Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 6 of 206
Found at i:1826849 original size:18 final size:17
Alignment explanation
Indices: 1826822--1826937 Score: 92
Period size: 19 Copynumber: 6.4 Consensus size: 17
1826812 TGAAAATTTA
* *
1826822 TTTTTGAAACATGAGAAT
1 TTTTTAAAACACGA-AAT
1826840 TTTTTAAAACACGAAATTT
1 TTTTTAAAACACGAAA--T
1826859 TTTTTAAAAACACGGAAAT
1 TTTTT-AAAACAC-GAAAT
* *
1826878 TTTTGAAACACAAGAAATT
1 TTTTTAAA-ACACGAAA-T
1826897 TTTTTGAAAACACGAAAAT
1 TTTTT-AAAACACG-AAAT
*
1826916 TTTTT-AAACACG-ATT
1 TTTTTAAAACACGAAAT
1826931 TTTTTAA
1 TTTTTAA
1826938 GAAGTGCCGT
Statistics
Matches: 82, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
15 7 0.09
16 1 0.01
17 9 0.11
18 19 0.23
19 29 0.35
20 13 0.16
21 4 0.05
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTTTAAAACACGAAAT
Found at i:1826861 original size:19 final size:18
Alignment explanation
Indices: 1826839--1826937 Score: 98
Period size: 19 Copynumber: 5.4 Consensus size: 18
1826829 AACATGAGAA
1826839 TTTTTTAAAACACGAAATT
1 TTTTTTAAAACACGAAA-T
1826858 TTTTTTAAAAACACGGAAA-
1 TTTTTT-AAAACAC-GAAAT
* *
1826877 TTTTTGAAACACAAGAAAT
1 TTTTTTAAA-ACACGAAAT
*
1826896 TTTTTTGAAAACACGAAAA
1 TTTTTT-AAAACACGAAAT
1826915 TTTTTT-AAACACG--AT
1 TTTTTTAAAACACGAAAT
1826930 TTTTTTAA
1 TTTTTTAA
1826938 GAAGTGCCGT
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.10
16 1 0.01
17 7 0.10
18 7 0.10
19 32 0.47
20 10 0.15
21 4 0.06
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (18 bp):
TTTTTTAAAACACGAAAT
Found at i:1826925 original size:38 final size:39
Alignment explanation
Indices: 1826815--1826926 Score: 140
Period size: 38 Copynumber: 2.9 Consensus size: 39
1826805 GGAATTTTGA
* * *
1826815 AAATTTATTTTTG-AAACATGAGAATTTTTTAAA-ACACG
1 AAATTT-TTTTTGAAAACACGAAAATTTTTTAAACACAAG
* * *
1826853 AAATTTTTTTTAAAAACACGGAAATTTTTGAAACACAAG
1 AAATTTTTTTTGAAAACACGAAAATTTTTTAAACACAAG
1826892 AAA-TTTTTTTGAAAACACGAAAATTTTTTAAACAC
1 AAATTTTTTTTGAAAACACGAAAATTTTTTAAACAC
1826927 GATTTTTTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
37 5 0.08
38 51 0.81
39 7 0.11
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (39 bp):
AAATTTTTTTTGAAAACACGAAAATTTTTTAAACACAAG
Found at i:1827226 original size:27 final size:27
Alignment explanation
Indices: 1827196--1827250 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1827186 TGCCTTATTT
*
1827196 ATTGAAATT-ATTTAAATTTAAAATAAA
1 ATTGAAATTAAATTAAA-TTAAAATAAA
*
1827223 ATTGAAATTAAATTAAATTAAATTAAA
1 ATTGAAATTAAATTAAATTAAAATAAA
1827250 A
1 A
1827251 ATATAAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
ATTGAAATTAAATTAAATTAAAATAAA
Found at i:1827235 original size:5 final size:5
Alignment explanation
Indices: 1827216--1827249 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1827206 TTTAAATTTA
*
1827216 AAATA AAATT GAAATT AAATT AAATT AAATT AAA
1 AAATT AAATT -AAATT AAATT AAATT AAATT AAA
1827250 AATATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (5 bp):
AAATT
Found at i:1827433 original size:16 final size:15
Alignment explanation
Indices: 1827403--1827448 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1827393 GCAAGTTGAA
1827403 TCCCTTTTTTCTTTT
1 TCCCTTTTTTCTTTT
1827418 TCCCTTTTTTCTTTT
1 TCCCTTTTTTCTTTT
* *
1827433 TTCCTCTTTT-TTTT
1 TCCCTTTTTTCTTTT
1827447 TC
1 TC
1827449 TCATTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TCCCTTTTTTCTTTT
Found at i:1827640 original size:16 final size:16
Alignment explanation
Indices: 1827613--1827658 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
1827603 TTGGACAGGC
1827613 CTGCTATTTTTTTGCTG
1 CTGCT-TTTTTTTGCTG
* *
1827630 CTGGTTTTTTTTACTG
1 CTGCTTTTTTTTGCTG
1827646 CTGCTTTTTTTTG
1 CTGCTTTTTTTTG
1827659 GGCTGATCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.04, C:0.15, G:0.17, T:0.63
Consensus pattern (16 bp):
CTGCTTTTTTTTGCTG
Found at i:1827765 original size:20 final size:18
Alignment explanation
Indices: 1827742--1827802 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 18
1827732 TTTATTTTTC
1827742 CTTTTTTCTTTCCATTTCTT
1 CTTTTTTCTTT-C-TTTCTT
*
1827762 CTTTCTTCTTTCTTTCTT
1 CTTTTTTCTTTCTTTCTT
*
