):
AGATCAGAAATCAGAACAGAATTC
Found at i:6656 original size:48 final size:48
Alignment explanation
Indices: 6585--6678 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
6575 TCATTAACGA
6585 AGATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
1 AGATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
* ** **
6633 AGATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAAT
1 AGATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAAT
6679 TCAAGTTGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18
Consensus pattern (48 bp):
AGATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
Found at i:6693 original size:24 final size:24
Alignment explanation
Indices: 6588--6695 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
6578 TTAACGAAGA
*
6588 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
6611 AACAGATATCAGAACAGAA-TCCAG
1 -TCAGAAATCAGAACAGAATTCAAG
*
6635 ATCAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAACAGAATTCAAG
***
6660 TCATTTATCAGAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
**
6684 TTGGAAATCAGA
1 TCAGAAATCAGA
6696 TAAAATATTA
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
23 2 0.03
24 61 0.92
25 3 0.05
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:9176 original size:8 final size:8
Alignment explanation
Indices: 9156--9203 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
9146 GGTCAACTCC
9156 GGTCAAC-
1 GGTCAACG
9163 GGTCAACG
1 GGTCAACG
9171 GGTCAACG
1 GGTCAACG
9179 GGTCAACG
1 GGTCAACG
9187 GGT---CG
1 GGTCAACG
9192 GGTCAACG
1 GGTCAACG
9200 GGTC
1 GGTC
9204 GGGTAAACGG
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.14
7 7 0.19
8 25 0.68
ACGTcount: A:0.21, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:9221 original size:18 final size:18
Alignment explanation
Indices: 9200--9243 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
9190 CGGGTCAACG
9200 GGTCGGGTAAACGGGTCA
1 GGTCGGGTAAACGGGTCA
*
9218 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCA
9236 GGTCGGGT
1 GGTCGGGT
9244 TGTGACCGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.18
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCA
Found at i:9238 original size:13 final size:13
Alignment explanation
Indices: 9163--9221 Score: 73
Period size: 13 Copynumber: 4.3 Consensus size: 13
9153 TCCGGTCAAC
9163 GGTCAACGGGTCAACG
1 GGTCAACGGGT---CG
9179 GGTCAACGGGTCG
1 GGTCAACGGGTCG
9192 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
9205 GGTAAACGGGTCA
1 GGTCAACGGGTCG
9218 GGTC
1 GGTC
9222 GGGTAAACGG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
13 29 0.73
16 11 0.28
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:11200 original size:2 final size:2
Alignment explanation
Indices: 11193--11219 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11183 TTTTTAAAAC
11193 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11220 CCCCCATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11405 original size:12 final size:12
Alignment explanation
Indices: 11380--11449 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
11370 ACGAAGATAT
* *
11380 CAGAAATCAAAA
1 CAGAATTCAGAA
11392 CAGAATTCAGAA
1 CAGAATTCAGAA
11404 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
11416 CAGAATCCAGAT
1 CAGAATTCAGAA
*
11428 CAGAAATCAGAA
1 CAGAATTCAGAA
11440 CAGAATTCAG
1 CAGAATTCAG
11450 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:11412 original size:24 final size:24
Alignment explanation
Indices: 11378--11472 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
11368 TAACGAAGAT
*
11378 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
11402 AACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
11426 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* ***
11450 GTCATTTATCAGAACAGAATTCA
1 ATCAGAAATCAGAACAGAATTCA
11473 AGTTGGAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:11449 original size:48 final size:48
Alignment explanation
Indices: 11378--11469 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
11368 TAACGAAGAT
11378 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
* ** **
11426 ATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAAT
11470 TCAAGTTGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
Found at i:11484 original size:24 final size:24
Alignment explanation
Indices: 11379--11486 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
11369 AACGAAGATA
*
11379 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
11402 AACAGATATCAGAACAGAA-TCCAG
1 -TCAGAAATCAGAACAGAATTCAAG
*
11426 ATCAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAACAGAATTCAAG
***
11451 TCATTTATCAGAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
**
11475 TTGGAAATCAGA
1 TCAGAAATCAGA
11487 TAAAATATTT
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
23 2 0.03
24 61 0.92
25 3 0.05
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:13972 original size:7 final size:7
Alignment explanation
Indices: 13960--13991 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
13950 TGGTCAACTC
13960 CGGTCAA
1 CGGTCAA
13967 CGGTCAA
1 CGGTCAA
13974 CGGGTCAA
1 C-GGTCAA
13982 CGGTCAA
1 CGGTCAA
13989 CGG
1 CGG
13992 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:13981 original size:8 final size:8
Alignment explanation
Indices: 13961--14007 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
13951 GGTCAACTCC
13961 GGTCAAC-
1 GGTCAACG
13968 GGTCAACG
1 GGTCAACG
13976 GGTCAAC-
1 GGTCAACG
13983 GGTCAACG
1 GGTCAACG
13991 GGT---CG
1 GGTCAACG
13996 GGTCAACG
1 GGTCAACG
14004 GGTC
1 GGTC
14008 GGGTCGGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:13981 original size:15 final size:15
Alignment explanation
Indices: 13961--14007 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
13951 GGTCAACTCC
13961 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
13976 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
13991 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
14004 GGTC
1 GGTC
14008 GGGTCGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:14001 original size:13 final size:13
Alignment explanation
Indices: 13968--14012 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
13958 TCCGGTCAAC
*
13968 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
13983 GGTCAACGGGTCG
1 GGTCAACGGGTCG
13996 GGTCAACGGGTCG
1 GGTCAACGGGTCG
14009 GGTC
1 GGTC
14013 GGGTAAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:14012 original size:18 final size:18
Alignment explanation
Indices: 13989--14034 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
13979 CAACGGTCAA
*
13989 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
14007 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
14025 CGGGTCGGGT
1 CGGGTCGGGT
14035 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.20, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:17629 original size:64 final size:63
Alignment explanation
Indices: 17559--17739 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
17549 TTGGAACACT
* ***
17559 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * * **
17623 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTTGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
17687 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
17740 CAATTAATTC
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
64 53 0.55
65 44 0.45
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:17711 original size:19 final size:19
Alignment explanation
Indices: 17687--17737 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
17677 GAAAATATTC
17687 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
17706 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
17725 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
17738 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:17713 original size:65 final size:65
Alignment explanation
Indices: 17580--17739 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
17570 TGCACCAAGT
* ***
17580 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* * **
17644 GTGCATCGATGCATCAAATGCATTTGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
17708 A
65 A
* *
17709 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
17740 CAATTAATTC
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.44
65 46 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:20544 original size:31 final size:31
Alignment explanation
Indices: 20490--20617 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
20480 GAACCTCGAC
* * *
20490 AACTGTCCATAGGTCTCGA-AGAACCTAGGTA
1 AACTGTCCATATGT-TCCATAGAACATAGGTA
* *
20521 AATTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * * *
20552 TACTGTCCATATATCTCAAAAG-ACATAGGTAA
1 AACTGTCCATATGT-TCCATAGAACATAGGT-A
20584 AACTGTCCATATGTTCCATAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
20615 AAC
1 AAC
20618 CCTCGACTCT
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
30 2 0.03
31 51 0.65
32 25 0.32
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:21502 original size:20 final size:20
Alignment explanation
Indices: 21477--21514 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21467 TTTCCCTTGA
21477 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
