Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 6 of 153
Found at i:1725465 original size:2 final size:2
Alignment explanation
Indices: 1725460--1725484 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1725450 AGCGTGTGTT
1725460 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1725485 AGTAAAAGAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1748371 original size:6 final size:6
Alignment explanation
Indices: 1748360--1748400 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
1748350 TGTATGTATA
1748360 TATGTC TATGTC TATGTC TATGTC TATGTC TATGTC TATGT
1 TATGTC TATGTC TATGTC TATGTC TATGTC TATGTC TATGT
1748401 ATGGATGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (6 bp):
TATGTC
Found at i:1759526 original size:18 final size:18
Alignment explanation
Indices: 1759492--1759527 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1759482 GAGACGGTGA
*
1759492 CCTTTAGTTTCTGCCTCT
1 CCTTTAGTTCCTGCCTCT
*
1759510 CCTTTAGTTCCTTCCTCT
1 CCTTTAGTTCCTGCCTCT
1759528 TTTTTGCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.36, G:0.08, T:0.50
Consensus pattern (18 bp):
CCTTTAGTTCCTGCCTCT
Found at i:1763553 original size:10 final size:11
Alignment explanation
Indices: 1763530--1763554 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1763520 CTGTCTTTTC
1763530 TTTTTCTTATT
1 TTTTTCTTATT
1763541 TTTTTCTTATT
1 TTTTTCTTATT
1763552 TTT
1 TTT
1763555 CCATTTCCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTATT
Found at i:1765977 original size:10 final size:10
Alignment explanation
Indices: 1765934--1765980 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
1765924 TAATTATTTT
1765934 AAAAT-TTAA
1 AAAATATTAA
*
1765943 AAAATGTTTAA
1 AAAAT-ATTAA
*
1765954 AAAATA-AAA
1 AAAATATTAA
1765963 AAAATATTAA
1 AAAATATTAA
1765973 AAAATATT
1 AAAATATT
1765981 TCTAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 13 0.41
10 10 0.31
11 9 0.28
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAATATTAA
Found at i:1769140 original size:39 final size:39
Alignment explanation
Indices: 1769081--1769224 Score: 135
Period size: 39 Copynumber: 3.5 Consensus size: 39
1769071 GCCTTAATAC
* *
1769081 GACAGCTGAGAGCTTTTAACTCTCGCTAACTGTTTGGTG
1 GACAACTGAGAGCTTTTAACTCTCGCTAACTGTTTGGAG
** *
1769120 GACAACTGAGAGCTTTTAACTCTCGTTCTCGCTATTTGTTTAGAG
1 GACAACTGAGAGCTTTTAA----C--TCTCGCTAACTGTTTGGAG
* * *
1769165 GACAACTGAGAGCTCTTAACTGTCGTTAACTGTTTGGAG
1 GACAACTGAGAGCTTTTAACTCTCGCTAACTGTTTGGAG
* * *
1769204 GACAGCTGTGAGCTTTGAACT
1 GACAACTGAGAGCTTTTAACT
1769225 TACCGCACCA
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
39 49 0.58
41 1 0.01
43 1 0.01
45 33 0.39
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (39 bp):
GACAACTGAGAGCTTTTAACTCTCGCTAACTGTTTGGAG
Found at i:1769168 original size:45 final size:45
Alignment explanation
Indices: 1769101--1769191 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
1769091 AGCTTTTAAC
* * *
1769101 TCTCGCTAACTGTTTGGTGGACAACTGAGAGCTTTTAACTCTCGT
1 TCTCGCTAACTGTTTAGAGGACAACTGAGAGCTCTTAACTCTCGT
** *
1769146 TCTCGCTATTTGTTTAGAGGACAACTGAGAGCTCTTAACTGTCGT
1 TCTCGCTAACTGTTTAGAGGACAACTGAGAGCTCTTAACTCTCGT
1769191 T
1 T
1769192 AACTGTTTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (45 bp):
TCTCGCTAACTGTTTAGAGGACAACTGAGAGCTCTTAACTCTCGT
Found at i:1770386 original size:13 final size:13
Alignment explanation
Indices: 1770368--1770394 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1770358 TCTCCTCCTC
1770368 TGAGTTAATTATT
1 TGAGTTAATTATT
1770381 TGAGTTAATTATT
1 TGAGTTAATTATT
1770394 T
1 T
1770395 ATAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (13 bp):
TGAGTTAATTATT
Found at i:1777373 original size:13 final size:13
Alignment explanation
Indices: 1777355--1777379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1777345 ATGAACATTT
1777355 TATTTCTCAAAAG
1 TATTTCTCAAAAG
1777368 TATTTCTCAAAA
1 TATTTCTCAAAA
1777380 TTACTTTTCC
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:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
TATTTCTCAAAAG
Found at i:1779293 original size:25 final size:24
Alignment explanation
Indices: 1779245--1779332 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 24
1779235 GAATAGCTAT
** *
1779245 TAACGGGAAGCTCACAAGAACCATA
1 TAACGGGAAGCT-ATGAGAGCCATA
*
1779270 TAACGGGAAGCTATAGAGGGCCATA
1 TAACGGGAAGCTAT-GAGAGCCATA
* * *
1779295 TATCGGGATGCTCATGAGAGCTA-A
1 TAACGGGAAGCT-ATGAGAGCCATA
*
1779319 TAACGGGACGCTAT
1 TAACGGGAAGCTAT
1779333 TTCTAGCTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.04
24 12 0.24
25 35 0.69
26 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.18
Consensus pattern (24 bp):
TAACGGGAAGCTATGAGAGCCATA
Found at i:1784220 original size:38 final size:37
Alignment explanation
Indices: 1784179--1784251 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 37
1784169 GACATTTCAA
1784179 AAAAAGTCAA-ATAGATTTTTTAATAAAAATATTGACT
1 AAAAAGTCAATATA-ATTTTTTAATAAAAATATTGACT
*
1784216 AAAAAGTCAATTTTAATTTTTTAATAAAAATATTGA
1 AAAAAGTCAA-TATAATTTTTTAATAAAAATATTGA
1784252 TTTTCAATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 10 0.30
38 21 0.64
39 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (37 bp):
AAAAAGTCAATATAATTTTTTAATAAAAATATTGACT
Found at i:1785753 original size:15 final size:15
Alignment explanation
Indices: 1785718--1785750 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1785708 TGATATAAAA
1785718 TAAATATTTCATATT
1 TAAATATTTCATATT
*
1785733 TAAATATTT-TTATT
1 TAAATATTTCATATT
1785747 TAAA
1 TAAA
1785751 ATAGGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATATTTCATATT
Found at i:1788459 original size:32 final size:32
Alignment explanation
Indices: 1788399--1788461 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1788389 GACTGTCATT
* *
1788399 ATAATTATTTTTTATCCAACAAGTTAAGGTTC
1 ATAATTAATTTTTATCCAACAAGATAAGGTTC
1788431 ATAATTAATTTTTATCCAA-ACAGATAAGGTT
1 ATAATTAATTTTTATCCAACA-AGATAAGGTT
1788462 AGGTTAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (32 bp):
ATAATTAATTTTTATCCAACAAGATAAGGTTC
Found at i:1789680 original size:19 final size:20
Alignment explanation
Indices: 1789671--1789707 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
1789661 TAATGATATT
1789671 TAATTTTTTTTAAAAAATTG
1 TAATTTTTTTTAAAAAATTG
1789691 TAA-TTTTTTTAAAAAAT
1 TAATTTTTTTTAAAAAAT
1789708 AATTAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TAATTTTTTTTAAAAAATTG
Found at i:1793523 original size:24 final size:24
Alignment explanation
Indices: 1793496--1793547 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1793486 TTAGTAAGTC
*
1793496 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1793520 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1793544 AAAT
1 AAAT
1793548 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1798302 original size:40 final size:41
Alignment explanation
Indices: 1798117--1798302 Score: 193
Period size: 40 Copynumber: 4.6 Consensus size: 41
1798107 CCAGCATGAT
* *
1798117 TGCTCTTCGGAACCTAGCCCGGATATAA-CACCAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATAATCACTAGCACGAA
* **
1798157 TGCTCTTCGGAACTTAGTCCGGATA-CCTCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATAATCACTAGCACGAA
* * * * * *
1798197 TGCTCTTCGGAATTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGAACTTAGCCCGGATATAATCACTAGCACGAA
** *
1798238 TGC-CTTCGGGTCTTAGCCCGGATATAATCACTAGCTC-AA
1 TGCTCTTCGGAACTTAGCCCGGATATAATCACTAGCACGAA
*
1798277 TTGC-CTTCGGGACTTAGCCCGGATAT
1 -TGCTCTTCGGAACTTAGCCCGGATAT
1798303 CATTCAAATG
Statistics
Matches: 121, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 2 0.02
40 106 0.88
41 13 0.11
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (41 bp):
TGCTCTTCGGAACTTAGCCCGGATATAATCACTAGCACGAA
Found at i:1798631 original size:29 final size:29
Alignment explanation
Indices: 1798592--1798670 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
1798582 CTTAATAATC
*
1798592 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
1798622 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
1798651 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