1827780 CTCTTTTTCTCTTTTTTCTT
1 CT-TTTTTCT-TTCTTTCTT
1827800 CTT
1 CTT
1827803 CTCCTTCGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 20 0.56
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTTTTCTTTCTTTCTT
Found at i:1827766 original size:7 final size:7
Alignment explanation
Indices: 1827756--1827804 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
1827746 TTTCTTTCCA
1827756 TTTCTTC
1 TTTCTTC
1827763 TTTCTTC
1 TTTCTTC
1827770 TTTCTTTC
1 TTTC-TTC
1827778 TTCTCTT-
1 TT-TCTTC
1827785 TTTC-TC
1 TTTCTTC
*
1827791 TTTTTTC
1 TTTCTTC
1827798 -TTCTTC
1 TTTCTTC
1827804 T
1 T
1827805 CCTTCGGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
5 1 0.03
6 10 0.29
7 15 0.43
8 7 0.20
9 2 0.06
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTCTTC
Found at i:1827776 original size:11 final size:10
Alignment explanation
Indices: 1827757--1827802 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
1827747 TTCTTTCCAT
*
1827757 TTCTTCTTTC
1 TTCTTTTTTC
1827767 TTCTTTCTTTC
1 TTCTTT-TTTC
1827778 TTCTCTTTTTC
1 TTCT-TTTTTC
1827789 -TCTTTTTTC
1 TTCTTTTTTC
1827798 TTCTT
1 TTCTT
1827803 CTCCTTCGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 6 0.19
10 12 0.38
11 12 0.38
12 2 0.06
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:1828110 original size:16 final size:17
Alignment explanation
Indices: 1828091--1828123 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1828081 TTTTTGCTGA
*
1828091 TTTTTCTTTTTT-TTTC
1 TTTTACTTTTTTCTTTC
1828107 TTTTACTTTTTTCTTTC
1 TTTTACTTTTTTCTTTC
1828124 CCCCTTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTACTTTTTTCTTTC
Found at i:1828148 original size:12 final size:12
Alignment explanation
Indices: 1828133--1828177 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1828123 CCCCCTTTCT
1828133 TTTTCCTTCTTC
1 TTTTCCTTCTTC
*
1828145 TTTTTCTTCTTC
1 TTTTCCTTCTTC
* *
1828157 CTTTCTTTCTTC
1 TTTTCCTTCTTC
1828169 TTCTTCCTT
1 TT-TTCCTT
1828178 GTTCGGCCCC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCCTTCTTC
Found at i:1828171 original size:18 final size:17
Alignment explanation
Indices: 1828126--1828177 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
1828116 TTTCTTTCCC
1828126 CCTTTCTTTTTC--CTT
1 CCTTTCTTTTTCTTCTT
1828141 -C-TTCTTTTTCTTCTT
1 CCTTTCTTTTTCTTCTT
1828156 CCTTTCTTTCTTCTTCTT
1 CCTTTCTTT-TTCTTCTT
1828174 CCTT
1 CCTT
1828178 GTTCGGCCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.28
14 1 0.03
15 3 0.09
16 1 0.03
17 6 0.19
18 12 0.38
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
CCTTTCTTTTTCTTCTT
Found at i:1828433 original size:20 final size:18
Alignment explanation
Indices: 1828408--1828456 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
1828398 ATGAGGCTGC
1828408 TGTTTTTGCTTGATTTCTTT
1 TGTTTTTGCTTG-TTT-TTT
*
1828428 TGTTTTTTCTTGTTTTTT
1 TGTTTTTGCTTGTTTTTT
*
1828446 T-TCTTTGCTTG
1 TGTTTTTGCTTG
1828457 GTTCTTGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 4 0.15
19 3 0.12
20 11 0.42
ACGTcount: A:0.02, C:0.10, G:0.14, T:0.73
Consensus pattern (18 bp):
TGTTTTTGCTTGTTTTTT
Found at i:1828665 original size:30 final size:30
Alignment explanation
Indices: 1828631--1828718 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 30
1828621 GCCAAAATAA
*
1828631 AATTTTGAGAAAATTTTAGGGTTAAAATGT
1 AATTTTGAGAAAAGTTTAGGGTTAAAATGT
* *
1828661 AA-TTT-ACAAAAGTTTAGGGGTAGAAATGT
1 AATTTTGAGAAAAGTTTAGGGTTA-AAATGT
* *
1828690 AATTTTGAG-AAAGTTTGGGGTCAAAATGT
1 AATTTTGAGAAAAGTTTAGGGTTAAAATGT
1828719 TTTTTTTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 14 0.29
29 17 0.35
30 16 0.33
31 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
AATTTTGAGAAAAGTTTAGGGTTAAAATGT
Found at i:1832837 original size:19 final size:19
Alignment explanation
Indices: 1832811--1832868 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1832801 TAATACAATA
1832811 AAATATTTATTATATTTAT
1 AAATATTTATTATATTTAT
** *
1832830 TTATATTT-TTA-ATATAAT
1 AAATATTTATTATAT-TTAT
1832848 AAAGTATTTATTATATTTAT
1 AAA-TATTTATTATATTTAT
1832868 A
1 A
1832869 GTAGCATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
17 2 0.07
18 7 0.24