21497 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
21515 TTAACATATG
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:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:23076 original size:2 final size:2
Alignment explanation
Indices: 23069--23129 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
23059 ATAGAAAGAA
23069 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
23111 AC AC AC AC AC AT AC AC AC A
1 AC AC AC AC AC AC AC AC AC A
23130 TATATATATA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:23134 original size:2 final size:2
Alignment explanation
Indices: 23129--23163 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23119 ACATACACAC
23129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23164 GTTTAGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27167 original size:22 final size:24
Alignment explanation
Indices: 27142--27188 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
27132 TAGAATCGAG
27142 AAACTC-CAAGAGA-AACTTATCA
1 AAACTCACAAGAGATAACTTATCA
*
27164 AAACTCAACAAGAGATGACTTATCA
1 AAACTC-ACAAGAGATAACTTATCA
27189 GTGGTATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (24 bp):
AAACTCACAAGAGATAACTTATCA
Found at i:28282 original size:89 final size:89
Alignment explanation
Indices: 28131--28296 Score: 244
Period size: 89 Copynumber: 1.9 Consensus size: 89
28121 CCATATACTC
* ** * **
28131 ATTATATATACAATAAAGATTGAGTTGTCCCTATAAAGCAATTGGTTAATCGTCCTGGCTTTATG
1 ATTATATATACAATAAACATTGAGTTACCCCCATAAAGCAATTGGTTAATCCCCCTGGCTTTATG
28196 GATAATATTCAGATAACCTATATT
66 GATAATATTCAGATAACCTATATT
* *
28220 ATTATATATACAATAAACCTTGAGTTACCCCCCTAAAGCAATTGGTTAATCACCCCT-GCTTTAT
1 ATTATATATACAATAAACATTGAGTTACCCCCATAAAGCAATTGGTTAATC-CCCCTGGCTTTAT
28284 GGATAATATTCAG
65 GGATAATATTCAG
28297 CTAGCATGTT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
89 65 0.96
90 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (89 bp):
ATTATATATACAATAAACATTGAGTTACCCCCATAAAGCAATTGGTTAATCCCCCTGGCTTTATG
GATAATATTCAGATAACCTATATT
Found at i:31012 original size:123 final size:122
Alignment explanation
Indices: 30649--32582 Score: 2486
Period size: 123 Copynumber: 15.7 Consensus size: 122
30639 CACTCGAGGG
* * * ** * * *
30649 ATCAACATTTCCAAAAAGAGTTCATAATAAGAAGAACTTGTTTGAGAAGAAAGAATAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGA-AAGGAAGAAGAAGTTCATA
* * * * * * **
30714 ATCTAAAGAACTTCTTCAGCCTTTTTCTCGACTCTATCGTATAAGGAGATAGAGCTGC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* *
30772 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAGAATGAAGAA-AATTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGA-AAGGAAGAAGAAGTTCATA
* * * * * *
30836 ATATAAAGAACTTATTCAACCTTTTGCTCAACTCTATCACAGAAGGATATAGAGCAGC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
30894 GTCAACATTTTCAGAATGAGTTCGTAATAAGAAGAACTCATCTGAATAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAA-AGGAAGAAGAAGTTCATA
* *
30959 ATCTGAAGAACTTATTCAACCTTTTGCTCAACTCTATCGCAGAAGAAGATAGAGCAAC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* *
31017 ATCAACATTTCGAGAAGGAGTTTGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAA-AGGAAGAAGAAGTTCATA
* *
31082 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAAAAGGAGATAGAGCAGC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
31140 ATCAAACATTTCCAGAAAGAATTCGTAATAAGAAGAACTCATCTAAGAAGGAAGAAGAAGTTCAT
1 ATC-AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGA-AAGGAAGAAGAAGTTCAT
** * * * *
31205 AATCTTTAGAACTTGTTCAACCTTTTGCTTGACTCTATCGCAGAATGAGATAGAGCATC
64 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * * * * *
31264 ATCAACATTTGCAAAAGGAGTTTGTAATAAGAAAAACTCATATGAAAAGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAAGGAAGAAGAAGTTCATAA
* * * * *
31329 TCTGAAAAACTTGTTCAAACTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCATC
66 TCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * * * *
31386 ATCAACATTTTCAAAAGGAGTTTGTAATAAGAAAAACTCATCTGAGAAAGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGA-AAGGAAGAAGAAGTTCATA
* * * * * *
31451 ATCTGAAAAACTTGTTCAACATTTTACTTGACTCTATCGCAGAAGGAGATAGAGCAGC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
31509 ATCAACATTTCCAGAAGGAGTTTGTAATAAGAATAACTCATCTGAGAAGGAAGAAGAAATTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGA-AAGGAAGAAGAAGTTCATA
* * * * *
31574 ATCTAAAGAACTTATTCAACCTTTTTCTCGACTCTATCACAGAAGGAGATAG-GTAGC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
31631 ATCAACATTTCCAGAAAGATTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAA-AGGAAGAAGAAGTTCATA
* *
31696 ATCTAAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAATGAGATAGAGCAAC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
31754 ATCAACATTTCCAGAAGGATTTCATAATAAGAAGAACTCATCTGAGGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGA-AAGGAAGAAGAAGTTCATA
* * *
31819 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCACAGAAGAAGATAGAGTAAC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * * *
31877 ATCAAATATTTCCAAAAAGAGTTCGTAATAAGAAGAACTCATCTGAGAAGAAAGAAGAAGTTCAT
1 ATC-AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGA-AAGGAAGAAGAAGTTCAT
* * * *
31942 AATCTGAAGAACTTATTCAACCTTTTTCTCAACTCTATCACAAAAGGAGATAGAGCAAC
64 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * * *
32001 ATCAAATATTTCCAGAAAGAGTTCGTAATAAGAAGAACACATCTGAGAAGGAAGAAGAAATTCAT
1 ATC-AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGA-AAGGAAGAAGAAGTTCAT
* * * ** *
32066 AATCTAAAGAACTTGTTCAACCTTTTGTTTAACTCTATCGCAGAAGGAGATAGAGCAGC
64 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * * * *
32125 ATTAAACATTTCGAGAAAGAGTTCGTAATAAGAAGAACTAATCTGAAGAGGAAGTAGAAGTTCAT
1 A-TCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAA-AGGAAGAAGAAGTTCAT
* * * * *
32190 AATCTGAAGAAATTATTCAATCTTTTGCTTGACTCTATCGCAAAAGGAGATAGAACAAC
64 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * * * * * * *
32249 GTCAACATTTCTAGAAGGAGTACATAATGAGAATAACTCATCTGGAGAGAAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCT-GAAAGGAAGAAGAAGTTCATA
* *
32314 ATCTGAAGAACTTATTCAACCTTTGGCTCGACTCTATTGCAGAAGGAGATAGAGCAAC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * *
32372 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTTACCTGAAGAGAAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAA-AGGAAGAAGAAGTTCATA
* *
32437 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGTAGAAGGAGATAGATCAAC
65 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
* * * *
32495 ATCAACATTTCCAGAAGAAGTTCATAATAAGAATAACTCATCTAAAAAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCT-GAAAGGAAGAAGAAGTTCATA
** *
32560 ATGAGAAGAACTTGTTCAACCTT
65 ATCTGAAGAACTTATTCAACCTT
32583 AGCTTGATTC
Statistics
Matches: 1610, Mismatches: 187, Indels: 28
0.88 0.10 0.02
Matches are distributed among these distances:
121 2 0.00
122 331 0.21
123 838 0.52
124 437 0.27
125 2 0.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAAGGAAGAAGAAGTTCATAA
TCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC
Found at i:47823 original size:30 final size:30
Alignment explanation
Indices: 47787--47872 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
47777 ATAGAACTTG
* *
47787 CGGTTCACACCGGTTTTACCAGTTTTCATC
1 CGGTTCACACCGGTTTTACCAGTTCTCAGC
* * *
47817 CGGTTCACACTGATTTTACCGGTTCTCAGC
1 CGGTTCACACCGGTTTTACCAGTTCTCAGC
*
47847 CGGTTC-TACCGGTTTTCAACCAGTTC
1 CGGTTCACACCGGTTTT--ACCAGTTC
47873 ATTGCAAAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 7 0.16
30 31 0.69
31 7 0.16
ACGTcount: A:0.16, C:0.30, G:0.19, T:0.35
Consensus pattern (30 bp):
CGGTTCACACCGGTTTTACCAGTTCTCAGC
Found at i:47872 original size:20 final size:20
Alignment explanation
Indices: 47833--47872 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
47823 ACACTGATTT
* *
47833 TACCGGTTCTCAGCCGGTTC
1 TACCGGTTCTCAACCAGTTC
*
47853 TACCGGTTTTCAACCAGTTC
1 TACCGGTTCTCAACCAGTTC
47873 ATTGCAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.33, G:0.20, T:0.33
Consensus pattern (20 bp):
TACCGGTTCTCAACCAGTTC
Found at i:56713 original size:67 final size:67
Alignment explanation
Indices: 56605--56738 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
56595 AAGAAGGTGA
56605 TTGATAATTTCTGAGGACGATCTTCAAAGATGTAATATATTTTAAATACAAATTAAAATTATCAT
1 TTGATAATTTCTGAGGACGATCTTCAAAGATGTAATATATTTTAAATACAAATTAAAATTATCAT
56670 AT
66 AT
*
56672 TTGATAATTTCTGAGGACGATCTTCAAAGATGTAATATATTTTAAATACAAATTAAAATTATTAT
1 TTGATAATTTCTGAGGACGATCTTCAAAGATGTAATATATTTTAAATACAAATTAAAATTATCAT
56737 AT
66 AT
56739 ATATATATAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (67 bp):
TTGATAATTTCTGAGGACGATCTTCAAAGATGTAATATATTTTAAATACAAATTAAAATTATCAT
AT
Found at i:58032 original size:21 final size:22
Alignment explanation
Indices: 58008--58051 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
57998 AAATATTTTC
58008 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
58029 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
58051 T
1 T
58052 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:58366 original size:20 final size:18
Alignment explanation
Indices: 58335--58380 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
58325 TAATTTAAAC
*
58335 ATATACAATTAAAATATAA
1 ATATAAAATTAAAAT-TAA
58354 ATAATAAAATTAAAATTAA