1798671 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:1798713 original size:43 final size:43
Alignment explanation
Indices: 1798652--1798733 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
1798642 TGCATTTCAA
1798652 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
1798695 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAGCACT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACT
1798734 AAGCCAATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.27, C:0.37, G:0.16, T:0.21
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:1798740 original size:26 final size:26
Alignment explanation
Indices: 1798710--1798759 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1798700 CACACTTAGT
*
1798710 GCCAATCTCACAACCGTGAGCACTAA
1 GCCAATCTCACAACCGTGAACACTAA
1798736 GCCAATCTCACAACCGTGAACACT
1 GCCAATCTCACAACCGTGAACACT
1798760 TATTGCTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.36, G:0.14, T:0.16
Consensus pattern (26 bp):
GCCAATCTCACAACCGTGAACACTAA
Found at i:1799009 original size:26 final size:26
Alignment explanation
Indices: 1798973--1799022 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1798963 AGTCATAACA
1798973 CTCTTTCAAAATTGCATCACTTATGC
1 CTCTTTCAAAATTGCATCACTTATGC
1798999 CTCTTTCAAAATTGCATCACTTAT
1 CTCTTTCAAAATTGCATCACTTAT
1799023 ACCCTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (26 bp):
CTCTTTCAAAATTGCATCACTTATGC
Found at i:1801172 original size:24 final size:24
Alignment explanation
Indices: 1801144--1801224 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
1801134 GAGCCATTGG
1801144 ATGTGAATGAAACGAAGAGATGGA
1 ATGTGAATGAAACGAAGAGATGGA
* * * **
1801168 ATGTGAACCG-CATGTTGAGCCATTGG-
1 ATGTGAA-TGAAACGAAGAG--A-TGGA
1801194 ATGTGAATGAAACGAAGAGATGGA
1 ATGTGAATGAAACGAAGAGATGGA
1801218 ATGTGAA
1 ATGTGAA
1801225 CCGCATGTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 3 0.07
24 20 0.49
25 2 0.05
26 13 0.32
27 3 0.07
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (24 bp):
ATGTGAATGAAACGAAGAGATGGA
Found at i:1801207 original size:50 final size:50
Alignment explanation
Indices: 1801132--1801233 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
1801122 TGGTTTAAAT
1801132 TTGAGCCATTGGATGTGAATGAAACGAAGAGATGGAATGTGAACCGCATG
1 TTGAGCCATTGGATGTGAATGAAACGAAGAGATGGAATGTGAACCGCATG
1801182 TTGAGCCATTGGATGTGAATGAAACGAAGAGATGGAATGTGAACCGCATG
1 TTGAGCCATTGGATGTGAATGAAACGAAGAGATGGAATGTGAACCGCATG
1801232 TT
1 TT
1801234 AGTATTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (50 bp):
TTGAGCCATTGGATGTGAATGAAACGAAGAGATGGAATGTGAACCGCATG
Found at i:1803412 original size:42 final size:44
Alignment explanation
Indices: 1803359--1803444 Score: 131
Period size: 42 Copynumber: 2.0 Consensus size: 44
1803349 TTGGGAAAAT
* *
1803359 AATTCTCTTATTCTAATAAACTATTTAAACATAAAA-AAAATAA
1 AATTCTCTTATTCTAATAAACTACTAAAACATAAAATAAAATAA
*
1803402 AATT-TCTTATTCTAATAAACTACTAAAAGATAAAATAAAATAA
1 AATTCTCTTATTCTAATAAACTACTAAAACATAAAATAAAATAA
1803445 TCTTAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 28 0.72
43 11 0.28
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (44 bp):
AATTCTCTTATTCTAATAAACTACTAAAACATAAAATAAAATAA
Found at i:1804481 original size:22 final size:23
Alignment explanation
Indices: 1804453--1804516 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
1804443 TTTAGGGTTT
1804453 GGGATTTAAGGTTTAGGGCTA-G
1 GGGATTTAAGGTTTAGGGCTAGG
*
1804475 GGGATTTAAGGTTTAGGGGTTAGG
1 GGGATTTAAGGTTTA-GGGCTAGG
* *
1804499 GGGATTTAGGGGTTAGGG
1 GGGATTTAAGGTTTAGGG
1804517 ATTTGGAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.41
23 8 0.22
24 14 0.38
ACGTcount: A:0.20, C:0.02, G:0.47, T:0.31
Consensus pattern (23 bp):
GGGATTTAAGGTTTAGGGCTAGG
Found at i:1804519 original size:15 final size:15
Alignment explanation
Indices: 1804430--1804520 Score: 55
Period size: 15 Copynumber: 6.1 Consensus size: 15
1804420 TTTTAAGGAG
* *
1804430 TAGGGGGTATGGATT
1 TAGGGGTTAGGGATT
*
1804445 TA-GGGTTTGGGATT
1 TAGGGGTTAGGGATT
* * *
1804459 TAAGGTTTAGGG--C
1 TAGGGGTTAGGGATT
*
1804472 TAGGGGATTTAAGG-TT
1 TAGGGG--TTAGGGATT
1804488 TAGGGGTTAGGGGGATT
1 TAGGGGTTA--GGGATT
1804505 TAGGGGTTAGGGATT
1 TAGGGGTTAGGGATT
1804520 T
1 T
1804521 GGAGTTTACG
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
13 4 0.07
14 14 0.24
15 21 0.36
16 8 0.14
17 11 0.19
ACGTcount: A:0.20, C:0.01, G:0.44, T:0.35
Consensus pattern (15 bp):
TAGGGGTTAGGGATT
Found at i:1804907 original size:19 final size:19
Alignment explanation
Indices: 1804883--1804924 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1804873 AAATATAAGA
1804883 AAAAATAAAATAAAAAAAT
1 AAAAATAAAATAAAAAAAT
* *
1804902 AAAAATGAAATAAAAAACT
1 AAAAATAAAATAAAAAAAT
1804921 AAAA
1 AAAA
1804925 TTTATACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAATAAAATAAAAAAAT
Found at i:1811109 original size:23 final size:23
Alignment explanation
Indices: 1811083--1811157 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
1811073 ATAAGTGCCA
*
1811083 CACTGATACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1811106 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1811129 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1811152 CACTGA
1 CACTGA
1811158 CCAATAACAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1811784 original size:26 final size:26
Alignment explanation
Indices: 1811750--1811803 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1811740 CAAAATCACA
1811750 ACTTTATGCACACTTTACCATCTTTC
1 ACTTTATGCACACTTTACCATCTTTC
*
1811776 ACTTTATGCACACTTTACTATCTTTC
1 ACTTTATGCACACTTTACCATCTTTC
1811802 AC
1 AC
1811804 AATTTAGTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.24, C:0.30, G:0.04, T:0.43
Consensus pattern (26 bp):
ACTTTATGCACACTTTACCATCTTTC
Found at i:1813506 original size:21 final size:21
Alignment explanation
Indices: 1813480--1813529 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1813470 TTACAACTTA
1813480 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
* * *
1813501 AAGCAGAGGCTGCAGTGAGGG
1 AAGCAGAGGCAGCAGCGAGAG
1813522 AAGCAGAG
1 AAGCAGAG
1813530 CAGAGCAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:1813705 original size:21 final size:20
Alignment explanation
Indices: 1813679--1813719 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1813669 ATAATATGAA
* *
1813679 TTATATTTTATTTATTTATTT
1 TTATATTATA-TTATTCATTT
1813700 TTATATTATATTATTCATTT
1 TTATATTATATTATTCATTT
1813720 AATTTGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATATTATATTATTCATTT
Found at i:1814092 original size:43 final size:43
Alignment explanation
Indices: 1813882--1814107 Score: 256
Period size: 43 Copynumber: 5.3 Consensus size: 43
1813872 CACCAAACAA
* * * ** *
1813882 TAGCGGCATTTGTGGGAAAAGCACCGCTAAAAGTCATGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGACATGACCTT
** * * *
1813925 TAGCAACGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGACTTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGACATGACCTT
* * *
1813968 TAGCGGCGCTTGTGGGAAAAGCGCAGCTAAAAGACATGACATT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGACATGACCTT
* *
1814011 TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGACATGACCTT
* * *
1814054 TAGTGGCGTTTGAGGGAAAAACGCCGCT-AAAGAACATGACCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAG-ACATGACCTT
*
1814097 TAGCGACGTTT
1 TAGCGGCGTTT
1814108 ATAGAAATAA
Statistics
Matches: 154, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 4 0.03
43 150 0.97
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGACATGACCTT
Found at i:1814244 original size:22 final size:22
Alignment explanation
Indices: 1814201--1814244 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1814191 TAGTGGCGCT
* **
1814201 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAAACCTA
1814223 AAAAAACGCCGCTAAAAACCTA
1 AAAAAACGCCGCTAAAAACCTA
1814245 TTTTGGTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:1816910 original size:26 final size:26
Alignment explanation
Indices: 1816870--1816921 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1816860 CCACAAAATG