19 11 0.38
20 7 0.24
21 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
AAATATTTATTATATTTAT
Found at i:1832888 original size:38 final size:37
Alignment explanation
Indices: 1832799--1832887 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 37
1832789 TAAAATTATA
* * *
1832799 TTTAATACAATAAAATATTTATTATATTTATTTATATT
1 TTTAATATAAT-AAATATTTATTATATTTATGTACATT
1832837 TTTAATATAATAAAGTATTTATTATATTTATAGTAGCATTT
1 TTTAATATAATAAA-TATTTATTATATTTAT-GTA-CA-TT
1832878 TTTAATATAA
1 TTTAATATAA
1832888 ATATTTTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
37 3 0.07
38 26 0.59
39 2 0.05
40 1 0.02
41 12 0.27
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (37 bp):
TTTAATATAATAAATATTTATTATATTTATGTACATT
Found at i:1835439 original size:24 final size:24
Alignment explanation
Indices: 1835400--1835454 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
1835390 AAAAATCCAG
*
1835400 TTTATTTTTTATTTTAA-TTAATT
1 TTTATTTTTTAATTTAATTTAATT
1835423 TTTATTTTTATAATTTAATTTAATT
1 TTTATTTTT-TAATTTAATTTAATT
*
1835448 TTAATTT
1 TTTATTT
1835455 AAAAAATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 9 0.32
24 7 0.25
25 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTATTTTTTAATTTAATTTAATT
Found at i:1842280 original size:2 final size:2
Alignment explanation
Indices: 1842273--1842311 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1842263 ATGGTGCTGC
1842273 AT AT 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 AT AT A
1842312 ATGGATGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1844128 original size:2 final size:2
Alignment explanation
Indices: 1844121--1844165 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1844111 NCATATTTGC
1844121 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
1844163 AT A
1 AT A
1844166 AATGTTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1854143 original size:2 final size:2
Alignment explanation
Indices: 1854136--1854176 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1854126 TAATATTTGC
1854136 AT AT AT 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 AT AT AT A
1854177 AATGTTTTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1854922 original size:14 final size:15
Alignment explanation
Indices: 1854903--1854936 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1854893 TGTTTTTAAA
1854903 TTTTAA-AATACGGG
1 TTTTAAGAATACGGG
*
1854917 TTTTAAGAATATGGG
1 TTTTAAGAATACGGG
1854932 TTTTA
1 TTTTA
1854937 TTTGATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (15 bp):
TTTTAAGAATACGGG
Found at i:1855416 original size:121 final size:121
Alignment explanation
Indices: 1855202--1855445 Score: 488
Period size: 121 Copynumber: 2.0 Consensus size: 121
1855192 AGGGTGTGGA
1855202 ATGGTATGATGGGTTTTCCTTAAAAGGAAATGAAAGGCTTAGGTGAGTTTAAAGCATTACAGAGA
1 ATGGTATGATGGGTTTTCCTTAAAAGGAAATGAAAGGCTTAGGTGAGTTTAAAGCATTACAGAGA
1855267 ACTGATACACCCAAACTCTTTCCTATCATGGCATTTAAGGATAGGACACTACACTC
66 ACTGATACACCCAAACTCTTTCCTATCATGGCATTTAAGGATAGGACACTACACTC
1855323 ATGGTATGATGGGTTTTCCTTAAAAGGAAATGAAAGGCTTAGGTGAGTTTAAAGCATTACAGAGA
1 ATGGTATGATGGGTTTTCCTTAAAAGGAAATGAAAGGCTTAGGTGAGTTTAAAGCATTACAGAGA
1855388 ACTGATACACCCAAACTCTTTCCTATCATGGCATTTAAGGATAGGACACTACACTC
66 ACTGATACACCCAAACTCTTTCCTATCATGGCATTTAAGGATAGGACACTACACTC
1855444 AT
1 AT
1855446 TTACTTACAA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 123 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (121 bp):
ATGGTATGATGGGTTTTCCTTAAAAGGAAATGAAAGGCTTAGGTGAGTTTAAAGCATTACAGAGA
ACTGATACACCCAAACTCTTTCCTATCATGGCATTTAAGGATAGGACACTACACTC
Found at i:1859289 original size:124 final size:124
Alignment explanation
Indices: 1859063--1859343 Score: 390
Period size: 124 Copynumber: 2.3 Consensus size: 124
1859053 TTATTTCGAG
* *
1859063 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGATAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCG-TTATACCAGGATGCTATCAGAGAAGAAATTGT
* * *
1859127 TAAATCGTGCCCTCGTGGACGCCATTTCGGTACAGTTGGTCATGTAAGAAATAA-T-TTTT
64 GAAATCGCGCCCTCGTGGACGCCATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
1859186 TTGACGTTTTCTGAGCAAATAGTATAAAATCGTTGATACCAGGATGCTAT-ATGAGAAGAAATTG