1 AT-ATAAAATTAAAATTAA
58373 ATATAAAA
1 ATATAAAA
58381 AGTAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.24
19 7 0.28
20 12 0.48
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
ATATAAAATTAAAATTAA
Found at i:58381 original size:19 final size:20
Alignment explanation
Indices: 58341--58380 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
58331 AAACATATAC
58341 AATTAAAATATAAATAATAA
1 AATTAAAATATAAATAATAA
58361 AATTAAAAT-TAAAT-ATAA
1 AATTAAAATATAAATAATAA
58379 AA
1 AA
58381 AGTAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 5 0.25
20 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AATTAAAATATAAATAATAA
Found at i:59566 original size:3 final size:3
Alignment explanation
Indices: 59552--59625 Score: 98
Period size: 3 Copynumber: 25.0 Consensus size: 3
59542 GTTGTATCTG
* * *
59552 TAA TAA -AA TAA TAA TAT TAA TAA TAA TAA TAA TAT TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59599 TAA TAA TAA TAA -ATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA
59626 AAAACCAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 3 0.05
3 58 0.94
4 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:60136 original size:113 final size:113
Alignment explanation
Indices: 59967--60455 Score: 811
Period size: 113 Copynumber: 4.4 Consensus size: 113
59957 AGAATCATGC
* *
59967 AAAAGATTGAACAAGTTATTCTCATTATGAACTT-TTCTTCCTTCTCCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
60031 TATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGCG
65 TATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGCG
60080 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
60145 ATGAACTCGACCTAGTAATGATGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGCG
60193 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* **
60258 ATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGAA
66 ATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGCG
60306 AAAAGTTGAACAAGTTCTTCTCATTATGAA----------CTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
60361 ATGAACTCGACCTGGTAATGTTAATCCATCGAATGATGAATTCAAACG
66 ATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGCG
60409 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
60456 TCATTATGAA
Statistics
Matches: 354, Mismatches: 11, Indels: 22
0.91 0.03 0.06
Matches are distributed among these distances:
103 99 0.28
112 27 0.08
113 228 0.64
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGCG
Found at i:60413 original size:103 final size:103
Alignment explanation
Indices: 60233--60445 Score: 392
Period size: 103 Copynumber: 2.1 Consensus size: 103
60223 CTTCTTCTTC
*
60233 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTAATCCATCGAATGATGAA
60298 TTCAAGAAAAAAGTTGAACAAGTTCTTCTCATTATGAA
66 TTCAAGAAAAAAGTTGAACAAGTTCTTCTCATTATGAA
60336 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTAATCCATCGAATGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTAATCCATCGAATGATGAA
*
60401 TTCAA-ACGAAAAGTTGAACAAGTTCTTCTCATTATGAA
66 TTCAAGA-AAAAAGTTGAACAAGTTCTTCTCATTATGAA
60439 CTTCTTC
1 CTTCTTC
60446 TTCCTTCTTC
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
102 1 0.01
103 106 0.99
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (103 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTAATCCATCGAATGATGAA
TTCAAGAAAAAAGTTGAACAAGTTCTTCTCATTATGAA
Found at i:60456 original size:226 final size:217
Alignment explanation
Indices: 59967--60453 Score: 789
Period size: 216 Copynumber: 2.2 Consensus size: 217
59957 AGAATCATGC
*
59967 AAAAGATTGAACAAGTTATTCTCATTATGAACTT-TTCTTCCTTCTCCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTCCAGATGAGTTCTTCTCAT
**
60031 TATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTT
65 TATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGAAAAAAGTTGAACAAGTT
60096 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTAGT
130 CTTCTCATTATGAA--------T-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTAGT
* *
60161 AATGATGATCCATCGAATGATGAATTCAAGCG
186 AATGATAATCCATCGAATGATGAATTCAAACG
*
60193 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTCCAGATGAGTTCTTCTCATT
*
60258 ATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGAAAAAAGTTGAACAAGTTC
66 ATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGAAAAAAGTTGAACAAGTTC
* *
60323 TTCTCATTATGAA-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTAATC
131 TTCTCATTATGAATCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTAGTAATGATAATC
60387 CATCGAATGATGAATTCAAACG
196 CATCGAATGATGAATTCAAACG
60409 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
60454 TCTCATTATG
Statistics
Matches: 251, Mismatches: 9, Indels: 12
0.92 0.03 0.04
Matches are distributed among these distances:
216 114 0.45
225 27 0.11
226 110 0.44
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (217 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTCCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGATGATCCATCGAATGATGAATTCAAGAAAAAAGTTGAACAAGTTC
TTCTCATTATGAATCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTAGTAATGATAATC
CATCGAATGATGAATTCAAACG
Found at i:60929 original size:22 final size:22
Alignment explanation
Indices: 60904--60958 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
60894 GATAAAGCTT
*
60904 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
60926 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
60948 TCATCTTTGAA
1 TCATCTTTGAA
60959 GAGTGTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:64582 original size:8 final size:8
Alignment explanation
Indices: 64569--64593 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
64559 CGGCGGAATA
64569 GGTTTTGG
1 GGTTTTGG
64577 GGTTTTGG
1 GGTTTTGG
64585 GGTTTTGG
1 GGTTTTGG
64593 G
1 G
64594 TGTTCTTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (8 bp):
GGTTTTGG
Found at i:64649 original size:21 final size:21
Alignment explanation
Indices: 64623--64662 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
64613 TAGAACCCCA
*
64623 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
64644 GGGGGGAATCGATTCCCCT
1 GGGGGGAATCGATTCCCCT
64663 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:64671 original size:23 final size:21
Alignment explanation
Indices: 64624--64703 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
64614 AGAACCCCAG
* ***
64624 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTCAA
64645 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC-AA
* * *
64668 GGGGGAAACGGTT-CCCTCAT
1 GGGGGAATCGATTCCCCTCAA
*
64688 GGGGGGATCGATTCCC
1 GGGGGAATCGATTCCC
64704 TCTGCACCAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 11 0.24
21 20 0.43
22 4 0.09
23 11 0.24
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAA
Found at i:68557 original size:22 final size:21
Alignment explanation
Indices: 68515--68554 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
68505 GAGTTTGTTT
*
68515 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
68536 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
68555 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:73529 original size:114 final size:114
Alignment explanation
Indices: 73329--73662 Score: 578
Period size: 114 Copynumber: 2.9 Consensus size: 114
73319 GATCATGCAG
* * * * *
73329 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
73394 ATACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
73443 TTCATCTTTTAAATCTAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
73508 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
73557 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
73622 ACACTTCCAGAAGATGCTATTGGGACTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
73663 CGAGAACATG
Statistics
Matches: 208, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 208 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:77773 original size:27 final size:27
Alignment explanation
Indices: 77743--77794 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
77733 TTATGCAAAT
77743 ATGCAAATGTAAATACAAACGTAAAAA
1 ATGCAAATGTAAATACAAACGTAAAAA
* *
77770 ATGCAAATGTAAATGCAAATGTAAA
1 ATGCAAATGTAAATACAAACGTAAA
77795 TATGTGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (27 bp):
ATGCAAATGTAAATACAAACGTAAAAA
Found at i:77783 original size:12 final size:12
Alignment explanation
Indices: 77743--77795 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
77733 TTATGCAAAT
77743 ATGCAAATGTAA
1 ATGCAAATGTAA
* *
77755 ATACAAACGTAAAAA
1 ATGCAAATGT---AA
77770 ATGCAAATGTAA
1 ATGCAAATGTAA
77782 ATGCAAATGTAA
1 ATGCAAATGTAA
77794 AT
1 AT
77796 ATGTGAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 24 0.71
15 10 0.29
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (12 bp):
ATGCAAATGTAA
Found at i:77895 original size:7 final size:7
Alignment explanation
Indices: 77854--77896 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
77844 ATAAGAGTAT
77854 AAATGCA
1 AAATGCA
* *
77861 CAATGAA
1 AAATGCA
*
77868 AAATGTA
1 AAATGCA
77875 AAGATGCA
1 AA-ATGCA
77883 AAATGCA
1 AAATGCA
77890 AAATGCA
1 AAATGCA
77897 TGTATGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (7 bp):
AAATGCA
Found at i:79445 original size:21 final size:20
Alignment explanation
Indices: 79382--79445 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