1816870 AAAGTAAAGACAAAAAGTTGTTCAAT
1 AAAGTAAAGACAAAAAGTTGTTCAAT
*
1816896 AAAGTAAAGATAAAAAGTTGTTCAAT
1 AAAGTAAAGACAAAAAGTTGTTCAAT
1816922 TTTTGATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.25
Consensus pattern (26 bp):
AAAGTAAAGACAAAAAGTTGTTCAAT
Found at i:1820847 original size:13 final size:13
Alignment explanation
Indices: 1820829--1820856 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1820819 TATTTTTAAA
1820829 ATATGTATTTTAT
1 ATATGTATTTTAT
1820842 ATATGTATTTTAT
1 ATATGTATTTTAT
1820855 AT
1 AT
1820857 TTTATGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (13 bp):
ATATGTATTTTAT
Found at i:1821775 original size:110 final size:110
Alignment explanation
Indices: 1821570--1821776 Score: 326
Period size: 110 Copynumber: 1.9 Consensus size: 110
1821560 TTTTGTAAAA
* * *
1821570 AATAAGGCAATGTTTTGCATTTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTTCGGTTT
1 AATAAGGCAATATTTTGCATTTGGAAATTCAAGGAAACGTGCCCTAATGTGCTGGGTTTCGGATT
*
1821635 TCTCGTTCGACCAAATAGCCGAATATCTTTTTAAAAAATTTTCAG
66 TCTCGTTCGACCAAATAGCCAAATATCTTTTTAAAAAATTTTCAG
* * *
1821680 AATAAGGCAATATTTTGCGTTTGGAAATTCAAGGAAACGTGCCCTAATGTGTTGGGTTT-TGATT
1 AATAAGGCAATATTTTGCATTTGGAAATTCAAGGAAACGTGCCCTAATGTGCTGGGTTTCGGATT
* *
1821744 TCTCGTTGGACCAAATAGCCAAATATCCTTTTA
66 TCTCGTTCGACCAAATAGCCAAATATCTTTTTA
1821777 TATTTTAATC
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
109 33 0.38
110 55 0.62
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (110 bp):
AATAAGGCAATATTTTGCATTTGGAAATTCAAGGAAACGTGCCCTAATGTGCTGGGTTTCGGATT
TCTCGTTCGACCAAATAGCCAAATATCTTTTTAAAAAATTTTCAG
Found at i:1822972 original size:42 final size:41
Alignment explanation
Indices: 1822906--1823049 Score: 139
Period size: 42 Copynumber: 3.4 Consensus size: 41
1822896 TATGTGAGGA
* *
1822906 TCTTTAGCAGCGCTTATATGAGAAACGCCGCTA-AAGTTA-GG
1 TCTTTAGCGGCGCTT-T-TGAGAAACGCCGCTATAAGTAATGG
* *
1822947 ATCTTTAGCGGCGCTTTTGGAAGAAACGCTGCTATAAGTGATGG
1 -TCTTTAGCGGCGCTTTT-G-AGAAACGCCGCTATAAGTAATGG
* * * *
1822991 CCTTTAGTGGCGCTTTTTGATAAACACCGCTATAAGTAATGG
1 TCTTTAGCGGCGC-TTTTGAGAAACGCCGCTATAAGTAATGG
*
1823033 TCTTTAGCGGAGCTTTT
1 TCTTTAGCGGCGCTTTT
1823050 TTACAAATGC
Statistics
Matches: 85, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
40 1 0.01
41 6 0.07
42 55 0.65
43 17 0.20
44 6 0.07
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (41 bp):
TCTTTAGCGGCGCTTTTGAGAAACGCCGCTATAAGTAATGG
Found at i:1827148 original size:19 final size:20
Alignment explanation
Indices: 1827112--1827158 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1827102 AATTTTTTTC
*
1827112 TATAAAATACATATACAAAAT
1 TATAAAATACA-ATACAAAAA
1827133 TATAAAATAC-ATACAAAAA
1 TATAAAATACAATACAAAAA
1827152 TATAAAA
1 TATAAAA
1827159 ATATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 15 0.60
21 10 0.40
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (20 bp):
TATAAAATACAATACAAAAA
Found at i:1827161 original size:20 final size:21
Alignment explanation
Indices: 1827112--1827158 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1827102 AATTTTTTTC
*
1827112 TATAAAATACATATACAAAAT
1 TATAAAATACATACACAAAAT
1827133 TATAAAATACATACA-AAAA-
1 TATAAAATACATACACAAAAT
1827152 TATAAAA
1 TATAAAA
1827159 ATATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.28
20 4 0.16
21 14 0.56
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (21 bp):
TATAAAATACATACACAAAAT
Found at i:1830693 original size:38 final size:38
Alignment explanation
Indices: 1830642--1830724 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 38
1830632 AACGAAGGGT
1830642 AAAAAC-AAAGTTTTGTGTTTGAAAGATGAAAAACAGA
1 AAAAACGAAAGTTTTGTGTTTGAAAGATGAAAAACAGA
*
1830679 AAAAACGATAGTTTTGTGTTTGAAAGATGAAAAACAGA
1 AAAAACGAAAGTTTTGTGTTTGAAAGATGAAAAACAGA
1830717 AAAAACGA
1 AAAAACGA
1830725 GTGCTAGATG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 6 0.14
38 38 0.86
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (38 bp):
AAAAACGAAAGTTTTGTGTTTGAAAGATGAAAAACAGA
Found at i:1832513 original size:15 final size:15
Alignment explanation
Indices: 1832493--1832521 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1832483 CGCAGGGCCA
1832493 GTTGCAAGTGAGGTC
1 GTTGCAAGTGAGGTC
1832508 GTTGCAAGTGAGGT
1 GTTGCAAGTGAGGT
1832522 GTCGCGAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.41, T:0.28
Consensus pattern (15 bp):
GTTGCAAGTGAGGTC
Found at i:1835234 original size:16 final size:16
Alignment explanation
Indices: 1835209--1835240 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1835199 ATCTGTGGGG
1835209 ACGAAAGATTTTTCAA
1 ACGAAAGATTTTTCAA
*
1835225 ACGAAGGATTTTTCAA
1 ACGAAAGATTTTTCAA
1835241 CCCTTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (16 bp):
ACGAAAGATTTTTCAA
Found at i:1836417 original size:19 final size:20
Alignment explanation
Indices: 1836381--1836427 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1836371 AACTTTTTTC
*
1836381 TATAAAATACATATACAAAAT
1 TATAAAATACA-ATACAAAAA
1836402 TATAAAATAC-ATACAAAAA
1 TATAAAATACAATACAAAAA
1836421 TATAAAA
1 TATAAAA
1836428 ATATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 15 0.60
21 10 0.40
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (20 bp):
TATAAAATACAATACAAAAA
Found at i:1836430 original size:20 final size:21
Alignment explanation
Indices: 1836381--1836427 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1836371 AACTTTTTTC
*
1836381 TATAAAATACATATACAAAAT
1 TATAAAATACATACACAAAAT
1836402 TATAAAATACATACA-AAAA-
1 TATAAAATACATACACAAAAT
1836421 TATAAAA
1 TATAAAA
1836428 ATATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.28
20 4 0.16
21 14 0.56
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (21 bp):
TATAAAATACATACACAAAAT
Found at i:1838200 original size:17 final size:18
Alignment explanation
Indices: 1838166--1838211 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
1838156 CCGTTATGTC
1838166 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
1838181 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
1838198 CGCGACCGCGACCG
1 CGCGACCGCGACCG
1838212 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:1840418 original size:18 final size:18
Alignment explanation
Indices: 1840397--1840498 Score: 71
Period size: 18 Copynumber: 5.3 Consensus size: 18
1840387 TATTTTGTTC
1840397 ATTATTTTTAATATTATT
1 ATTATTTTTAATATTATT
*
1840415 ATTATTTTCT-TTATTATT
1 ATTATTTT-TAATATTATT
* *
1840433 ATTATATTTACTATTATT
1 ATTATTTTTAATATTATT
* * *
1840451 ATCATCTTTACTATTGCTATT
1 ATTATTTTTAATA-T--TATT
1840472 AGTATATTTATTAATATTATT
1 A-T-TATTT-TTAATATTATT
*
1840493 GTTATT
1 ATTATT
1840499 ATTGTTATGT
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
17 1 0.01
18 40 0.60
19 6 0.09
20 1 0.01
21 9 0.13
22 1 0.01
23 4 0.06
24 5 0.07
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTATTTTTAATATTATT
Found at i:1840428 original size:15 final size:15
Alignment explanation
Indices: 1840397--1840452 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1840387 TATTTTGTTC
*
1840397 ATTATTTTTA-ATATT
1 ATTATTATTATAT-TT
* *
1840412 ATTATTATTTTCTTT
1 ATTATTATTATATTT
1840427 ATTATTATTATATTT
1 ATTATTATTATATTT
*
1840442 ACTATTATTAT
1 ATTATTATTAT
1840453 CATCTTTACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 33 0.97
16 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTATTATTATATTT
Found at i:1840692 original size:34 final size:34
Alignment explanation
Indices: 1840653--1840719 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
1840643 TCTACATATA
* * *
1840653 TATTTTTTATTTAAATATGTATATTATATATTAT
1 TATTTTATATCTAAATATATATATTATATATTAT
* * *
1840687 TATTTTATATCTATATATATATTTTTTATATTA
1 TATTTTATATCTAAATATATATATTATATATTA
1840720 AAATATGTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (34 bp):
TATTTTATATCTAAATATATATATTATATATTAT
Found at i:1840701 original size:21 final size:20
Alignment explanation
Indices: 1840672--1840719 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
1840662 TTTAAATATG
1840672 TATATTATATAT-TATTATTT
1 TATATTATATATATATT-TTT
1840692 TATATCTATATATATATTTTT
1 TATAT-TATATATATATTTTT
1840713 TATATTA
1 TATATTA