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGTT-ATACCAGGATGCTATCA-GAGAAGAAATTG
* * * *
1859250 TGAAATCGCGCCCTCGTGGATGCGATTTCGCTATAGTTGGTCATGTAGGAAATAATTATTTT
63 TGAAATCGCGCCCTCGTGGACGCCATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
* *
1859312 TTGACGTTTCTGAGCAAATAGTGTCAAATCGT
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGT
1859344 GCCCTCGTGG
Statistics
Matches: 141, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
123 9 0.06
124 96 0.68
125 26 0.18
126 10 0.07
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGTTATACCAGGATGCTATCAGAGAAGAAATTGTGA
AATCGCGCCCTCGTGGACGCCATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
Found at i:1862559 original size:56 final size:56
Alignment explanation
Indices: 1862499--1862606 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
1862489 TGTAAAACTG
* ** * *
1862499 TGTAAAATTATTATGCCCA-AAAACTTTTGTTAATGGTTAGTCAA-ATTATCAATTTA
1 TGTAAAATTATTAAG-CCAGAAAAAGTGTGTTAATGGGTAGT-AAGATTATCAATTTA
1862555 TGTAAAATTATTAAGCCAGAAAAAGTGTGTTAATGGGTAGTAAGATTATCAA
1 TGTAAAATTATTAAGCCAGAAAAAGTGTGTTAATGGGTAGTAAGATTATCAA
1862607 ATTAGGTTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
55 5 0.11
56 40 0.89
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (56 bp):
TGTAAAATTATTAAGCCAGAAAAAGTGTGTTAATGGGTAGTAAGATTATCAATTTA
Found at i:1862639 original size:28 final size:26
Alignment explanation
Indices: 1862607--1863123 Score: 498
Period size: 28 Copynumber: 20.0 Consensus size: 26
1862597 AGATTATCAA
*
1862607 ATTAGGTTAGGGTTTTTAACT-AA-T
1 ATTAGGTTAGGGTTTTTAATTAAATT
*
1862631 -TTAGGTTAGGG-TTTTAACT-AA--
1 ATTAGGTTAGGGTTTTTAATTAAATT
1862652 ATTAGGTTAGGGTTTTTAATTAAATT
1 ATTAGGTTAGGGTTTTTAATTAAATT
1862678 AAATTAGGTTAGGGTTTTTAATTAAATT
1 --ATTAGGTTAGGGTTTTTAATTAAATT
1862706 AAATTAGGTTAGGGTTTTTAATTAAATT
1 --ATTAGGTTAGGGTTTTTAATTAAATT
*
1862734 AGGTTAAGGTTTAGGGTTTTTAAATAAATT
1 A--TT-AGG-TTAGGGTTTTTAATTAAATT
1862764 A-T-GGTTAGGGTTTTTAATT-AA--
1 ATTAGGTTAGGGTTTTTAATTAAATT
1862785 ATTAGGTTAGGGTTTTTAATTAAATT
1 ATTAGGTTAGGGTTTTTAATTAAATT
1862811 AAATTAGGGTTAGGGTTTTTAATTAAATT
1 --ATTA-GGTTAGGGTTTTTAATTAAATT
1862840 AAATTAGGGTTAGGGTTTTTAATT-AA--
1 --ATTA-GGTTAGGGTTTTTAATTAAATT
1862866 ATTAGGTTAGGGTTTTTAATTAAATT
1 ATTAGGTTAGGGTTTTTAATTAAATT
*
1862892 AAATTAGGTTAGGGTTTTTAAAATAAATT
1 --ATTAGGTTAGGGTTTTT-AATTAAATT
*
1862921 AGGTTAGGATTTAGGGTTTTTAAATAAATT
1 A--TTAGG--TTAGGGTTTTTAATTAAATT
1862951 A-T-GGTTAGGGTTTTTAATT-AA--
1 ATTAGGTTAGGGTTTTTAATTAAATT
1862972 ATTAGGTTAGGGTTTTTAATTAAATT
1 ATTAGGTTAGGGTTTTTAATTAAATT
* *
1862998 AGGTTAGGGTTTAGAGTTTTTAAAT-AA--
1 A--TTA-GG-TTAGGGTTTTTAATTAAATT
1863025 ATTAGGTTAGGGTTTTTAATTAAATT
1 ATTAGGTTAGGGTTTTTAATTAAATT
*
1863051 AAATTAGTTTAGGGTTTTTAATTAAATT
1 --ATTAGGTTAGGGTTTTTAATTAAATT
*
1863079 A-T-GGTTACGG-TTTTAATT-AA--
1 ATTAGGTTAGGGTTTTTAATTAAATT
*
1863099 ATTAGGTTAGGGTTTTTAATCAAAT
1 ATTAGGTTAGGGTTTTTAATTAAAT
1863124 AATATCAAAA
Statistics
Matches: 431, Mismatches: 14, Indels: 95
0.80 0.03 0.18
Matches are distributed among these distances:
20 1 0.00
21 3 0.01
22 32 0.07
23 101 0.23
24 52 0.12
25 6 0.01
26 5 0.01
27 4 0.01
28 107 0.25
29 66 0.15
30 43 0.10
31 11 0.03
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.46
Consensus pattern (26 bp):
ATTAGGTTAGGGTTTTTAATTAAATT
Found at i:1862970 original size:187 final size:184
Alignment explanation
Indices: 1862605--1863109 Score: 691
Period size: 187 Copynumber: 2.8 Consensus size: 184
1862595 TAAGATTATC
* * * **
1862605 AAATTAGGTTAGGGTTTTTAACT-AA-T---TTA-GG-TTAG-GGTTTTAACTAAATTAGGTTAG
1 AAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTTAGAGTTTTTAAATAAATTAAATTAG
1862662 GGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAA
66 GGTTTTT-ATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAA
1862727 TTAAATTAGGTTAAGGTTTAGGGTTTTTAAATAAATTATGGTTAGGGTTTTTAATT
130 TTAAATTAGGTT-AGGTTTAGGGTTTTTAAATAAATTATGGTTAGGGTTTTTAATT
* *
1862783 AAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGG-TTAGGGTTTTTAATTAAATTAAATTAG
1 AAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTTAGAGTTTTTAAATAAATTAAATTAG