79372 TAATGAAATT
79382 TAATATT-TGAAAATAA-AA
1 TAATATTATGAAAATAATAA
* *
79400 TAATA-AAT-AAAAAATATAA
1 TAATATTATGAAAATA-ATAA
79419 TAAATATTATGAAAATAATAA
1 T-AATATTATGAAAATAATAA
79440 GTAATA
1 -TAATA
79446 AAAAAATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
17 5 0.14
18 7 0.20
19 3 0.09
20 4 0.11
21 10 0.29
22 6 0.17
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
TAATATTATGAAAATAATAA
Found at i:79451 original size:18 final size:18
Alignment explanation
Indices: 79396--79452 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
79386 ATTTGAAAAT
79396 AAAATAATAAAT-A-AAA
1 AAAATAATAAATAATAAA
* * **
79412 AATATAATAAATATTATG
1 AAAATAATAAATAATAAA
*
79430 AAAATAATAAGTAATAAA
1 AAAATAATAAATAATAAA
79448 AAAAT
1 AAAAT
79453 TTGAAATAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 11 0.37
18 19 0.63
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (18 bp):
AAAATAATAAATAATAAA
Found at i:80105 original size:21 final size:22
Alignment explanation
Indices: 80081--80124 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
80071 AAATATTTTC
80081 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
80102 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
80124 T
1 T
80125 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:80435 original size:20 final size:18
Alignment explanation
Indices: 80408--80453 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 18
80398 TAATTTAAAC
80408 ATATAAAATTAAAATATAA
1 ATATAAAATTAAAAT-TAA
80427 ATAATAAAATTAAAATTAA
1 AT-ATAAAATTAAAATTAA
80446 ATATAAAA
1 ATATAAAA
80454 AGTAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.23
19 7 0.27
20 13 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATATAAAATTAAAATTAA
Found at i:81588 original size:3 final size:3
Alignment explanation
Indices: 81574--81650 Score: 97
Period size: 3 Copynumber: 26.0 Consensus size: 3
81564 GTTGTATCTG
*
81574 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
*
81619 -AA TAA TAA TTA TAA TAA -AA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
81651 AAAACCAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.09
3 53 0.82
4 6 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:81626 original size:39 final size:39
Alignment explanation
Indices: 81574--81651 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
81564 GTTGTATCTG
81574 TAATAAAATAATAATAATAATAATAATAT-TAATAATAAA
1 TAATAAAATAATAATAATAATAA-AATATATAATAATAAA
*
81613 TAATAAAATAATAATTATAATAAAATATATAATAATAAA
1 TAATAAAATAATAATAATAATAAAATATATAATAATAAA
81652 AAACCAAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 5 0.14
39 32 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (39 bp):
TAATAAAATAATAATAATAATAAAATATATAATAATAAA
Found at i:86047 original size:17 final size:17
Alignment explanation
Indices: 86025--86089 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
86015 CGTATAAATG
86025 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
** *
86042 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGACCT-ATC---A
*
86063 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCA
86080 TCCCGAAGGA
1 TCCCGAAGGA
86090 TGTAATCTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 21 0.57
18 3 0.08
20 2 0.05
21 11 0.30
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:86068 original size:21 final size:21
Alignment explanation
Indices: 86042--86110 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
86032 GGACCTATCA
86042 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
86063 TCCCGAAGGA---C--CTGTCA
1 TCCCGAAGGATGTCATCTGT-G
*
86080 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
86101 TCCCGTAGGA
1 TCCCGAAGGA
86111 CCTATCATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGATGTCATCTGTG
Found at i:86074 original size:38 final size:38
Alignment explanation
Indices: 86023--86118 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
86013 CTCGTATAAA
*
86023 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
86061 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
86099 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
86119 ATGTCTTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:92956 original size:17 final size:17
Alignment explanation
Indices: 92934--92998 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
92924 CGTATAAATG
92934 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
** *
92951 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGACCT-ATC---A
*
92972 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCA
92989 TCCCGAAGGA
1 TCCCGAAGGA
92999 TGTAATCTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 21 0.57
18 3 0.08
20 2 0.05
21 11 0.30
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:92977 original size:21 final size:21
Alignment explanation
Indices: 92951--93019 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
92941 GGACCTATCA
92951 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
92972 TCCCGAAGGA---C--CTGTCA
1 TCCCGAAGGATGTCATCTGT-G
*
92989 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
93010 TCCCGTAGGA
1 TCCCGAAGGA
93020 CCTATCATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGATGTCATCTGTG
Found at i:92983 original size:38 final size:38
Alignment explanation
Indices: 92932--93027 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
92922 CTCGTATAAA
*
92932 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
92970 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
93008 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
93028 ATGTCTTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:93704 original size:36 final size:35
Alignment explanation
Indices: 93646--93714 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 35
93636 TTCATTTAGG
93646 GGAATCGATACCCCCCCAGGGGAATCTGTTCCCGA
1 GGAATCGATACCCCCCCAGGGGAATCTGTTCCCGA
93681 GGAATCGATA-CCCCCCAGGGGGGAATCTGTTCCC
1 GGAATCGATACCCCCCCA--GGGGAATCTGTTCCC
93715 CCTGTACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 7 0.22
35 10 0.31
36 15 0.47
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (35 bp):
GGAATCGATACCCCCCCAGGGGAATCTGTTCCCGA
Found at i:99827 original size:89 final size:88
Alignment explanation
Indices: 99703--99884 Score: 283
Period size: 89 Copynumber: 2.1 Consensus size: 88
99693 CCTATTATTC
* *
99703 ATCATTCTTTGTTCTTAATCGAGTCTAGAACTTTCTAAGTTTGAATCTTCAACAAAATCAAAGTT
1 ATCATTCTTTGTTCTTAATCGAGTCTAGAACTTTCTAAGTTTCAATCTTCAACAAAAGCAAAGTT
*
99768 CATTAATCCGTCACCGCTTCCCT
66 CATTAATCCGCCACCGCTTCCCT
* * * *
99791 ATCATGTCTTTGTTTTTAATCGAGTCTAGAACTTTCTAAGTTTCATTCTTCAACAAGAGCAACGT
1 ATCAT-TCTTTGTTCTTAATCGAGTCTAGAACTTTCTAAGTTTCAATCTTCAACAAAAGCAAAGT
*
99856 TTATTAATCCGCCACCGCTTCCCT
65 TCATTAATCCGCCACCGCTTCCCT
99880 ATCAT
1 ATCAT
99885 CGCTGGTAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
88 5 0.06
89 80 0.94
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (88 bp):
ATCATTCTTTGTTCTTAATCGAGTCTAGAACTTTCTAAGTTTCAATCTTCAACAAAAGCAAAGTT
CATTAATCCGCCACCGCTTCCCT
Found at i:101744 original size:77 final size:77
Alignment explanation
Indices: 101658--101811 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
101648 TTGTTGCTGG
101658 TACTTCCATCCTACATTGTAAGAATAACTAATTAGTAGTTGTTAAACATTTTAAAAGGGAAGAAA
1 TACTTCCATCCTACATTGTAAGAATAACTAATTAGTAGTTGTTAAACATTTTAAAAGGGAAGAAA
101723 AACTAAACTCCA
66 AACTAAACTCCA
101735 TACTTCCATCCTACATTGTAAGAATAACTAATTAGTAGTTGTTAAACATTTTAAAAGGGAAGAAA
1 TACTTCCATCCTACATTGTAAGAATAACTAATTAGTAGTTGTTAAACATTTTAAAAGGGAAGAAA
101800 AACTAAACTCCA
66 AACTAAACTCCA
101812 AGCCAAAAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.30
Consensus pattern (77 bp):
TACTTCCATCCTACATTGTAAGAATAACTAATTAGTAGTTGTTAAACATTTTAAAAGGGAAGAAA
AACTAAACTCCA
Found at i:102982 original size:159 final size:158
Alignment explanation
Indices: 102694--103010 Score: 616
Period size: 159 Copynumber: 2.0 Consensus size: 158
102684 TTCCCTCGCT
102694 GAAACCCAAAGAAAAGAAAAAAAAACTCTTTTTTAATTAATGATTCCGCAAAACTATAAAATCTT
1 GAAACCCAAAGAAAAGAAAAAAAAACTCTTTTTTAATTAATGATTCCGCAAAACTATAAAATCTT
102759 CCAAAAATTTCCGGGGATTTAAAATAGCAGTCAGCCTTCTTAGTAACCAAACAAACAGCTGGAAG
66 CCAAAAATTTCCGGGGATTTAAAATAGCAGTCAGCCTTCTTAGTAACCAAACAAACAGCTGGAAG
102824 AAAATTCAATGGACTGAATAAGAATGAA
131 AAAATTCAATGGACTGAATAAGAATGAA
*
102852 GAAACCCAAAGAAAAGAAAAAAAAAACTCTTTTTTATTTAATGATTCCGCAAAACTATAAAATCT
1 GAAACCCAAAGAAAAG-AAAAAAAAACTCTTTTTTAATTAATGATTCCGCAAAACTATAAAATCT
102917 TCCAAAAATTTCCGGGGATTTAAAATAGCAGTCAGCCTTCTTAGTAACCAAACAAACAGCTGGAA
65 TCCAAAAATTTCCGGGGATTTAAAATAGCAGTCAGCCTTCTTAGTAACCAAACAAACAGCTGGAA
102982 GAAAATTCAATGGACTGAATAAGAATGAA
130 GAAAATTCAATGGACTGAATAAGAATGAA
103011 AAGCAGAAGA
Statistics
Matches: 157, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
158 16 0.10
159 141 0.90
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (158 bp):
GAAACCCAAAGAAAAGAAAAAAAAACTCTTTTTTAATTAATGATTCCGCAAAACTATAAAATCTT
CCAAAAATTTCCGGGGATTTAAAATAGCAGTCAGCCTTCTTAGTAACCAAACAAACAGCTGGAAG
AAAATTCAATGGACTGAATAAGAATGAA
Found at i:110054 original size:105 final size:105
Alignment explanation
Indices: 109838--110319 Score: 822
Period size: 105 Copynumber: 4.6 Consensus size: 105
109828 TTTGTCGGAT
* * * *