1840720 AAATATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.27
21 15 0.58
22 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTATATATATATTTTT
Found at i:1840709 original size:19 final size:19
Alignment explanation
Indices: 1840640--1840711 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 19
1840630 TTTTATATAC
*
1840640 ATATCTACATATATATTTT
1 ATATCTATATATATATTTT
* * * * *
1840659 TTATTTAAATATGTATATT
1 ATATCTATATATATATTTT
1840678 ATA--TAT-TAT-TATTTT
1 ATATCTATATATATATTTT
1840693 ATATCTATATATATATTTT
1 ATATCTATATATATATTTT
1840712 TTATATTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
15 8 0.20
16 3 0.07
17 5 0.12
18 3 0.07
19 22 0.54
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (19 bp):
ATATCTATATATATATTTT
Found at i:1840725 original size:19 final size:22
Alignment explanation
Indices: 1840672--1840725 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 22
1840662 TTTAAATATG
*
1840672 TATAT-TATATAT-TATTATTT
1 TATATCTATAAATATATTATTT
*
1840692 TATATCTATATATATATT-TTT
1 TATATCTATAAATATATTATTT
1840713 TATAT-TA-AAATAT
1 TATATCTATAAATAT
1840726 GTATATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 5 0.16
20 7 0.23
21 15 0.48
22 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TATATCTATAAATATATTATTT
Found at i:1840725 original size:21 final size:21
Alignment explanation
Indices: 1840678--1840740 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
1840668 TATGTATATT
*
1840678 ATATATTATTATTTTATATCT-AT
1 ATATA-TATT-TTTTATAT-TAAA
1840701 ATATATATTTTTTATATTAAA
1 ATATATATTTTTTATATTAAA
* * *
1840722 ATATGTATATTATATATTA
1 ATATATATTTTTTATATTA
1840741 TCTTATGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 25 0.71
22 4 0.11
23 5 0.14
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATATATTTTTTATATTAAA
Found at i:1841009 original size:19 final size:19
Alignment explanation
Indices: 1840987--1841024 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1840977 TTATCTTTTC
*
1840987 TTATTTCAT-TTGTATTATT
1 TTATTT-ATGTTGCATTATT
1841006 TTATTTATGTTGCATTATT
1 TTATTTATGTTGCATTATT
1841025 ATTGTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (19 bp):
TTATTTATGTTGCATTATT
Found at i:1861391 original size:29 final size:30
Alignment explanation
Indices: 1861359--1861424 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 30
1861349 ATTTAGGACC
* * *
1861359 AAATTTAGCTC-AAGAAAAGAATAAGGGTT
1 AAATTTAACTCAAAAAAAAGAATAAGGGCT
1861388 AAATTTAACTCAAAAAAAAAAGAATAAGGGCT
1 AAATTTAACTC--AAAAAAAAGAATAAGGGCT
1861420 AAATT
1 AAATT
1861425 GATAAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 10 0.32
32 21 0.68
ACGTcount: A:0.55, C:0.08, G:0.15, T:0.23
Consensus pattern (30 bp):
AAATTTAACTCAAAAAAAAGAATAAGGGCT
Found at i:1861502 original size:28 final size:29
Alignment explanation
Indices: 1861448--1861506 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 29
1861438 TATACATAAA
*
1861448 TACTAAGGGCTAATTTTTTTTATTATGCC
1 TACTAAGGGCTAATTTTTGTTATTATGCC
1861477 TACTAAGGGCTAA-TTTTGTTATTATGCC
1 TACTAAGGGCTAATTTTTGTTATTATGCC
1861505 TA
1 TA
1861507 ATGAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (29 bp):
TACTAAGGGCTAATTTTTGTTATTATGCC
Found at i:1861929 original size:17 final size:17
Alignment explanation
Indices: 1861909--1861941 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1861899 ATTTAATATA
1861909 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
1861926 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
1861942 TAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:1882519 original size:19 final size:19
Alignment explanation
Indices: 1882495--1882531 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1882485 TTATTCTAAA
1882495 ATTTATCTACCTAAATAAG
1 ATTTATCTACCTAAATAAG
1882514 ATTTATCTACCTAAATAA
1 ATTTATCTACCTAAATAA
1882532 CTTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (19 bp):
ATTTATCTACCTAAATAAG
Found at i:1884922 original size:20 final size:20
Alignment explanation
Indices: 1884897--1884946 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1884887 TGGCTTAAAA
1884897 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1884917 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1884934 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1884947 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1889561 original size:20 final size:20
Alignment explanation
Indices: 1889536--1889585 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1889526 TGGCTTAAAA
1889536 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1889556 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1889573 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1889586 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1890714 original size:72 final size:72
Alignment explanation
Indices: 1890604--1890809 Score: 295
Period size: 72 Copynumber: 2.9 Consensus size: 72
1890594 TAATCAGAGT
* * * *
1890604 TCCAACAACTCGTCCTTAGAAGTAATAAATATTAATATTTTAAATAGATATAGCCAAAATAATAT
1 TCCAACAACTAGTCCTTGGAAGTAATAAATATTAATATTTTAAATAAATGTAGCCAAAATAATAT
1890669 AATGAGG
66 AATGAGG
* ** *
1890676 TCCAACAACTTGTGGTTGGAAGTAATAAATATTAATATTTAAAATAAATGTAGCCAAAATAATAT
1 TCCAACAACTAGTCCTTGGAAGTAATAAATATTAATATTTTAAATAAATGTAGCCAAAATAATAT
* * *
1890741 ATTTATG
66 AATGAGG
* *
1890748 TCCAACAACTAGTCCTTGGATGTAATAAATATTAATATTTTAAATAAACGTAGCCAAAATAA
1 TCCAACAACTAGTCCTTGGAAGTAATAAATATTAATATTTTAAATAAATGTAGCCAAAATAA
1890810 AATCCAACAA
Statistics
Matches: 118, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 118 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (72 bp):
TCCAACAACTAGTCCTTGGAAGTAATAAATATTAATATTTTAAATAAATGTAGCCAAAATAATAT
AATGAGG
Found at i:1891553 original size:20 final size:20
Alignment explanation
Indices: 1891516--1891555 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1891506 TTGTTTTCCG
**
1891516 TATTATATAATTTTAATTAA
1 TATTATATAATTAAAATTAA
*
1891536 TATTTTATAATTAAAATTAA
1 TATTATATAATTAAAATTAA
1891556 AAATTTATGT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTATATAATTAAAATTAA
Found at i:1891678 original size:39 final size:40
Alignment explanation
Indices: 1891635--1891715 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
1891625 AAATCTATTT
* *
1891635 ATAACAACTTAATTTT-TATTTAAATTTATATATAATTCA
1 ATAACAACTTAATTTTGTATTTAAATTTAAATATAAATCA
1891674 ATAACAACTTAATTTTGTATTTAAATTTAAATATAAATCA
1 ATAACAACTTAATTTTGTATTTAAATTTAAATATAAATCA
1891714 AT
1 AT
1891716 CTTATAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 16 0.41
40 23 0.59
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (40 bp):
ATAACAACTTAATTTTGTATTTAAATTTAAATATAAATCA
Found at i:1897937 original size:18 final size:18
Alignment explanation
Indices: 1897911--1897956 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1897901 CAGAAACATG
*
1897911 TACAGATGTAAATACGGA
1 TACAGATGTAAATACAGA
* *
1897929 TACAAATGTAAATATAGA
1 TACAGATGTAAATACAGA
1897947 TACAGATGTA
1 TACAGATGTA
1897957 TTTATCCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (18 bp):
TACAGATGTAAATACAGA
Found at i:1899908 original size:18 final size:18
Alignment explanation
Indices: 1899880--1899923 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1899870 AACCTATTAT
1899880 AATTGTTTTTTGA-ATTTTG
1 AATT-TTTTTT-ATATTTTG
*
1899899 AATTTTTTTTATTTTTTG
1 AATTTTTTTTATATTTTG
1899917 AATTTTT
1 AATTTTT
1899924 AAATTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 18 0.78
19 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (18 bp):
AATTTTTTTTATATTTTG
Found at i:1901816 original size:17 final size:17
Alignment explanation
Indices: 1901794--1901827 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1901784 ATCCACTAAT
*
1901794 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1901811 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1901828 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1906455 original size:17 final size:17
Alignment explanation
Indices: 1906433--1906466 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1906423 ATCCACTAAT
*