1862847 GGTTAGGGTTT-TT-AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTT
66 GGTT----TTTATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTT
*
1862910 TAAAATAAATTAGGTTAGGATTTAGGGTTTTTAAATAAATTATGGTTAGGGTTTTTAATT
127 T-AATTAAATTAGGTTAGG-TTTAGGGTTTTTAAATAAATTATGGTTAGGGTTTTTAATT
** **
1862970 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGAGTTTTTAAATAAATTAGGTTAG
1 AAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTTAGAGTTTTTAAATAAATTAAATTAG
* *
1863035 GGTTTTTAATTAAATTAAATTAGTTTAGGGTTTTTAATTAAATT--A-T-GGTTACGG-TTTTAA
66 GGTTTTT-ATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAA
1863095 TTAAATTAGGTTAGG
130 TTAAATTAGGTTAGG
1863110 GTTTTTAATC
Statistics
Matches: 295, Mismatches: 15, Indels: 31
0.87 0.04 0.09
Matches are distributed among these distances:
178 22 0.07
179 2 0.01
180 1 0.00
181 16 0.05
182 4 0.01
183 10 0.03
184 10 0.03
185 23 0.08
186 56 0.19
187 121 0.41
188 27 0.09
189 3 0.01
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.46
Consensus pattern (184 bp):
AAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTTAGAGTTTTTAAATAAATTAAATTAG
GGTTTTTATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAAT
TAAATTAGGTTAGGTTTAGGGTTTTTAAATAAATTATGGTTAGGGTTTTTAATT
Found at i:1863123 original size:23 final size:23
Alignment explanation
Indices: 1862605--1863123 Score: 421
Period size: 23 Copynumber: 20.2 Consensus size: 23
1862595 TAAGATTATC
*
1862605 AAATTAGGTTAGGGTTTTTAACT
1 AAATTAGGTTAGGGTTTTTAATT
* *
1862628 AATTTAGGTTAGGG-TTTTAACT
1 AAATTAGGTTAGGGTTTTTAATT
1862650 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
1862678 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
1862706 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
1862729 AAATTAGGTTAAGGTTTAGGGTTTTTAAAT
1 -AA--A--TT-AGG-TTAGGGTTTTTAATT
1862759 AAATTATGGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
1862783 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
1862811 AAATTAGGGTTAGGGTTTTTAATTAAATT
1 AAATTA-GGTTAGGG-TT-T--TT-AATT
1862840 AAATTAGGGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
1862864 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
*
1862892 AAATTAGGTTAGGGTTTTTAAAATA
1 AAATTAGGTTAGGGTTTTT--AATT
*
1862917 AATTAGGTTAGGATTTAGGGTTTTTAAAT
1 AA--A--TTAGG--TTAGGGTTTTTAATT
1862946 AAATTATGGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
1862970 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
1862993 AAATTAGGTTAGGGTTTAGAGTTTTTAAAT
1 AAATTAGGTTA--G----G-GTTTTTAATT
1863023 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
*
1863051 AAATTAGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
1863074 AAATTATGGTTACGG-TTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
*
1863097 AAATTAGGTTAGGGTTTTTAATC
1 AAATTAGGTTAGGGTTTTTAATT
1863120 AAAT
1 AAAT
1863124 AATATCAAAA
Statistics
Matches: 432, Mismatches: 16, Indels: 96
0.79 0.03 0.18
Matches are distributed among these distances:
22 28 0.06
23 97 0.22
24 66 0.15
25 27 0.06
26 12 0.03
27 12 0.03
28 97 0.22
29 48 0.11
30 34 0.08
31 11 0.03
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTTAATT
Found at i:1864296 original size:7 final size:7
Alignment explanation
Indices: 1864286--1864310 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1864276 ATATATACAT
1864286 AATACTA
1 AATACTA
1864293 AATACTA
1 AATACTA
1864300 AATACTA
1 AATACTA
1864307 AATA
1 AATA
1864311 TCAATCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:1865245 original size:14 final size:15
Alignment explanation
Indices: 1865228--1865261 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1865218 AATAATTATC
1865228 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
1865242 TAAAAATATCATAAA
1 TAAAAATATCATAAA
1865257 TAAAA
1 TAAAA
1865262 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:1865372 original size:8 final size:9
Alignment explanation
Indices: 1865352--1865402 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
1865342 GCCATTGTTG
1865352 AAAATATTA
1 AAAATATTA
1865361 AAAATATTA
1 AAAATATTA
*
1865370 AAATTATTTTA
1 AAA--ATATTA
*
1865381 AAAA-AATA
1 AAAATATTA
*
1865389 AAAATATTT