109838 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGT-GAATTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
109902 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
109942 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
110007 GGAACAGGCTCTTCTCATTACGAACCTTCTCTTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
110047 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
110112 GGAACAAGTTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* * *
110152 GAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
110217 GGAACGGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* * *
110257 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTTCTTCTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGA
110320 TTGTTGTTGA
Statistics
Matches: 360, Mismatches: 17, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
104 52 0.14
105 308 0.86
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:111264 original size:34 final size:33
Alignment explanation
Indices: 111226--111344 Score: 121
Period size: 34 Copynumber: 3.4 Consensus size: 33
111216 TCTCGAACCC
111226 TTCTTTTTCTTTTTTCTTTTCATTTTTTCTTTTT
1 TTCTTTTT-TTTTTTCTTTTCATTTTTTCTTTTT
*
111260 TTCTTTTTTTTCTTTTTTTTCATTTTTTCATTTTTT
1 TTCTTTTTTTT-TTTCTTTTCATTTTTTC--TTTTT
* * **
111296 TTATTTTTTCTTTTTCACTTTTTCATTTTTTCATTCA
1 TTCTTTTTT-TTTTT--C-TTTTCATTTTTTCTTTTT
111333 TTCTTTTTTTTT
1 TTCTTTTTTTTT
111345 CAAGCATAGT
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
33 3 0.04
34 24 0.34
36 19 0.27
37 12 0.17
39 13 0.18
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (33 bp):
TTCTTTTTTTTTTTCTTTTCATTTTTTCTTTTT
Found at i:111270 original size:17 final size:17
Alignment explanation
Indices: 111237--111343 Score: 100
Period size: 17 Copynumber: 6.5 Consensus size: 17
111227 TCTTTTTCTT
111237 TTTTCTTTTCATTTTTTC
1 TTTT-TTTTCATTTTTTC
*
111255 -TTTTTTTCTTTTTTTTC
1 TTTTTTTTC-ATTTTTTC
111272 TTTTTTTTCATTTTTTC
1 TTTTTTTTCATTTTTTC
111289 ATTTTTTTT-ATTTTTTC
1 -TTTTTTTTCATTTTTTC
*
111306 ---TTTTTCACTTTTTC
1 TTTTTTTTCATTTTTTC
* **
111320 -ATTTTTTCATTCATTC
1 TTTTTTTTCATTTTTTC
111336 TTTTTTTT
1 TTTTTTTT
111344 TCAAGCATAG
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
13 5 0.07
14 7 0.09
16 16 0.21
17 31 0.41
18 16 0.21
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTTCATTTTTTC
Found at i:111318 original size:9 final size:8
Alignment explanation
Indices: 111242--111330 Score: 92
Period size: 8 Copynumber: 11.0 Consensus size: 8
111232 TTCTTTTTTC
111242 TTTTCATT
1 TTTTCATT
*
111250 TTTTCTTT
1 TTTTCATT
*
111258 TTTTCTTTT
1 TTTTC-ATT
*
111267 TTTTCTTTT
1 TTTTC-ATT
111276 TTTTCATT
1 TTTTCATT
111284 TTTTCATTT
1 TTTTCA-TT
*
111293 TTTTTATT
1 TTTTCATT
111301 TTTTC--T
1 TTTTCATT
*
111307 TTTTCACT
1 TTTTCATT
111315 TTTTCATT
1 TTTTCATT
111323 TTTTCATT
1 TTTTCATT
111331 CATTCTTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
6 6 0.08
8 42 0.58
9 24 0.33
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTCATT
Found at i:114890 original size:14 final size:14
Alignment explanation
Indices: 114871--114897 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
114861 AAATGAATGT
114871 AAAGAATGAAGAAC
1 AAAGAATGAAGAAC
114885 AAAGAATGAAGAA
1 AAAGAATGAAGAA
114898 TGAAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAGAATGAAGAAC
Found at i:125949 original size:4 final size:4
Alignment explanation
Indices: 125936--126029 Score: 56
Period size: 4 Copynumber: 23.8 Consensus size: 4
125926 ATTTTGTAAG
* * *
125936 AAAT -AAT AAAT AAAT -ATT AAAT AAAT CAAAG AAAA AAAT AAAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT AAAT
* *
125983 AAAT AAAA AAAT AAAT CAAAGG AAA- AAAT AAA- ATAA- AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT -AAA-T AAAT AAAT AAAT A-AAT AAAT AAAT AAA
126030 AGGAAAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
3 14 0.19
4 45 0.62
5 13 0.18
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:125956 original size:11 final size:11
Alignment explanation
Indices: 125936--126029 Score: 52
Period size: 11 Copynumber: 8.3 Consensus size: 11
125926 ATTTTGTAAG
125936 AAATAATAAAT
1 AAATAATAAAT
*
125947 AAATATTAAAT
1 AAATAATAAAT
125958 AAATCAA-AGAA-
1 AAAT-AATA-AAT
125969 AAA-AATAAAAT
1 AAATAAT-AAAT
* *
125980 AAAAAATAAAA
1 AAATAATAAAT
*
125991 AAATAAATCAAAGG
1 AAAT-AAT-AAA-T
*
126005 AAAAAATAAAAT
1 AAATAAT-AAAT
126017 AAA-AATAAAT
1 AAATAATAAAT
126027 AAA
1 AAA
126030 AGGAAAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
9 2 0.03
10 9 0.14
11 31 0.47
12 12 0.18
13 9 0.14
14 3 0.05
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:125976 original size:17 final size:17
Alignment explanation
Indices: 125954--126014 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
125944 AATAAATATT
125954 AAATAAATCAAAGAAAA
1 AAATAAATCAAAGAAAA
* *
125971 AAATAAAATAAAAAATAAAA
1 AAAT-AAAT--CAAAGAAAA
*
125991 AAATAAATCAAAGGAAA
1 AAATAAATCAAAGAAAA
126008 AAATAAA
1 AAATAAA
126015 ATAAAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
17 17 0.47
18 4 0.11
19 4 0.11
20 11 0.31
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (17 bp):
AAATAAATCAAAGAAAA
Found at i:125976 original size:32 final size:33
Alignment explanation
Indices: 125943--126051 Score: 109
Period size: 37 Copynumber: 3.3 Consensus size: 33
125933 AAGAAATAAT
*
125943 AAATAAATATTAAATAAATCAAAGAAAAAAATA
1 AAATAAATAATAAATAAATCAAAGAAAAAAATA
* *
125976 AAATAAAAAATAAAAAAATAAATCAAAGGAAAAAATA
1 AAAT---AAAT-AATAAATAAATCAAAGAAAAAAATA
*
126013 AAATAAA-AATAAAT-AA--AAGGAAAAAAATA
1 AAATAAATAATAAATAAATCAAAGAAAAAAATA
*
126042 AAAAAAATAA
1 AAATAAATAA
126052 ATTTTAAAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
29 17 0.27
30 2 0.03
31 2 0.03
32 6 0.09
33 4 0.06
34 3 0.05
36 4 0.06
37 26 0.41
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (33 bp):
AAATAAATAATAAATAAATCAAAGAAAAAAATA
Found at i:125995 original size:37 final size:38
Alignment explanation
Indices: 125936--126030 Score: 140
Period size: 37 Copynumber: 2.5 Consensus size: 38
125926 ATTTTGTAAG
*
125936 AAATAATAAATAAATATTAAATAAATCAAAGAAAAAAATA
1 AAATAAAAAATAAATA--AAATAAATCAAAGAAAAAAATA
*
125976 AAATAAAAAATAAA-AAAATAAATCAAAGGAAAAAATA
1 AAATAAAAAATAAATAAAATAAATCAAAGAAAAAAATA
126013 AAAT-AAAAATAAATAAAA
1 AAATAAAAAATAAATAAAA
126031 GGAAAAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
36 9 0.17
37 29 0.56
39 1 0.02
40 13 0.25
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (38 bp):
AAATAAAAAATAAATAAAATAAATCAAAGAAAAAAATA
Found at i:126031 original size:28 final size:28
Alignment explanation
Indices: 125967--126102 Score: 112
Period size: 28 Copynumber: 5.1 Consensus size: 28
125957 TAAATCAAAG
*
125967 AAAA-AAATAAAA-TAAAAAAT--AA-A
1 AAAATAAATAAAAGGAAAAAATAAAATA
*
125990 AAAATAAATCAAAGGAAAAAATAAAATA
1 AAAATAAATAAAAGGAAAAAATAAAATA
126018 AAAATAAATAAAAGGAAAAAA-ATAAA-A
1 AAAATAAATAAAAGGAAAAAATA-AAATA
** **
126045 AAAATAAATTTTAA--AAGTAATAAAATA
1 AAAATAAA-TAAAAGGAAAAAATAAAATA
*
126072 AAAAT-AATAAGAAGTAAAAAATAAAATA
1 AAAATAAATAA-AAGGAAAAAATAAAATA
126100 AAA
1 AAA
126103 CAAATAATAA
Statistics
Matches: 90, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
23 4 0.04
24 7 0.08
25 8 0.09
26 11 0.12
27 19 0.21
28 41 0.46
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (28 bp):
AAAATAAATAAAAGGAAAAAATAAAATA
Found at i:126046 original size:37 final size:38
Alignment explanation
Indices: 125958--126102 Score: 111
Period size: 37 Copynumber: 3.7 Consensus size: 38
125948 AATATTAAAT
* *
125958 AAATCAAAG-AAAAAAATAAAATAAAAAATAAAAAAAT
1 AAATAAAAGAAAAAAAATAAAATAAAAAATAAAAAAAG
* *
125995 AAATCAAAG-GAAAAAATAAAAT-AAAAATAAATAAAAGG
1 AAATAAAAGAAAAAAAATAAAATAAAAAATAAA-AAAA-G
* * *
126033 AAA-AAAATAAAAAAAATAAATTTTAAAAGTAATAAAATAA-
1 AAATAAAAGAAAAAAAATAAA--ATAAAA--AATAAAAAAAG
126073 AAATAATAAGAAGTAAAAAATAAAATAAAA
1 AAATAA-AAGAA--AAAAAATAAAATAAAA
126103 CAAATAATAA
Statistics
Matches: 87, Mismatches: 9, Indels: 19
0.76 0.08 0.17
Matches are distributed among these distances:
36 9 0.10
37 28 0.32
38 13 0.15
40 4 0.05
41 5 0.06
42 12 0.14
43 6 0.07
44 10 0.11
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.17
Consensus pattern (38 bp):
AAATAAAAGAAAAAAAATAAAATAAAAAATAAAAAAAG
Found at i:126068 original size:9 final size:8
Alignment explanation
Indices: 126005--126114 Score: 51
Period size: 7 Copynumber: 14.5 Consensus size: 8
125995 AAATCAAAGG
126005 AAAA-AAT
1 AAAATAAT
126012 AAAAT-A-
1 AAAATAAT
126018 AAAATAAAT
1 AAAAT-AAT
* *
126027 AAAAGGAAA
1 AAAA-TAAT
126036 AAAATAA-
1 AAAATAAT
126043 AAAA-AAT
1 AAAATAAT
**
126050 -AAATTTT
1 AAAATAAT
126057 AAAAGTAAT
1 AAAA-TAAT
126066 AAAAT-A-
1 AAAATAAT
126072 AAAATAAT
1 AAAATAAT
* *
126080 AAGA-AGT
1 AAAATAAT
126087 AAAA-AAT
1 AAAATAAT
*
126094 AAAATAAA
1 AAAATAAT
126102 ACAAATAAT
1 A-AAATAAT
126111 AAAA
1 AAAA
126115 ACATACTAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
6 15 0.19
7 23 0.30
8 16 0.21
9 23 0.30
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (8 bp):
AAAATAAT
Found at i:126073 original size:5 final size:5
Alignment explanation
Indices: 125970--126052 Score: 50
Period size: 5 Copynumber: 16.6 Consensus size: 5
125960 ATCAAAGAAA
* *
125970 AAAAT AAAAT AAAA- AATAAA AAAAT -AAAT CAAAGGAA AAAAT AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT -AAA--AT AAAAT AAAAT