1906433 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1906450 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1906467 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1911934 original size:73 final size:73
Alignment explanation
Indices: 1911807--1911964 Score: 298
Period size: 73 Copynumber: 2.2 Consensus size: 73
1911797 AAATCACAAT
*
1911807 TTCATAAGGAATATCACGATTCCACAACCACTTCCAATCAAAGTGAAGTGTAGTTTCTATGCCTT
1 TTCATAAGGAATATCACGATTCCACAACCACTTCCAATCAAAGTGAAGTATAGTTTCTATGCCTT
1911872 CATATGAA
66 CATATGAA
*
1911880 TTCATAAGGAATATCACGATTCCACAACCACTTCCAATCAAAGTTAAGTATAGTTTCTATGCCTT
1 TTCATAAGGAATATCACGATTCCACAACCACTTCCAATCAAAGTGAAGTATAGTTTCTATGCCTT
1911945 CATATGAA
66 CATATGAA
1911953 TTCATAAGGAAT
1 TTCATAAGGAAT
1911965 TTAGGGTTTA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 83 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (73 bp):
TTCATAAGGAATATCACGATTCCACAACCACTTCCAATCAAAGTGAAGTATAGTTTCTATGCCTT
CATATGAA
Found at i:1915359 original size:21 final size:21
Alignment explanation
Indices: 1915333--1915373 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1915323 ATCTGCTCAA
* *
1915333 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1915354 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1915374 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1922810 original size:43 final size:42
Alignment explanation
Indices: 1922743--1922872 Score: 165
Period size: 43 Copynumber: 3.0 Consensus size: 42
1922733 CATAGGATTT
1922743 TCGATATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCA
* **
1922786 TCGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGCCAATGGCA
1 TCGA-TATGTG-TTACGTGTAAGACCAC-GTCTGGGACGTTGGCA
*
1922829 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCA
1922872 T
1 T
1922873 TGTACGAGTC
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
42 2 0.03
43 67 0.91
44 5 0.07
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (42 bp):
TCGATATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:1929098 original size:33 final size:33
Alignment explanation
Indices: 1929060--1929128 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1929050 AAATATATTG
* *
1929060 ATATTTGTAATAGTTATTTGAAAT-ATTTCACAT
1 ATATTTGAAATAATTATTTGAAATAATTT-ACAT
*
1929093 ATATTTGAAATAATTTTTTGAAATAATTTACAT
1 ATATTTGAAATAATTATTTGAAATAATTTACAT
1929126 ATA
1 ATA
1929129 AAATCAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (33 bp):
ATATTTGAAATAATTATTTGAAATAATTTACAT
Found at i:1929114 original size:13 final size:13
Alignment explanation
Indices: 1929096--1929121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1929086 TTCACATATA
1929096 TTTGAAATAATTT
1 TTTGAAATAATTT
1929109 TTTGAAATAATTT
1 TTTGAAATAATTT
1929122 ACATATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTGAAATAATTT
Found at i:1929627 original size:206 final size:198
Alignment explanation
Indices: 1929315--1929836 Score: 621
Period size: 206 Copynumber: 2.6 Consensus size: 198
1929305 ACAATGCATA
*
1929315 TAAAAAAATATTTGATGTATAAAAATTATATATATAGAAAAATATA--AAAAAATTAGTTGATGT
1 TAAAAAAATATTTGA--TATAAAAATTATATATAAAGAAAAATATATCAAAAAATTAGTTGATG-
* * * * *
1929378 TTTTTAAAAAATAAAAAATAAATAACACAATGATACTTATGAATATATTTTCACTATATCCACAA
63 TTTTTAAAAAATAAATAAT-ATTAACATAATGATACATATGAATATATTTTCA-TATATCAACAA
* * * * *
1929443 TGCAAGTGAAAAAAAATAATGATATTTGAAATAATTATTTTTATAATATTAAAATTTATGTTACC
126 TGCAAGTG--AAAAAATAAAGAGATTTGAAATAATTAATTTTAT-ATATTAAAATTTACGATACC
1929508 CACAATGTACG
188 CACAATGTACG
* * * *
1929519 TAAAAACATTTTTTTTATATAAAGAATTATTTATAAAGAAAAATATATCAAAAAATTAGTTGATG
1 TAAAAA-A-ATATTTGATATAAA-AATTATATATAAAGAAAAATATATCAAAAAATTAGTTGATG
* * *
1929584 TTTTT-AAAAATACATATAATTTTAACATAATGATACATATGAATATATATTCATCATATCAATA
63 TTTTTAAAAAATA-A-ATAATATTAACATAATGATACATATGAATATATTTTCAT-ATATCAACA
* * *
1929648 ATGTAAGTGAAAAAATAAAGAGATTTGAAATAATTAATTTTATATGTTAGAATTTACGATACCCA
125 ATGCAAGTGAAAAAATAAAGAGATTTGAAATAATTAATTTTATATATTAAAATTTACGATACCCA
1929713 CAATGTACG
190 CAATGTACG
*
1929722 TAAAAAAATATTTGACATAAAAA--ATATATAAAGAAAAATATATCAAAAAATTAGTTGATGTTT
1 TAAAAAAATATTTGATATAAAAATTATATATAAAGAAAAATATATCAAAAAATTAGTTGATGTTT
* *
1929785 TTAAAAAATAAA-ATATATTAACATAAT--TATATATAAAT-TATTTTCATTATAT
66 TTAAAAAATAAATA-ATATTAACATAATGATACATATGAATATATTTTCA-TATAT
1929837 AATTACATAT
Statistics
Matches: 277, Mismatches: 30, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
194 11 0.04
195 10 0.04
196 1 0.00
197 13 0.05
198 42 0.15
199 7 0.03
200 2 0.01
201 10 0.04
202 1 0.00
203 33 0.12
204 43 0.16
205 30 0.11
206 54 0.19
207 20 0.07
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.36
Consensus pattern (198 bp):
TAAAAAAATATTTGATATAAAAATTATATATAAAGAAAAATATATCAAAAAATTAGTTGATGTTT
TTAAAAAATAAATAATATTAACATAATGATACATATGAATATATTTTCATATATCAACAATGCAA
GTGAAAAAATAAAGAGATTTGAAATAATTAATTTTATATATTAAAATTTACGATACCCACAATGT
ACG
Found at i:1931506 original size:13 final size:13
Alignment explanation
Indices: 1931490--1931515 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1931480 CTTTGCATAT
1931490 TGTCTTCAACAGG
1 TGTCTTCAACAGG
1931503 TGTCTTCAACAGG
1 TGTCTTCAACAGG
1931516 CTCGCACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:1935362 original size:25 final size:24
Alignment explanation
Indices: 1935304--1935362 Score: 57
Period size: 25 Copynumber: 2.3 Consensus size: 24
1935294 CAGATGGCCA
**
1935304 AAAGTAAAAAAATCTAGATATTTTT
1 AAAG-AAAAAAATCTAGATATTCCT
1935329 AAAGTAAAAAAATCTAGATATAATCCT
1 AAAG-AAAAAAATCTAGATAT--TCCT
1935356 AAA-AAAA
1 AAAGAAAA
1935363 GGCACCGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 25 0.83
27 5 0.17
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (24 bp):
AAAGAAAAAAATCTAGATATTCCT
Found at i:1935657 original size:17 final size:14
Alignment explanation
Indices: 1935633--1935680 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
1935623 TTTTTTGTTT
1935633 TTTGTTCTTTTTCC
1 TTTGTTCTTTTTCC
1935647 TGTTGTCTTCTTTGTT-C
1 T-TTG--TTCTTT-TTCC
1935664 TTTGTTCTTTTTCC
1 TTTGTTCTTTTTCC
1935678 TTT
1 TTT
1935681 TTTTGATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.07
14 11 0.38
15 3 0.10
16 3 0.10
17 8 0.28
18 2 0.07
ACGTcount: A:0.00, C:0.19, G:0.10, T:0.71
Consensus pattern (14 bp):
TTTGTTCTTTTTCC
Found at i:1944144 original size:17 final size:20
Alignment explanation
Indices: 1944103--1944147 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1944093 TTTTTTTTTC
1944103 TATAAAATACATATACAAAAT
1 TATAAAATACA-ATACAAAAT
1944124 TATAAAATAC-ATA-AAAA-
1 TATAAAATACAATACAAAAT
1944141 TATAAAA
1 TATAAAA
1944148 ATATTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.29
18 4 0.17
19 3 0.12
21 10 0.42
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (20 bp):
TATAAAATACAATACAAAAT
Found at i:1946432 original size:17 final size:17
Alignment explanation
Indices: 1946410--1946443 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1946400 ATCCACTAAT
*
1946410 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1946427 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1946444 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1951071 original size:17 final size:17
Alignment explanation
Indices: 1951049--1951082 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1951039 ATCCACTAAT
*
1951049 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1951066 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1951083 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1954027 original size:27 final size:26
Alignment explanation
Indices: 1953980--1954036 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
1953970 AATATATTAT
* *
1953980 TTTTAATTAATTAAGCATGAAATATGA
1 TTTTAATAAATTAAGCATGAAA-ATCA
*
1954007 TTTTAATAAAATTAAG-TTGAAAATCA
1 TTTTAAT-AAATTAAGCATGAAAATCA
1954033 TTTT
1 TTTT
1954037 TCCATTGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.27
27 12 0.46
28 7 0.27
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (26 bp):
TTTTAATAAATTAAGCATGAAAATCA
Found at i:1964759 original size:29 final size:29
Alignment explanation
Indices: 1964694--1964760 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