1 AAAATATTA
1865398 AAAAT
1 AAAAT
1865403 TTTCTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 6 0.18
9 20 0.59
11 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATATTA
Found at i:1865390 original size:19 final size:19
Alignment explanation
Indices: 1865352--1865401 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1865342 GCCATTGTTG
*
1865352 AAAATA-TTAAAAATATTA
1 AAAATATTTAAAAATAATA
*
1865370 AAATTATTTTAAAAA-AATA
1 AAAATA-TTTAAAAATAATA
1865389 AAAATATTTAAAA
1 AAAATATTTAAAA
1865402 TTTTCTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.44
19 8 0.30
20 7 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATATTTAAAAATAATA
Found at i:1865392 original size:28 final size:29
Alignment explanation
Indices: 1865359--1865416 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
1865349 TTGAAAATAT
1865359 TAAAAATA-TTAAAATTATT-TTAAAAAAA
1 TAAAAATATTTAAAATT-TTCTTAAAAAAA
1865387 TAAAAATATTTAAAATTTTCTTAAAAAAA
1 TAAAAATATTTAAAATTTTCTTAAAAAAA
1865416 T
1 T
1865417 GAAATTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAAAATATTTAAAATTTTCTTAAAAAAA
Found at i:1865475 original size:22 final size:21
Alignment explanation
Indices: 1865450--1865500 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
1865440 TAATATGGAT
*
1865450 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
1865472 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
1865494 TTGAGAG
1 TTGAGAG
1865501 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:1865523 original size:52 final size:52
Alignment explanation
Indices: 1865453--1865552 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
1865443 TATGGATTTG
* * * *
1865453 AGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGAAAGGAATTTGAGAGTTTA
*
1865505 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTTAAAGGAATTTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGAAAGGAATTTGAGAG
1865553 AATTTTTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGAAAGGAATTTGAGAGTTTA
Found at i:1865530 original size:22 final size:22
Alignment explanation
Indices: 1865505--1865573 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
1865495 TGAGAGTTTA
*
1865505 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
* *
1865527 AGAGAATTTTTAAAGGAATTTG
1 AGAGAATTTTTGAAGGAAATTG
1865549 AGAGAATTTTTGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
1865571 AGA
1 AGA
1865574 TAGGATTTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:1883911 original size:24 final size:24
Alignment explanation
Indices: 1883878--1883924 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1883868 TGTTTCCATG
1883878 AAAGAGGGTGACATATTCTTTGGT
1 AAAGAGGGTGACATATTCTTTGGT
*
1883902 AAAGATGGTGACATATTCTTTGG
1 AAAGAGGGTGACATATTCTTTGG
1883925 ACTGTCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.34
Consensus pattern (24 bp):
AAAGAGGGTGACATATTCTTTGGT
Found at i:1891056 original size:11 final size:11
Alignment explanation
Indices: 1891040--1891127 Score: 60
Period size: 11 Copynumber: 8.4 Consensus size: 11
1891030 TATTTTTTGG
*
1891040 TTTTAAAATAC
1 TTTTAAAATAA
1891051 TTTTAAAATACA
1 TTTTAAAATA-A
*
1891063 TTTT---TTAA
1 TTTTAAAATAA
* *
1891071 TTCTAAAATAT
1 TTTTAAAATAA
*
1891082 TTTTAAAATAC
1 TTTTAAAATAA
**
1891093 TTTT--TTTAA
1 TTTTAAAATAA
*
1891102 TTTTAAAATAT
1 TTTTAAAATAA
1891113 TTTTAAAATAA
1 TTTTAAAATAA
1891124 TTTT
1 TTTT
1891128 TTGGGATTTA
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
8 4 0.07
9 8 0.14
11 41 0.72
12 4 0.07
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAA
Found at i:1891066 original size:31 final size:31
Alignment explanation
Indices: 1891031--1891129 Score: 146
Period size: 31 Copynumber: 3.2 Consensus size: 31
1891021 AAATATATTT
** *
1891031 ATTTTTTGGTTTTAAAATACTTTTAAAATAC
1 ATTTTTTAATTTTAAAATATTTTTAAAATAC
*
1891062 ATTTTTTAATTCTAAAATATTTTTAAAATAC
1 ATTTTTTAATTTTAAAATATTTTTAAAATAC
*
1891093 TTTTTTTAATTTTAAAATATTTTTAAAATA-
1 ATTTTTTAATTTTAAAATATTTTTAAAATAC
1891123 ATTTTTT
1 ATTTTTT
1891130 GGGATTTAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 6 0.10
31 55 0.90
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (31 bp):
ATTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:1892574 original size:2 final size:2
Alignment explanation
Indices: 1892561--1892597 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1892551 AATAAAAACG
*
1892561 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1892598 TAAAATGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1893623 original size:4 final size:4
Alignment explanation
Indices: 1893614--1893669 Score: 71
Period size: 4 Copynumber: 14.0 Consensus size: 4
1893604 ATAGATTTGT
*
1893614 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A-AC A-AA ATAA GATCAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA -AT-AA
1893662 ATAA ATAA
1 ATAA ATAA
1893670 GAGAAAACCA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 4 0.09
4 37 0.79
5 4 0.09
6 2 0.04
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:1894611 original size:7 final size:7
Alignment explanation
Indices: 1894599--1894627 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1894589 AAAATACTTT
1894599 AAAATAA
1 AAAATAA
1894606 AAAATAA
1 AAAATAA
1894613 AAAATAA
1 AAAATAA
1894620 AAAATAA
1 AAAATAA
1894627 A
1 A
1894628 TATTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:1895073 original size:17 final size:18
Alignment explanation
Indices: 1895051--1895084 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1895041 TTAATTGAGT
1895051 TCATCTTAG-TTAATAAC
1 TCATCTTAGATTAATAAC
1895068 TCATCTTAGATTAATAA
1 TCATCTTAGATTAATAA
1895085 ATGAGTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (18 bp):
TCATCTTAGATTAATAAC
Found at i:1901152 original size:46 final size:46
Alignment explanation
Indices: 1901099--1901284 Score: 293
Period size: 46 Copynumber: 4.0 Consensus size: 46
1901089 ACATTGCTAT
*
1901099 AACTCAGTATGGTTTTCTTCATTGAAATAACATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACAACATACCTACTTTTCAC
* *
1901145 AACTCAGTATTGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACAACATACCTACTTTTCAC
*
1901191 AACTCAGTATGGTTTTCTTCATTAAAAC-ACAATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACAAC-ATACCTACTTTTCAC
* * *
1901237 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTATTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACAACATACCTACTTTTCAC
1901283 AA
1 AA
1901285 TTTGCCATGG
Statistics
Matches: 128, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 1 0.01
46 126 0.98
47 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.38
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCATTGAAACAACATACCTACTTTTCAC
Found at i:1902529 original size:17 final size:17
Alignment explanation
Indices: 1902507--1902570 Score: 103
Period size: 17 Copynumber: 3.8 Consensus size: 17
1902497 AAATTCTTTT
1902507 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
1902524 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
1902541 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
1902558 TAATTCA-AAAATT
1 TAAATCACAAAATT
1902571 ATTCTAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
16 6 0.13
17 39 0.87
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:1904797 original size:27 final size:28
Alignment explanation
Indices: 1904767--1904834 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
1904757 CTTTTAGCGG
*
1904767 CGCTTTACGA-AGCGCCGCAAAGAACGC
1 CGCTTAACGACAGCGCCGCAAAGAACGC
* *
1904794 CGC-TAATGACAGCGTCGCAAAGAACGC
1 CGCTTAACGACAGCGCCGCAAAGAACGC
*
1904821 CGC-TAATGACAGCG
1 CGCTTAACGACAGCG
1904835 TCGGTAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 4 0.11
27 33 0.89
ACGTcount: A:0.31, C:0.31, G:0.26, T:0.12
Consensus pattern (28 bp):
CGCTTAACGACAGCGCCGCAAAGAACGC
Found at i:1904835 original size:27 final size:27
Alignment explanation
Indices: 1904777--1904837 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
1904767 CGCTTTACGA
*
1904777 AGCGCCGCAAAGAACGCCGCTAATGAC
1 AGCGTCGCAAAGAACGCCGCTAATGAC
1904804 AGCGTCGCAAAGAACGCCGCTAATGAC
1 AGCGTCGCAAAGAACGCCGCTAATGAC
1904831 AGCGTCG
1 AGCGTCG
1904838 GTAACTTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.28, T:0.10
Consensus pattern (27 bp):
AGCGTCGCAAAGAACGCCGCTAATGAC