* *
126017 AAAA- ATAAAT AAAAG GAAA- AAAAT AAAA- AAAAT AAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
126053 TTTTAAAAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
4 14 0.23
5 39 0.63
6 5 0.08
7 3 0.05
8 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.05, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:126114 original size:54 final size:54
Alignment explanation
Indices: 126009--126114 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
125999 CAAAGGAAAA
* **
126009 AATAAAATAAAAATAAATAAAAGGAAAAAAATAAAAAAAATAAATTTTAAAAGT
1 AATAAAATAAAAATAAATAAAAGGAAAAAAATAAAAAAAACAAATAATAAAAGT
*
126063 AATAAAATAAAAAT-AATAAGAA-GTAAAAAATAAAATAAAACAAATAATAAAA
1 AATAAAATAAAAATAAATAA-AAGGAAAAAAATAAAA-AAAACAAATAATAAAA
126115 ACATACTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 17 0.37
54 29 0.63
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (54 bp):
AATAAAATAAAAATAAATAAAAGGAAAAAAATAAAAAAAACAAATAATAAAAGT
Found at i:127061 original size:12 final size:12
Alignment explanation
Indices: 127033--127081 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
127023 ATTAAAATTA
*
127033 AATAA-ATAAGT
1 AATAATATAAAT
*
127044 ATTAATATAAAT
1 AATAATATAAAT
127056 AATAATATAAAT
1 AATAATATAAAT
127068 AATAATAATAAAT
1 AATAAT-ATAAAT
127081 A
1 A
127082 TTATTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 4 0.12
12 22 0.67
13 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:127154 original size:44 final size:43
Alignment explanation
Indices: 127102--127278 Score: 210
Period size: 44 Copynumber: 4.3 Consensus size: 43
127092 AATATATATA
* *
127102 AATATATATATTATATTTATTTTCCAAAAT-GTTTTCAAAACTAT
1 AATATATATA-TATA-TTATTTTCAAAAATAATTTTCAAAACTAT
*
127146 AATATATATATATATATATATTCAAAAATAATTTTCAAAACTAT
1 AATATATATATATAT-TATTTTCAAAAATAATTTTCAAAACTAT
* *
127190 AATATATATATATA-TATTTTAAAAAATCATTTTCAAAAC--T
1 AATATATATATATATTATTTTCAAAAATAATTTTCAAAACTAT
*
127230 -ATATA-ATATATA-TATTTTCAAAAATAATTTTCAAAATTAT
1 AATATATATATATATTATTTTCAAAAATAATTTTCAAAACTAT
127270 -ATA-ATATAT
1 AATATATATAT
127279 TTTCAAAAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
38 29 0.24
39 6 0.05
40 9 0.08
42 23 0.19
43 15 0.13
44 37 0.31
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.44
Consensus pattern (43 bp):
AATATATATATATATTATTTTCAAAAATAATTTTCAAAACTAT
Found at i:127289 original size:36 final size:38
Alignment explanation
Indices: 127150--127288 Score: 171
Period size: 40 Copynumber: 3.7 Consensus size: 38
127140 AACTATAATA
*
127150 TATATATATATATATATTC-AAAAATAATTTTCAAAAC
1 TATATATATATATATTTTCAAAAAATAATTTTCAAAAC
* *
127187 TATAATATATATATATATATTTTAAAAAATCATTTTCAAAAC
1 --T-ATATATATATATAT-TTTCAAAAAATAATTTTCAAAAC
127229 TATATAATATATATATTTTC-AAAAATAATTTTCAAAA-
1 TATAT-ATATATATATTTTCAAAAAATAATTTTCAAAAC
127266 T-TATATA-ATATATTTTCAAAAAA
1 TATATATATATATATTTTCAAAAAA
127289 ACCAATTTTT
Statistics
Matches: 90, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
34 10 0.11
35 8 0.09
36 3 0.03
37 1 0.01
38 16 0.18
39 8 0.09
40 25 0.28
41 2 0.02
42 17 0.19
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.42
Consensus pattern (38 bp):
TATATATATATATATTTTCAAAAAATAATTTTCAAAAC
Found at i:130573 original size:2 final size:2
Alignment explanation
Indices: 130566--130595 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
130556 ATTTAAGATA
130566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
130596 CATCGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:131150 original size:21 final size:21
Alignment explanation
Indices: 131124--131173 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
131114 ATTTATCGTG
*
131124 ATTGCGAGC-GTCGCGGGCGCT
1 ATTGCG-GCTGTCGCGGACGCT
*
131145 ATTGCGGCTGTCGCGGATGCT
1 ATTGCGGCTGTCGCGGACGCT
131166 ATTGCGGC
1 ATTGCGGC
131174 CATCGCAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.10, C:0.26, G:0.40, T:0.24
Consensus pattern (21 bp):
ATTGCGGCTGTCGCGGACGCT
Found at i:132006 original size:21 final size:20
Alignment explanation
Indices: 131964--132007 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
131954 GTTTGTTGAA
*
131964 TTATTACAAAATTGATATGT
1 TTATTACAAAATTGATAAGT
131984 TTATTA-AAAATAATGATAAGT
1 TTATTACAAAAT--TGATAAGT
132005 TTA
1 TTA
132008 AGGACTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 6 0.29
21 10 0.48
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (20 bp):
TTATTACAAAATTGATAAGT
Found at i:137181 original size:2 final size:2
Alignment explanation
Indices: 137174--137205 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
137164 TTGTAATTCT
137174 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
137206 TGCTTGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:144976 original size:20 final size:20
Alignment explanation
Indices: 144944--144983 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
144934 GATTAAAATG
144944 ATTTAAAAGTAATATATTAA
1 ATTTAAAAGTAATATATTAA
*
144964 ATTTATAAA-TAATATTTTAA
1 ATTTA-AAAGTAATATATTAA
144984 TAAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTTAAAAGTAATATATTAA
Found at i:146437 original size:3 final size:3
Alignment explanation
Indices: 146429--146483 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
146419 TTTAATTATT
* *
146429 TAA TAA TAA TAA TAA TAA -AA GAAA TAA -AA TAA TAA TAA T-A TATT
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A
146473 TAA TAA TAA TA
1 TAA TAA TAA TA
146484 TTAAAAAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
2 6 0.14
3 34 0.77
4 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:146969 original size:113 final size:113
Alignment explanation
Indices: 146711--147309 Score: 979
Period size: 113 Copynumber: 5.3 Consensus size: 113
146701 GATGTAATCT
* * * * * * *
146711 AGCAAAAAGTTGAACAAATTCTTCTTATTATGAATTTCTTC-TCATTCTTCAGCTGAGTTCTTCT
1 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
146775 TATTATGAAC-TCCTTCTGGAAATGTTGATCCATCG-GTGATGAATTAA
66 CATTATGAACTTCC-TCTGGAAAAGTTAATCCATCGAGTGATGAATTCA
*
146822 AGCAAAAGGTTAAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
146887 CATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCA
66 CATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCA
146935 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
147000 CATTATGAACTTCCTCTAGAAAAGTTAATCCATCGAGTGATGAATTCA
66 CATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCA
147048 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
147113 CATTATAAACTTCCTCTGGAAAAGTTAATCCATAGAGTGATGAATTCA
66 CATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCA
* *
147161 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
147226 CATTATGAAATTCCTCTAGAAAAGTTAATCCATTGAGTGATGAATTCA
66 CATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCA
*
147274 AGTAAAAGGTTAAACAAGTTCTTCTCATTATGAACT
1 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACT
147310 CTGGAAAAGT
Statistics
Matches: 460, Mismatches: 25, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
111 35 0.08
112 49 0.11
113 376 0.82
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (113 bp):
AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCA
Found at i:147307 original size:38 final size:38
Alignment explanation
Indices: 147265--147376 Score: 87
Period size: 38 Copynumber: 3.1 Consensus size: 38
147255 CCATTGAGTG
147265 ATGAATTCAAGTAAAAGGTTAAACAAGTTCTTCTCATT
1 ATGAATTCAAGTAAAAGGTTAAACAAGTTCTTCTCATT
* * * * * * * *
147303 ATGAACTC-TGGAAAA-GTT----TA-TCCATC-GAGTG
1 ATGAATTCAAGTAAAAGGTTAAACAAGTTCTTCTCA-TT
147334 ATGAATTCAAGTAAAAGGTTAAACAAGTTCTTCTCATT
1 ATGAATTCAAGTAAAAGGTTAAACAAGTTCTTCTCATT
147372 ATGAA
1 ATGAA
147377 CTTCTTATTC
Statistics
Matches: 49, Mismatches: 16, Indels: 18
0.59 0.19 0.22
Matches are distributed among these distances:
30 1 0.02
31 12 0.24
32 6 0.12
33 3 0.06
36 3 0.06
37 6 0.12
38 17 0.35
39 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (38 bp):
ATGAATTCAAGTAAAAGGTTAAACAAGTTCTTCTCATT
Found at i:147333 original size:69 final size:69
Alignment explanation
Indices: 147217--147378 Score: 261
Period size: 69 Copynumber: 2.3 Consensus size: 69
147207 TCTTCAGATG
*
147217 AGTTCTTCTCATTATGAAATTCCTCTAGAAAAGTTAATCCATTGAGTGATGAATTCAAGTAAAAG
1 AGTTCTTCTCATTATG-AA---CTCTAGAAAAGTTAATCCATCGAGTGATGAATTCAAGTAAAAG
147282 GTTAAACA
62 GTTAAACA
* *
147290 AGTTCTTCTCATTATGAACTCTGGAAAAGTTTATCCATCGAGTGATGAATTCAAGTAAAAGGTTA
1 AGTTCTTCTCATTATGAACTCTAGAAAAGTTAATCCATCGAGTGATGAATTCAAGTAAAAGGTTA
147355 AACA
66 AACA
147359 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
147379 TCTTATTCCT
Statistics
Matches: 86, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
69 68 0.79
72 2 0.02
73 16 0.19
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (69 bp):
AGTTCTTCTCATTATGAACTCTAGAAAAGTTAATCCATCGAGTGATGAATTCAAGTAAAAGGTTA
AACA
Found at i:147352 original size:182 final size:182
Alignment explanation
Indices: 147126--147491 Score: 606
Period size: 182 Copynumber: 2.0 Consensus size: 182
147116 TATAAACTTC
147126 CTCTGGAAAAGTTAATCCATAGAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTA
1 CTCTGGAAAAGTTAATCCATAGAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTA
* * *
147191 TGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAATTCCTCTAGAAAAGTTAATC
66 TGAACTTCTTATTCATTCTTCAGATGAGTTCTTCTCATTATGAAATTCATCTAGAAAAGTTAATC
* * * *
147256 CATTGAGTGATGAATTCAAGTAAAAGGTTAAACAAGTTCTTCTCATTATGAA
131 CATCGAGTGATGAATTCAAGAAAAAGGTTAAACAAGTTATTCTCATTATAAA
* * *
147308 CTCTGGAAAAGTTTATCCATCGAGTGATGAATTCAAGTAAAAGGTTAAACAAGTTCTTCTCATTA
1 CTCTGGAAAAGTTAATCCATAGAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTA
* * * *
147373 TGAACTTCTTATTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTTCATCTGGAAAAGTTAATC
66 TGAACTTCTTATTCATTCTTCAGATGAGTTCTTCTCATTATGAAATTCATCTAGAAAAGTTAATC
147438 CATCGAGTGATGAATTCAAGAAAAAGGTTAAACAAGTTATTCTCATTATAAA
131 CATCGAGTGATGAATTCAAGAAAAAGGTTAAACAAGTTATTCTCATTATAAA
147490 CT
1 CT
147492 TCTTCTTCCT
Statistics
Matches: 170, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 170 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (182 bp):
CTCTGGAAAAGTTAATCCATAGAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTA
TGAACTTCTTATTCATTCTTCAGATGAGTTCTTCTCATTATGAAATTCATCTAGAAAAGTTAATC
CATCGAGTGATGAATTCAAGAAAAAGGTTAAACAAGTTATTCTCATTATAAA
Found at i:147352 original size:295 final size:295
Alignment explanation
Indices: 146991--147528 Score: 916
Period size: 295 Copynumber: 1.8 Consensus size: 295
146981 TCTTCAGATG
146991 AGTTCTTCTCATTATGAACTTCCTCTAGAAAAGTTAATCCATCGAGTGATGAATTCAAGCAAAAG
1 AGTTCTTCTCATTATGAA---CCTCTAGAAAAGTTAATCCATCGAGTGATGAATTCAAGCAAAAG
*
147056 GTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAA
63 GTTAAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATAA
* * *
147121 ACTTCCTCTGGAAAAGTTAATCCATAGAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCT
128 ACTTCATCTGGAAAAGTTAATCCATAGAGTGATGAATTCAAGAAAAAGGTTAAACAAGTTATTCT
* *
147186 CATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAATTCCTCTAGAAAAGT
193 CATTATAAACTTCTTCTTCATTCTTCAGATGAGTT-TTCTCATTATGAAATTCCTCTAGAAAAGT
147251 TAATCCATTGAGTGATGAATTCAAGTAAAAGGTTAAACA
257 TAATCCATTGAGTGATGAATTCAAGTAAAAGGTTAAACA
* * *
147290 AGTTCTTCTCATTATGAA-CTCTGGAAAAGTTTATCCATCGAGTGATGAATTCAAGTAAAAGGTT
1 AGTTCTTCTCATTATGAACCTCTAGAAAAGTTAATCCATCGAGTGATGAATTCAAGCAAAAGGTT
* *
147354 AAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTTTTCTCATTATGAACT
66 AAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT
*
147419 TCATCTGGAAAAGTTAATCCATCGAGTGATGAATTCAAGAAAAAGGTTAAACAAGTTATTCTCAT
131 TCATCTGGAAAAGTTAATCCATAGAGTGATGAATTCAAGAAAAAGGTTAAACAAGTTATTCTCAT
*
147484 TATAAACTTCTTCTTCCTTCTTCAGATGAGTTTTCTCATTATGAA
196 TATAAACTTCTTCTTCATTCTTCAGATGAGTTTTCTCATTATGAA
147529 CTCTACCTGG
Statistics
Matches: 226, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
294 13 0.06
295 195 0.86
299 18 0.08
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (295 bp):
AGTTCTTCTCATTATGAACCTCTAGAAAAGTTAATCCATCGAGTGATGAATTCAAGCAAAAGGTT
AAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT
TCATCTGGAAAAGTTAATCCATAGAGTGATGAATTCAAGAAAAAGGTTAAACAAGTTATTCTCAT
TATAAACTTCTTCTTCATTCTTCAGATGAGTTTTCTCATTATGAAATTCCTCTAGAAAAGTTAAT
CCATTGAGTGATGAATTCAAGTAAAAGGTTAAACA
Found at i:147492 original size:113 final size:111
Alignment explanation
Indices: 147290--147532 Score: 393
Period size: 113 Copynumber: 2.2 Consensus size: 111
147280 AGGTTAAACA
* * *
147290 AGTTCTTCTCATTATGAA--CTCTGGAAAAGTTTATCCATCGAGTGATGAATTCAAGTAAAAGGT
1 AGTTTTTCTCATTATGAACTCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAAGAAAAAGGT
* *
147353 TAAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATG
66 TAAACAAGTTATTCTCATTATAAACTTCTTATTCCTTCTTCAGATG
147399 AGTTTTTCTCATTATGAACTTCATCTGGAAAAGTTAATCCATCGAGTGATGAATTCAAGAAAAAG
1 AGTTTTTCTCATTATGAAC-TC-TCTGGAAAAGTTAATCCATCGAGTGATGAATTCAAGAAAAAG
*
147464 GTTAAACAAGTTATTCTCATTATAAACTTCTTCTTCCTTCTTCAGATG
64 GTTAAACAAGTTATTCTCATTATAAACTTCTTATTCCTTCTTCAGATG
147512 AG-TTTTCTCATTATGAACTCT
1 AGTTTTTCTCATTATGAACTCT
147533 ACCTGGCAAT
Statistics
Matches: 124, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
109 17 0.14
110 1 0.01
111 2 0.02
112 17 0.14
113 87 0.70
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (111 bp):
AGTTTTTCTCATTATGAACTCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAAGAAAAAGGT
TAAACAAGTTATTCTCATTATAAACTTCTTATTCCTTCTTCAGATG
Found at i:148746 original size:18 final size:18
Alignment explanation
Indices: 148723--148772 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
148713 ATGTGAAAAA
148723 ATAAATTGAATTTCGAAT
1 ATAAATTGAATTTCGAAT
148741 ATAAATTGAATTTCGAAT
1 ATAAATTGAATTTCGAAT
148759 ATAAATTGAATTTC
1 ATAAATTGAATTTC
148773 AAAAAGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (18 bp):
ATAAATTGAATTTCGAAT
Found at i:149170 original size:17 final size:16
Alignment explanation
Indices: 149144--149186 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
149134 TTTTTCATCA
*
149144 TTTTCATCATTTTTTTC
1 TTTTCTTCA-TTTTTTC
149161 TTTTCTTCATTTTTTC
1 TTTTCTTCATTTTTTC
149177 TTCTTCTTCA
1 TT-TTCTTCA
149187 GGCATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTCTTCATTTTTTC
Found at i:152153 original size:20 final size:20
Alignment explanation
Indices: 152130--152180 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
152120 ATATCTATAC
152130 TCAGACCAGGCATATCTTGA
1 TCAGACCAGGCATATCTTGA
152150 TCAGACCAGGCATATCTTGA
1 TCAGACCAGGCATATCTTGA
*
152170 TAAGACCAGGC
1 TCAGACCAGGC
152181 GAAGATATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (20 bp):
TCAGACCAGGCATATCTTGA
Found at i:152593 original size:24 final size:24
Alignment explanation
Indices: 152529--152594 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
152519 AAATTTATGA
*
152529 AATAAA-TATAAAGAATGAGAAAT
1 AATAAAGTATAAAGAATGAAAAAT
*
152552 AATAAATGTA-AAAAAATGTAAAAAT
1 AATAAA-GTATAAAGAATG-AAAAAT
*
152577 -GTAAAGTATAAAGAATGA
1 AATAAAGTATAAAGAATGA
152595 TTGCCATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 10 0.29
24 18 0.51
25 7 0.20
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.23
Consensus pattern (24 bp):
AATAAAGTATAAAGAATGAAAAAT
Found at i:158342 original size:15 final size:15
Alignment explanation
Indices: 158316--158363 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
158306 TTCAACCATC
*
158316 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
158332 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
158349 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
158364 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:160393 original size:20 final size:20
Alignment explanation
Indices: 160320--160400 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
160310 CCAGAACCCC
*
160320 AGGGGGTATCGATTCCCTGT-
1 AGGGGGAATCGATTCCCT-TA
* *
160340 GGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATT-CCCTT--A
*
160363 AGGGGGAATCGGTTCCCTTA
1 AGGGGGAATCGATTCCCTTA
* *
160383 TGGGGGTATCGATTCCCT
1 AGGGGGAATCGATTCCCT
160401 CTGCACCAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 28 0.56
21 4 0.08
22 5 0.10
23 13 0.26
ACGTcount: A:0.16, C:0.22, G:0.35, T:0.27
Consensus pattern (20 bp):
AGGGGGAATCGATTCCCTTA
Found at i:169758 original size:2 final size:2
Alignment explanation
Indices: 169751--169775 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
169741 AATTTTAAGA
169751 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
169776 AATAAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:170033 original size:21 final size:21
Alignment explanation
Indices: 169996--170039 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
169986 GCCCTTTCTT
169996 AATATTGATAAATATATATTAA
1 AATATTGATAAATATAT-TTAA
170018 AATA-TGATTAAA-ATATTTAA
1 AATATTGA-TAAATATATTTAA
170038 AA
1 AA
170040 GTAATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 7 0.33
22 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
AATATTGATAAATATATTTAA
Found at i:170182 original size:29 final size:27
Alignment explanation
Indices: 170147--170225 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 27
170137 ATATGAACAT
170147 ATAAAATTTAAAATATAAATAAAAAA-TA
1 ATAAAA-TTAAAAT-TAAATAAAAAAGTA
*
170175 ACTAAAATTAACATTAAATATAAAAAGTA
1 A-TAAAATTAAAATTAAATA-AAAAAGTA
* *
170204 ATAAGACTTATAATTAAATAAA
1 ATAA-AATTAAAATTAAATAAA
170226 GGTATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
27 6 0.14
28 17 0.40
29 20 0.47
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.29
Consensus pattern (27 bp):
ATAAAATTAAAATTAAATAAAAAAGTA
Found at i:171471 original size:3 final size:3
Alignment explanation
Indices: 171463--171505 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
171453 TGTAATTATT
*
171463 TAA TAA TAA TAA TAA TAA -AA GAAA TAA -AA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
171506 TAAAAAATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
2 4 0.11
3 30 0.83
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:171500 original size:26 final size:27
Alignment explanation
Indices: 171464--171519 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
171454 GTAATTATTT
171464 AATAATAATAATAATA-AAAGAAATA-A
1 AATAATAATAATAATATAAA-AAATACA
171490 AATAATAATAATAATATAAAAAATACA
1 AATAATAATAATAATATAAAAAATACA
171517 AAT
1 AAT
171520 GGGTAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (27 bp):
AATAATAATAATAATATAAAAAATACA
Found at i:184746 original size:31 final size:31
Alignment explanation