1964684 AAAGATTGGT
* *
1964694 GACCAAATTTAGCTCAAGAAAAGAATAAG
1 GACCAAATTTAACTCAAAAAAAGAATAAG
**
1964723 GATTAAATTTAACTCAAAAAAAGAATAAG
1 GACCAAATTTAACTCAAAAAAAGAATAAG
*
1964752 GGCCAAATT
1 GACCAAATT
1964761 GATAAAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (29 bp):
GACCAAATTTAACTCAAAAAAAGAATAAG
Found at i:1966448 original size:21 final size:19
Alignment explanation
Indices: 1966424--1966471 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
1966414 AAAGTTTTTT
1966424 TTATAAAATACATATACAAAA
1 TTATAAAATAC--ATACAAAA
*
1966445 TTATAAAATGCATACAAAA
1 TTATAAAATACATACAAAA
*
1966464 ATATAAAA
1 TTATAAAA
1966472 ATATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
21 10 0.40
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.27
Consensus pattern (19 bp):
TTATAAAATACATACAAAA
Found at i:1972993 original size:12 final size:12
Alignment explanation
Indices: 1972976--1973000 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1972966 CTTGAAATGC
1972976 CTTCTCTTCACT
1 CTTCTCTTCACT
1972988 CTTCTCTTCACT
1 CTTCTCTTCACT
1973000 C
1 C
1973001 CTTTCTGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTCTTCACT
Found at i:1974380 original size:18 final size:18
Alignment explanation
Indices: 1974343--1974381 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1974333 TCACCTTAGC
* * *
1974343 TTTATTTTGTTTTTGCGT
1 TTTATTTTCTTTATGAGT
1974361 TTTATTTTCTTTATGAGT
1 TTTATTTTCTTTATGAGT
1974379 TTT
1 TTT
1974382 TAAATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.10, C:0.05, G:0.13, T:0.72
Consensus pattern (18 bp):
TTTATTTTCTTTATGAGT
Found at i:1983043 original size:115 final size:114
Alignment explanation
Indices: 1982729--1983174 Score: 635
Period size: 114 Copynumber: 3.9 Consensus size: 114
1982719 AAAATAAGCA
* ** * * *
1982729 TTAGCAGCGTTTTCCAGAAAGCGCCGC-AAAAAAGCTAAGCCCAACGACGTCGTTTTCTAAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
1982793 TCGGGGATTTAGCCGCTTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * *
1982842 TTAGCGGCGTTTTTGAGAAAGCACCACAAAAAAACCTAAGCCCAACCACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* ** *
1982907 TTGGGGATTTAGCGGCGTTTTT-AGAAAAGCGCCTTTAATGCTTAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAATGCTCAGGGCT
*
1982956 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAGAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAA-AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
1983021 TTCGAGGATATAGCGGCATTTTTAAGAAAGCGCCGCTAATGCCCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
1983071 TTAGCGGCGTTTTTGAGAAAGCGCAGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
1983136 TCGGGGATTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAA
66 TCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAA
1983175 AGGTCTTGTT
Statistics
Matches: 293, Mismatches: 35, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
113 24 0.08
114 154 0.53
115 113 0.39
116 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.25
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:1987730 original size:75 final size:75
Alignment explanation
Indices: 1987615--1987829 Score: 358
Period size: 75 Copynumber: 2.9 Consensus size: 75
1987605 TGAATGGATC
*
1987615 TTCGGTTCCTCAGAATGGAGTAGATATTAGTCCAACAAGTACTAATTCTCATAGTATTCCCTCTT
1 TTCGGCTCCTCAGAATGGAGTAGATATTAGTCCAACAAGTACTAATTCTCATAGTATTCCCTCTT
1987680 TAAATGGGTA
66 TAAATGGGTA
* *
1987690 TTTGGCTCCTCAGAATGGAGTAGATATTAGTCCAACAAGTACTAATTCTTATAGTATTCCCTCTT
1 TTCGGCTCCTCAGAATGGAGTAGATATTAGTCCAACAAGTACTAATTCTCATAGTATTCCCTCTT
1987755 TAAATGGGTA
66 TAAATGGGTA
* * * * *
1987765 TTCGGTTCCTCAAAATGAAGTAGATATTAGTCCAACAAGTACTAACTCTCATAGTATTCCTTCTT
1 TTCGGCTCCTCAGAATGGAGTAGATATTAGTCCAACAAGTACTAATTCTCATAGTATTCCCTCTT
1987830 ATTCTGGTGA
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 130 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (75 bp):
TTCGGCTCCTCAGAATGGAGTAGATATTAGTCCAACAAGTACTAATTCTCATAGTATTCCCTCTT
TAAATGGGTA
Found at i:1996080 original size:17 final size:17
Alignment explanation
Indices: 1996058--1996091 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1996048 ATCCACTAAT
*
1996058 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1996075 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1996092 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2000719 original size:17 final size:17
Alignment explanation
Indices: 2000697--2000730 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2000687 ATCCACTAAT
*
2000697 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2000714 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2000731 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2001003 original size:18 final size:17
Alignment explanation
Indices: 2000980--2001052 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 17
2000970 TTGCGAGGCG
2000980 CCGGGTCCGATGGAAGAC
1 CCGGGTCCGATGGAAG-C
**
2000998 CCGGGTCCGATGGCTGCC
1 CCGGGTCCGATGGAAG-C
**
2001016 CCGGGTCCGATGGCTGC
1 CCGGGTCCGATGGAAGC
2001033 CCTGGGTCCGATGGAAGC
1 CC-GGGTCCGATGGAAGC
2001051 CC
1 CC
2001053 CACCCTATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
17 3 0.06
18 46 0.94
ACGTcount: A:0.12, C:0.34, G:0.38, T:0.15
Consensus pattern (17 bp):
CCGGGTCCGATGGAAGC
Found at i:2001053 original size:36 final size:36
Alignment explanation
Indices: 2000980--2001053 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
2000970 TTGCGAGGCG
**
2000980 CCGGGTCCGATGGAAGACCCGGGTCCGATGGCTGCC
1 CCGGGTCCGATGGAAGACCCGGGTCCGATGGAAGCC
**
2001016 CCGGGTCCGATGGCTG-CCCTGGGTCCGATGGAAGCC
1 CCGGGTCCGATGGAAGACCC-GGGTCCGATGGAAGCC
2001052 CC
1 CC
2001054 ACCCTATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 3 0.09
36 30 0.91
ACGTcount: A:0.12, C:0.35, G:0.38, T:0.15
Consensus pattern (36 bp):
CCGGGTCCGATGGAAGACCCGGGTCCGATGGAAGCC
Found at i:2007750 original size:20 final size:21
Alignment explanation
Indices: 2007714--2007752 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2007704 TAGGCGCCAA
2007714 TGAATAAAATAATAATTTTTT
1 TGAATAAAATAATAATTTTTT
2007735 TGAATAAAAT-ATAATTTT
1 TGAATAAAATAATAATTTT
2007753 ATACTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TGAATAAAATAATAATTTTTT
Found at i:2007841 original size:27 final size:27
Alignment explanation
Indices: 2007800--2007883 Score: 141
Period size: 27 Copynumber: 3.1 Consensus size: 27
2007790 TAGTATTGGC
*
2007800 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
2007827 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
2007854 GCCTATCTGGGAGGTGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
2007881 GCC
1 GCC
2007884 ATACTGAAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.15, C:0.21, G:0.39, T:0.24
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:2007895 original size:27 final size:27
Alignment explanation
Indices: 2007800--2007902 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
2007790 TAGTATTGGC
2007800 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
* *
2007827 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
* *
2007854 GCCTATCTGGGAGGTGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
* *
2007881 GCC-ATACTGAAAGGTGCCAATG
1 GCCTAT-CTGGAAGGCGCCAATG
2007903 TTGTGATTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
26 2 0.03
27 67 0.97
ACGTcount: A:0.19, C:0.20, G:0.37, T:0.23
Consensus pattern (27 bp):
GCCTATCTGGAAGGCGCCAATGGTGGT
Found at i:2007996 original size:22 final size:22
Alignment explanation
Indices: 2007958--2008034 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
2007948 ACTACAGAAA
2007958 CAGAAGAAAGAAGAAGGAAGGAAG
1 CAGAAG-AA-AAGAAGGAAGGAAG
2007982 CAGAAGAAAAGAAGGAAGGAAG
1 CAGAAGAAAAGAAGGAAGGAAG
2008004 CAGAAGAAAAGAAGGAAGGAA-
1 CAGAAGAAAAGAAGGAAGGAAG
*
2008025 AAGAAGAAAA
1 CAGAAGAAAA
2008035 AAATTAGGTA
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
21 9 0.17
22 35 0.67
23 2 0.04
24 6 0.12
ACGTcount: A:0.62, C:0.04, G:0.34, T:0.00
Consensus pattern (22 bp):
CAGAAGAAAAGAAGGAAGGAAG
Found at i:2008713 original size:90 final size:90
Alignment explanation
Indices: 2008560--2008738 Score: 340
Period size: 90 Copynumber: 2.0 Consensus size: 90
2008550 TTATTTGCTG
*
2008560 AGTTAGCCAGTGTGGAGGCAACTGAAGATCCCACTCCATTAGGTGAAGAAGATGGAGTTGAAGCG
1 AGTTAGCCAATGTGGAGGCAACTGAAGATCCCACTCCATTAGGTGAAGAAGATGGAGTTGAAGCG
2008625 CCGTGTATGGTGGTTCCGGTATCGA
66 CCGTGTATGGTGGTTCCGGTATCGA
*
2008650 AGTTAGCCAATGTGGAGGCAACTGATGATCCCACTCCATTAGGTGAAGAAGATGGAGTTGAAGCG
1 AGTTAGCCAATGTGGAGGCAACTGAAGATCCCACTCCATTAGGTGAAGAAGATGGAGTTGAAGCG
2008715 CCGTGTATGGTGGTTCCGGTATCG
66 CCGTGTATGGTGGTTCCGGTATCG
2008739 TATGTTGATA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (90 bp):
AGTTAGCCAATGTGGAGGCAACTGAAGATCCCACTCCATTAGGTGAAGAAGATGGAGTTGAAGCG
CCGTGTATGGTGGTTCCGGTATCGA
Found at i:2011862 original size:27 final size:27
Alignment explanation
Indices: 2011832--2011914 Score: 148
Period size: 27 Copynumber: 3.1 Consensus size: 27
2011822 CCTATCAGGT
2011832 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
2011859 AGGCGCTAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
2011886 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
2011913 AG
1 AG
2011915 TAGACCTGTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.30, C:0.23, G:0.34, T:0.13
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:2012083 original size:11 final size:11
Alignment explanation
Indices: 2012067--2012094 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2012057 AGATTTTTTT
2012067 GGCCCGGGCCC
1 GGCCCGGGCCC
2012078 GGCCCGGGCCC
1 GGCCCGGGCCC
2012089 GGCCCG
1 GGCCCG
2012095 AAAAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.54, G:0.46, T:0.00
Consensus pattern (11 bp):
GGCCCGGGCCC
Found at i:2012130 original size:22 final size:24
Alignment explanation
Indices: 2012104--2012147 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2012094 GAAAAATATT
2012104 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
2012126 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
2012148 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:2012258 original size:9 final size:9
Alignment explanation
Indices: 2012244--2012271 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2012234 TTTTGTTACA
2012244 ACAATTAAT
1 ACAATTAAT
2012253 ACAATTAAT
1 ACAATTAAT
2012262 ACAATTAAT
1 ACAATTAAT
2012271 A
1 A
2012272 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:2012293 original size:68 final size:66
Alignment explanation
Indices: 2012214--2012355 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
2012204 TTAAGTTTGT
*
2012214 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
2012279 AAA
64 AAA
2012282 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
2012347 T
66 A
2012348 TTTACTAA
1 TTTACTAA
2012356 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:2012365 original size:16 final size:16
Alignment explanation
Indices: 2012344--2012385 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2012334 AATAATTTGA
*
2012344 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
2012360 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
2012376 TAGTTTTAAT
1 TAATTTTAAT
2012386 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:2012374 original size:59 final size:66
Alignment explanation
Indices: 2012214--2012377 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
2012204 TTAAGTTTGT
*
2012214 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
2012279 AAA
64 AAA
2012282 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
2012345 AAT
64 AAA
*
2012348 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
2012378 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:2012693 original size:21 final size:21
Alignment explanation
Indices: 2012664--2012707 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2012654 TGGATTAGTA
*
2012664 TTTTGTATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
2012685 TTTTATATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
2012706 TT
1 TT
2012708 GTGTTTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTATATGAATATTGTAATT
Found at i:2012839 original size:16 final size:16
Alignment explanation
Indices: 2012796--2012839 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
2012786 AAAATCAAAT
*
2012796 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
2012812 AAAGTTACATTATATA
1 AAAATTAAATTATATA
2012828 AAAATTAAATTA
1 AAAATTAAATTA
2012840 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:2012914 original size:37 final size:38
Alignment explanation
Indices: 2012872--2012952 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 38
2012862 AAAAAGACAG
2012872 TTATAATTAAACTTTTAATAAAATGATTTTT-ATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
2012909 TTATAATTAAACTTTTAATAAGATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
2012947 TTATAA
1 TTATAA
2012953 ACTTTATATG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 30 0.71
38 12 0.29
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:2013078 original size:60 final size:60
Alignment explanation
Indices: 2012985--2013106 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
2012975 ATATTAAACT
* * * *
2012985 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATTT-T-AAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT--ATTTATAAAATAATTAC
*
2013045 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTATTTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTATTTATAAAATAATTAC
2013105 AA
1 AA
2013107 TATTCATACA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 4 0.07
59 1 0.02
60 50 0.91
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTATTTATAAAATAATTAC
Found at i:2013171 original size:19 final size:19
Alignment explanation
Indices: 2013168--2013286 Score: 75
Period size: 19 Copynumber: 6.1 Consensus size: 19
2013158 CATACAAAAT
*
2013168 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
*
2013187 TACAAAATTATAATATTCA
1 TACAAAATTACAATATTCA
* *
2013206 TACAAAA-TACTA-ATCCAA
1 TACAAAATTACAATATTC-A
*
2013224 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
* *
2013247 TAAAATAATTACAATATTAA
1 TACAA-AATTACAATATTCA
2013267 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
2013286 T
1 T
2013287 TGGCGCCTCT
Statistics
Matches: 77, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
17 3 0.04
18 6 0.08
19 42 0.55
20 12 0.16
21 2 0.03
22 5 0.06
23 5 0.06
25 2 0.03
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.34
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:2013183 original size:27 final size:27
Alignment explanation
Indices: 2013147--2013203 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2013137 ATATCCCGAC
2013147 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
*
2013174 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
2013201 ATT
1 ATT
2013204 CATACAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:2013320 original size:27 final size:27
Alignment explanation
Indices: 2013282--2013348 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
2013272 AATTACAATA
2013282 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
2013309 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
2013336 TTCATTGGCGCCT
1 TTCATTGGCGCCT
2013349 ACCTGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:2013453 original size:16 final size:16
Alignment explanation
Indices: 2013430--2013463 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2013420 TAAAAAAATA
*
2013430 TAAAAAAATATTTTATT
1 TAAAAAAAT-TATTATT
2013447 TAAAAAAATTATTATT
1 TAAAAAAATTATTATT
2013463 T
1 T
2013464 TTTTATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAAAAATTATTATT
Found at i:2013591 original size:83 final size:82
Alignment explanation
Indices: 2013500--2013664 Score: 240
Period size: 83 Copynumber: 2.0 Consensus size: 82
2013490 GGCTCCAATG
* ***** *
2013500 AAAAAGTAACCTATTTTGGTAAATTTTTTTTCTGACATCCTATTTCAGTATTTTTTTTTCTATAC
1 AAAAAGTAACCTATTTTGGCAAAAAAAATTTCTGACATACTATTTCAGTA-TTTTTTTTCTATAC
*
2013565 CATTTGTGTAAAAAACCC
65 CATTTCTGTAAAAAACCC
*
2013583 AAAAAGTAACCTATTTTGGCAAAAAAAATTTCTGACATACTATTTCAGTATTTTTTTTCTATACT
1 AAAAAGTAACCTATTTTGGCAAAAAAAATTTCTGACATACTATTTCAGTATTTTTTTTCTATACC