Indices: 184693--184775 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
184683 CATTATTTTT
* * *
184693 TAATATTTTCGGTTA-TTTTTTAACGTCTAA
1 TAATGTTTTCGGTCATTTTTTTAACGCCTAA
*
184723 TAATGTTTTCGGTCATTTTTTTAATGCCTAA
1 TAATGTTTTCGGTCATTTTTTTAACGCCTAA
*
184754 TAATGTTTCCGGTCATTTTTTT
1 TAATGTTTTCGGTCATTTTTTT
184776 TAAAAATCCG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 13 0.28
31 34 0.72
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (31 bp):
TAATGTTTTCGGTCATTTTTTTAACGCCTAA
Found at i:188246 original size:137 final size:137
Alignment explanation
Indices: 187930--188246 Score: 384
Period size: 138 Copynumber: 2.3 Consensus size: 137
187920 ACTAAGGTTT
* * *
187930 AATTTATTAGGGTTTAATATTAGAGTCTACACTTTAGGTTTATTTTTATTTTAGTCCCTAATTTT
1 AATTTATTAGGGTTTAATATTAGAGCCTA-ACTTTAGGTTTAATTTCATTTTAGTCCCTAATTTT
* * * * *
187995 AGGGGAATATTTAAAATGGTCCCTGCCAATACTCGAGGTTTCATTTTAATTATTCGGCAGAACAG
65 AGGGGAATATGTAAAAGGGTCCCTGCCAATACTCGAGGTTCCATCTTAATTATTCGACAGAACAG
*
188060 ACTTGTAA
130 AATTGTAA
* * * *
188068 AATTTATTATGGTTTAATATTAGAGCCTGCACTTTATGTTTAATTTCATTTTAGTCCCTACTTTT
1 AATTTATTAGGGTTTAATATTAGAGCCT-AACTTTAGGTTTAATTTCATTTTAGTCCCTAATTTT
* * * * * ** * *
188133 AGGGGAATATGTAAAAGGGTCCC-GTCAATGCTTGGGGTTCCATCTTAATTATTTGATTGAATAT
65 AGGGGAATATGTAAAAGGGTCCCTGCCAATACTCGAGGTTCCATCTTAATTATTCGACAGAACAG
*
188197 AATTTTAA
130 AATTGTAA
*
188205 AATTTATTAGGGTTTAATATTAGAGCCTAAATTATAGGTTTA
1 AATTTATTAGGGTTTAATATTAGAGCCTAACTT-TAGGTTTA
188247 GTTCTATTAA
Statistics
Matches: 150, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
136 3 0.02
137 69 0.46
138 78 0.52
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (137 bp):
AATTTATTAGGGTTTAATATTAGAGCCTAACTTTAGGTTTAATTTCATTTTAGTCCCTAATTTTA
GGGGAATATGTAAAAGGGTCCCTGCCAATACTCGAGGTTCCATCTTAATTATTCGACAGAACAGA
ATTGTAA
Found at i:191413 original size:15 final size:16
Alignment explanation
Indices: 191383--191432 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
191373 AATATTAAAA
191383 ATAATTATTATATATAT
1 ATAA-TATTATATATAT
191400 ATAATATT-TATATAT
1 ATAATATTATATATAT
* *
191415 TTAAT-TTAAATATAT
1 ATAATATTATATATAT
191430 ATA
1 ATA
191433 CTCGGCCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 19 0.66
16 4 0.14
17 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAATATTATATATAT
Found at i:206481 original size:32 final size:32
Alignment explanation
Indices: 206407--206594 Score: 279
Period size: 32 Copynumber: 5.8 Consensus size: 32
206397 GAGTCGATGG
* * *
206407 TTACCAATGTCCTTT-GAGACATATGGACAGATT
1 TTACCTATGT-CTTTCGGGACATATGGACAG-TA
206440 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGTA
* *
206472 TTACCTATGTCTTTCGGGATATATGGATAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGTA
206504 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGTA
** *
206536 TTACCTATGTCTTTTAGGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAGTA
206568 TTACCTATGTCTTTCGGGACATATGGA
1 TTACCTATGTCTTTCGGGACATATGGA
206595 TAGTTACATA
Statistics
Matches: 142, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
32 119 0.84
33 23 0.16
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGTA
Found at i:207291 original size:11 final size:11
Alignment explanation
Indices: 207275--207311 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
207265 TTTTTATGAA
207275 AGTATTGTAGC
1 AGTATTGTAGC
207286 AGTATTGTAGC
1 AGTATTGTAGC
* *
207297 ATTATTGTAGT
1 AGTATTGTAGC
207308 AGTA
1 AGTA
207312 CCGTAACAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (11 bp):
AGTATTGTAGC
Found at i:212000 original size:18 final size:20
Alignment explanation
Indices: 211977--212018 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
211967 AGCATATATT
*
211977 CATACAA-ATCATAT-AACA
1 CATACAATACCATATAAACA
211995 CATACAATACCATATAAACA
1 CATACAATACCATATAAACA
212015 CATA
1 CATA
212019 TACTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (20 bp):
CATACAATACCATATAAACA
Found at i:212567 original size:62 final size:63
Alignment explanation
Indices: 212492--212627 Score: 238
Period size: 62 Copynumber: 2.2 Consensus size: 63
212482 GCTTCCCAGG
*
212492 TATCGATACCCCATGAATAATTTATAAATTTCTACCTTAT-GTATCGATACTCATCCATATGA
1 TATCGATACCCCATGAATAATTTATAAATTTCTACCATATGGTATCGATACTCATCCATATGA
* *
212554 TATCGATACCCCATGAATAATTTATAAATTTCTACCATATGGTATCGGTACTCATCCATATGG
1 TATCGATACCCCATGAATAATTTATAAATTTCTACCATATGGTATCGATACTCATCCATATGA
212617 TATCGATACCC
1 TATCGATACCC
212628 TCACTCGAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 39 0.56
63 31 0.44
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.35
Consensus pattern (63 bp):
TATCGATACCCCATGAATAATTTATAAATTTCTACCATATGGTATCGATACTCATCCATATGA
Found at i:214454 original size:148 final size:148
Alignment explanation
Indices: 214186--214482 Score: 567
Period size: 148 Copynumber: 2.0 Consensus size: 148
214176 ATTCAAATAG
*
214186 AACATATACTCATAGTAATGAAGTCAAAACAGTGTTTTTGAAATATGATTTACGTAAAACCATAA
1 AACATATACTCATAGTAATGAAGTCAAAACAGTGTTTTTGAAATACGATTTACGTAAAACCATAA
214251 AAATTAATATAAATATCTATTCAAAATTCTATTTTAGTAAAAAATCATTGGAAGTCGACTCATCA
66 AAATTAATATAAATATCTATTCAAAATTCTATTTTAGTAAAAAATCATTGGAAGTCGACTCATCA
214316 CAAGTCTTCTTCTCTTGT
131 CAAGTCTTCTTCTCTTGT
* *
214334 AACATATACTCATAGTAATGAAGTCAAAACATTGTTTTTGAAATACGATTTAGGTAAAACCATAA
1 AACATATACTCATAGTAATGAAGTCAAAACAGTGTTTTTGAAATACGATTTACGTAAAACCATAA
214399 AAATTAATATAAATATCTATTCAAAATTCTATTTTAGTAAAAAATCATTGGAAGTCGACTCATCA
66 AAATTAATATAAATATCTATTCAAAATTCTATTTTAGTAAAAAATCATTGGAAGTCGACTCATCA
214464 CAAGTCTTCTTCTCTTGT
131 CAAGTCTTCTTCTCTTGT
214482 A
1 A
214483 TTAATACATT
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
148 146 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (148 bp):
AACATATACTCATAGTAATGAAGTCAAAACAGTGTTTTTGAAATACGATTTACGTAAAACCATAA
AAATTAATATAAATATCTATTCAAAATTCTATTTTAGTAAAAAATCATTGGAAGTCGACTCATCA
CAAGTCTTCTTCTCTTGT
Found at i:219717 original size:3 final size:3
Alignment explanation
Indices: 219703--219748 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
219693 CTACAAAAAC
* * *
219703 ATT ATT -TT ATT ATT ATT ATC ATC ATC ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
219749 CATTTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:219735 original size:21 final size:21
Alignment explanation
Indices: 219709--219752 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
219699 AAACATTATT
219709 TTATTATTATTATCATCATCA
1 TTATTATTATTATCATCATCA
* *
219730 TTATTATTATTATTATTATCA
1 TTATTATTATTATCATCATCA
219751 TT
1 TT
219753 TATTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTATTATTATCATCATCA
Found at i:222461 original size:54 final size:54
Alignment explanation
Indices: 222278--222461 Score: 217
Period size: 54 Copynumber: 3.4 Consensus size: 54
222268 TAAAATTAAA
* * * *
222278 TATTTATTGTGCCAATTTAGTTATCTACAATAAATTAAAATTATTATAACCAAG
1 TATTTATTGTACCAATTTATTTATCTAAAATAAATTAAAATTATTATAATCAAG
* * *
222332 TACTTATTGTACCAATTTA-TTATTCTAAAATAAATTAAAATTATTATTATAAAG
1 TATTTATTGTACCAATTTATTTA-TCTAAAATAAATTAAAATTATTATAATCAAG
** * * * * *
222386 TATTTATTGTGTCAATTTATTTATCTATAATAAATCAATATTAATATCATCAAG
1 TATTTATTGTACCAATTTATTTATCTAAAATAAATTAAAATTATTATAATCAAG
*
222440 TATTTATTGTATCAATTTATTT
1 TATTTATTGTACCAATTTATTT
222462 GTGTACAATG
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 3 0.03
54 106 0.95
55 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (54 bp):
TATTTATTGTACCAATTTATTTATCTAAAATAAATTAAAATTATTATAATCAAG
Found at i:227148 original size:34 final size:34
Alignment explanation
Indices: 227110--227179 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
227100 CAATAAAGAT
*
227110 TATATTTTTCCAAAATAATTTTCTCATTTAATTC
1 TATATATTTCCAAAATAATTTTCTCATTTAATTC
*
227144 TATATATTTCCAAAATATTTTTCTCATTTAATTC
1 TATATATTTCCAAAATAATTTTCTCATTTAATTC
227178 TA
1 TA
227180 AAATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (34 bp):
TATATATTTCCAAAATAATTTTCTCATTTAATTC
Found at i:227189 original size:2 final size:2
Alignment explanation
Indices: 227182--227207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
227172 TAATTCTAAA
227182 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
227208 TTTCTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:230820 original size:123 final size:123
Alignment explanation
Indices: 230675--230932 Score: 435
Period size: 123 Copynumber: 2.1 Consensus size: 123
230665 GTATCCTATG
*
230675 ATGTAAACTCCACCATGAATACAAATACATAATATCTTATGTATCCTAAAATCCATTATCTATAT
1 ATGTAAACTCCACCACGAATACAAATACATAATATCTTATGTATCCTAAAATCCATTATCTATAT
*
230740 CAAAACTCGGTGTATCCCAAAACACTCTCCCAACATTCCTATATTATCCATCTCTACA
66 CAAAACTCGGTGTATCCCAAAACACTCTCCCAACATTCCTATAATATCCATCTCTACA
* * *
230798 ATGTAAACTCCACCACGAATACAAATACATAATATCTTATGTATCCTAAAATTCGTTATTTATAT
1 ATGTAAACTCCACCACGAATACAAATACATAATATCTTATGTATCCTAAAATCCATTATCTATAT
* * * *
230863 CAAAACTTGGTGTATCCCAAAATATTCTCCCAACATTCCTATAATATCCATCTTTACA
66 CAAAACTCGGTGTATCCCAAAACACTCTCCCAACATTCCTATAATATCCATCTCTACA
230921 ATGTAAACTCCA
1 ATGTAAACTCCA
230933 AAAGTTACAG
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 126 1.00
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.32
Consensus pattern (123 bp):
ATGTAAACTCCACCACGAATACAAATACATAATATCTTATGTATCCTAAAATCCATTATCTATAT
CAAAACTCGGTGTATCCCAAAACACTCTCCCAACATTCCTATAATATCCATCTCTACA
Done.