2013648 ATTTCTGTAAAAAACCC
66 ATTTCTGTAAAAAACCC
2013665 CGTTAAACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
82 30 0.41
83 43 0.59
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (82 bp):
AAAAAGTAACCTATTTTGGCAAAAAAAATTTCTGACATACTATTTCAGTATTTTTTTTCTATACC
ATTTCTGTAAAAAACCC
Found at i:2032216 original size:18 final size:18
Alignment explanation
Indices: 2032193--2032249 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
2032183 TACGACCGTT
2032193 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
2032211 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
2032229 TACGGTACTGTTCACGTA
1 TACGGCACTATTCACGTA
2032247 TAC
1 TAC
2032250 AGTAGTTGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:2037081 original size:28 final size:29
Alignment explanation
Indices: 2037032--2037089 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2037022 TACTATGGTT
*
2037032 AAAAAAAAGATAAGTATTTTAATTGAAACA
1 AAAAAAAAGATAAGTA-TTTAAATGAAACA
* *
2037062 AAAAAAAAGTTTAGTA-TTAAATGAAACA
1 AAAAAAAAGATAAGTATTTAAATGAAACA
2037090 TTGAAGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.44
30 14 0.56
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.26
Consensus pattern (29 bp):
AAAAAAAAGATAAGTATTTAAATGAAACA
Found at i:2046051 original size:37 final size:37
Alignment explanation
Indices: 2046009--2046083 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
2045999 GTTGCCGGTG
* *
2046009 TAAGAGGACGTCGGTTCGAGTGCGTTGAAGCGTATTA
1 TAAGAGGACGTCGGTTCGAGTACGTTGAAGCATATTA
*
2046046 TAAGAGGACGTGGGTTCGAGTACGTTGAAGCATATTA
1 TAAGAGGACGTCGGTTCGAGTACGTTGAAGCATATTA
2046083 T
1 T
2046084 CCTCTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.28
Consensus pattern (37 bp):
TAAGAGGACGTCGGTTCGAGTACGTTGAAGCATATTA
Found at i:2047611 original size:72 final size:72
Alignment explanation
Indices: 2047501--2047706 Score: 306
Period size: 72 Copynumber: 2.9 Consensus size: 72
2047491 TAATCAAAGT
* ** * * *
2047501 TCCAACAACTCGTCCTTAAAAGTAATAAATATTAATATTTTAAATAGATATAGCCAGAATAATAT
1 TCCAACAACTTGTCCTTGGAAGTAATAAATATTAATATTTTAAATAAATGTAGCCAAAATAATAT
2047566 AATGAGG
66 AATGAGG
*
2047573 TCCAACAACTTGTCGTTGGAAGTAATAAATATTAATATTTTAAATAAATGTAGCCAAAATAATAT
1 TCCAACAACTTGTCCTTGGAAGTAATAAATATTAATATTTTAAATAAATGTAGCCAAAATAATAT
* *
2047638 ATTGATG
66 AATGAGG
*
2047645 TCCAACAACTTGTCCTTGGATGTAATAAATATT-ATCATTTTAAATAAATGTAGCCAAAATAA
1 TCCAACAACTTGTCCTTGGAAGTAATAAATATTAAT-ATTTTAAATAAATGTAGCCAAAATAA
2047707 GATCCAACAA
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
71 2 0.02
72 120 0.98
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (72 bp):
TCCAACAACTTGTCCTTGGAAGTAATAAATATTAATATTTTAAATAAATGTAGCCAAAATAATAT
AATGAGG
Found at i:2048522 original size:18 final size:18
Alignment explanation
Indices: 2048499--2048552 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
2048489 CGAAGCAACA
2048499 GGTCCGATGGCGGCCCCG
1 GGTCCGATGGCGGCCCCG
*
2048517 GGTCCGACGGCGGCCCCG
1 GGTCCGATGGCGGCCCCG
* *
2048535 GTTCCGATGGCAGCCCCG
1 GGTCCGATGGCGGCCCCG
2048553 CCATAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.07, C:0.41, G:0.41, T:0.11
Consensus pattern (18 bp):
GGTCCGATGGCGGCCCCG
Found at i:2050953 original size:23 final size:23
Alignment explanation
Indices: 2050923--2050967 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2050913 TTCCATGAAC
2050923 TATGCTGCACACTTGGGTTTCAT
1 TATGCTGCACACTTGGGTTTCAT
2050946 TATGCTGCACACTTGGGTTTCA
1 TATGCTGCACACTTGGGTTTCA
2050968 AGTCTGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (23 bp):
TATGCTGCACACTTGGGTTTCAT
Found at i:2062592 original size:75 final size:75
Alignment explanation
Indices: 2062464--2062617 Score: 256
Period size: 75 Copynumber: 2.1 Consensus size: 75
2062454 TGCCCGAGTC
* * *
2062464 CTTTGAATGGATCTTCGGTTCCTCAGAATGGAGTAGATATTAGTCCAACAAGTACTAATTCTCAT
1 CTTTAAATGGATCTTCGGTTCCTCAGAATGAAGTAGATATTAGTCCAACAAGTACTAACTCTCAT
*
2062529 AGTATTCCCT
66 AATATTCCCT
*
2062539 CTTTAAATGGGTCTTCGGTTCCTCAGAATGAAGTAGATATTAGTCCAACAAGTACTAACTCTCAT
1 CTTTAAATGGATCTTCGGTTCCTCAGAATGAAGTAGATATTAGTCCAACAAGTACTAACTCTCAT
2062604 AATATTCCCT
66 AATATTCCCT
2062614 -TTTA
1 CTTTA
2062618 TTCTGGTGAT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
74 4 0.05
75 70 0.95
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (75 bp):
CTTTAAATGGATCTTCGGTTCCTCAGAATGAAGTAGATATTAGTCCAACAAGTACTAACTCTCAT
AATATTCCCT
Found at i:2064133 original size:20 final size:19
Alignment explanation
Indices: 2064108--2064315 Score: 89
Period size: 19 Copynumber: 11.1 Consensus size: 19
2064098 AGAAACGGAT
*
2064108 TTAAAATTTATTTAAAAATA
1 TTAAAAATTA-TTAAAAATA
2064128 TTAAAAATTATTAAAAAT-
1 TTAAAAATTATTAAAAATA
* *
2064146 TGTAAAAATTAATAAAAACA
1 T-TAAAAATTATTAAAAATA
*
2064166 TT-AAAATTTTGTAAAAATA
1 TTAAAAATTAT-TAAAAATA
** *
2064185 TATAATAAAAAATTTAGAAAT-
1 T-TAA-AAATTA-TTAAAAATA
* *
2064206 GTAAAAATGATTAAAACAT-
1 TTAAAAATTATTAAAA-ATA
* * *
2064225 TGT-AAAATT-TTCAACATC
1 T-TAAAAATTATTAAAAATA
*
2064243 TT-AAAATT-TTAAAAATT
1 TTAAAAATTATTAAAAATA
*
2064260 TTAAAAATTA--AAATATA
1 TTAAAAATTATTAAAAATA
** *
2064277 TTAAAAATT-TGTAAATTTTG
1 TTAAAAATTAT-TAAA-AATA
2064297 TTAAAAATTA-TAAAAATA
1 TTAAAAATTATTAAAAATA
2064315 T
1 T
2064316 ACACTTCATC
Statistics
Matches: 143, Mismatches: 28, Indels: 36
0.69 0.14 0.17
Matches are distributed among these distances:
17 31 0.22
18 25 0.17
19 50 0.35
20 26 0.18
21 1 0.01
22 9 0.06
23 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
TTAAAAATTATTAAAAATA
Found at i:2064145 original size:10 final size:10
Alignment explanation
Indices: 2064108--2064313 Score: 63
Period size: 9 Copynumber: 21.8 Consensus size: 10
2064098 AGAAACGGAT
*
2064108 TTAAAATTTA
1 TTAAAAATTA
2064118 TTTAAAAA-TA
1 -TTAAAAATTA
2064128 TTAAAAATTA
1 TTAAAAATTA
2064138 TTAAAAATT-
1 TTAAAAATTA
*
2064147 GTAAAAATTA
1 TTAAAAATTA
* *
2064157 ATAAAAA-CA
1 TTAAAAATTA
*
2064166 TT-AAAATTT
1 TTAAAAATTA
2064175 TGTAAAAATATA
1 T-TAAAAAT-TA
*
2064187 TAATAAAAAAT-
1 T--TAAAAATTA
*
2064198 TTAGAAA-T-
1 TTAAAAATTA
* *
2064206 GTAAAAATGA
1 TTAAAAATTA
2064216 TTAAAACATT-
1 TTAAAA-ATTA
*
2064226 GT-AAAATT-
1 TTAAAAATTA
* * *
2064234 TTCAACA-TC
1 TTAAAAATTA
2064243 TT-AAAATT-
1 TTAAAAATTA
2064251 TTAAAAATT-
1 TTAAAAATTA
2064260 TTAAAAATTA
1 TTAAAAATTA
*
2064270 --AAATA-TA
1 TTAAAAATTA
2064277 TTAAAAATT-
1 TTAAAAATTA
** *
2064286 TGTAAATTTTG
1 T-TAAAAATTA
2064297 TTAAAAATTA
1 TTAAAAATTA
2064307 -TAAAAAT
1 TTAAAAAT
2064314 ATACACTTCA
Statistics
Matches: 148, Mismatches: 27, Indels: 42
0.68 0.12 0.19
Matches are distributed among these distances:
7 2 0.01
8 24 0.16
9 59 0.40
10 39 0.26
11 15 0.10
12 3 0.02
13 6 0.04
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:2064161 original size:29 final size:28
Alignment explanation
Indices: 2064120--2064213 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 28
2064110 AAAATTTATT
*
2064120 TAAAAA-TATTAAAAATTATTAAAAATTG
1 TAAAAATTAATAAAAA-TATTAAAAATTG
* *
2064148 TAAAAATTAATAAAAACATTAAAATTTTG
1 TAAAAATTAATAAAAATATTAAAA-ATTG
*
2064177 TAAAAATATATAATAAAAA-ATTTAGAAA-TG
1 T-AAAA-AT-TAATAAAAATA-TTAAAAATTG
2064207 TAAAAAT
1 TAAAAAT
2064214 GATTAAAACA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
28 15 0.27
29 16 0.29
30 7 0.13
31 3 0.05
32 14 0.25
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (28 bp):
TAAAAATTAATAAAAATATTAAAAATTG
Found at i:2064213 original size:59 final size:57
Alignment explanation
Indices: 2064106--2064235 Score: 138
Period size: 58 Copynumber: 2.2 Consensus size: 57
2064096 CTAGAAACGG
* **
2064106 ATTTAAAATTTATTTAAAAATATTAAAAATTATTAAAAATTGTAAAAATTAATAAAAAC
1 ATTTAAAATTT-TGTAAAAATATTAAAAAAAATTAAAAATTGTAAAAA-TAATAAAAAC
* * *
2064165 A-TTAAAATTTTGTAAAAATATATAATAAAAAATTTAGAAA-TGTAAAAATGATTAAAAC
1 ATTTAAAATTTTGTAAAAATAT-TAA-AAAAAA-TTAAAAATTGTAAAAATAATAAAAAC
2064223 ATTGTAAAATTTT
1 ATT-TAAAATTTT
2064236 CAACATCTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
57 10 0.17
58 21 0.35
59 14 0.23
60 15 0.25
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (57 bp):
ATTTAAAATTTTGTAAAAATATTAAAAAAAATTAAAAATTGTAAAAATAATAAAAAC
Done.