Found at i:1904938 original size:43 final size:43
Alignment explanation
Indices: 1904886--1905257 Score: 636
Period size: 43 Copynumber: 8.7 Consensus size: 43
1904876 AGATCAAGAC
*
1904886 CTTTAGCGGCGCTTAGCCTAAAAACGCCACTATAGACCATGGT
1 CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
* *
1904929 CTTTCGCGGCGCTTAGCCAAAAAACTCCACTATAGACCATGGT
1 CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
*
1904972 CTTTAGCGGCGCTTAGACAAAAAACGCCACTATAGACCATGGT
1 CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
* *
1905015 CTTTAACGGCGCTTAGCCAAAAAACGGCACTATAGACCATGGT
1 CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
* *
1905058 CTTTAGCAGCGCTTAGCCAAAAAACGCCACTATAGACCATAGT
1 CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
*
1905101 CTTTAGCGGCGCTTAGACAAAAAACGCCACTATAGACCATGGT
1 CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
* *
1905144 CTTTAGCGGCGCTTAGCCGAAAAACGCTACTATAGACCATGGT
1 CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
1905187 CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
1 CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
*
1905230 CTTTAGCGGCGCTTATCCAAAAAACGCC
1 CTTTAGCGGCGCTTAGCCAAAAAACGCC
1905258 GCTAATTTTG
Statistics
Matches: 307, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 307 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTAGCCAAAAAACGCCACTATAGACCATGGT
Found at i:1905341 original size:14 final size:14
Alignment explanation
Indices: 1905324--1905353 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1905314 AATCAGAAGA
1905324 AACCAAATCTAACC
1 AACCAAATCTAACC
1905338 AACCAAATCTAACC
1 AACCAAATCTAACC
1905352 AA
1 AA
1905354 ATCTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (14 bp):
AACCAAATCTAACC
Found at i:1905669 original size:87 final size:87
Alignment explanation
Indices: 1905560--1905757 Score: 220
Period size: 87 Copynumber: 2.3 Consensus size: 87
1905550 TGTTGTTCTG
* * * * *
1905560 CTTCCCTCGCTGCAGTCGCTGCTTCTCTCGCTGCCGCATCTTCTTTAAGCTGCT-GCTGCAGTTG
1 CTTCTCTCGCTGCTGCCTCTGCTTCTCTCGCTGCCGCATCTACTTTAAGCTG-TAGCTGCAGTTG
1905624 CTCATA-CTTTCGTTGAACCTCAA
65 CTCATATCTTT-GTTGAACCTCAA
* * * * * *
1905647 CTTCTCTCGCTGCTGCCTCTGCTTCTCTCGTTGCTGCATCTACTTTAAGTTGTATCTGGAGTTGT
1 CTTCTCTCGCTGCTGCCTCTGCTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGCAGTTGC
* *
1905712 TCATATCTTTTTTGAACCTCAG
66 TCATATCTTTGTTGAACCTCAA
* * *
1905734 CTTCTCTCGATGTTGCCTCCGCTT
1 CTTCTCTCGCTGCTGCCTCTGCTT
1905758 TAAGTTGTGT
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
86 1 0.01
87 88 0.95
88 4 0.04
ACGTcount: A:0.12, C:0.31, G:0.18, T:0.39
Consensus pattern (87 bp):
CTTCTCTCGCTGCTGCCTCTGCTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGCAGTTGC
TCATATCTTTGTTGAACCTCAA
Found at i:1913252 original size:16 final size:16
Alignment explanation
Indices: 1913233--1913263 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1913223 CGTTTATGAG
1913233 TTAGGGATTTTAGAAC
1 TTAGGGATTTTAGAAC
1913249 TTAGGGATTTTAGAA
1 TTAGGGATTTTAGAA
1913264 TAGGGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.39
Consensus pattern (16 bp):
TTAGGGATTTTAGAAC
Found at i:1914854 original size:23 final size:23
Alignment explanation
Indices: 1914811--1914855 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1914801 TGCTTTTGTA
*
1914811 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
1914834 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
1914856 AATTAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:1915265 original size:2 final size:2
Alignment explanation
Indices: 1915217--1915251 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1915207 AACTAACACA
1915217 AT AT -T 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
1915252 GTTCATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1915430 original size:41 final size:41
Alignment explanation
Indices: 1915385--1915464 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
1915375 TTACCGGCGC
* *
1915385 TTCTCCAGGAACGCCGCTATAGACCGGAACATTAGCGGCAA
1 TTCTCCAGAAACGCCGCTATAGACCGGAACATCAGCGGCAA
* * * *
1915426 TTCTCCATAAACGCCGCTTTAGAGCGGAGCATCAGCGGC
1 TTCTCCAGAAACGCCGCTATAGACCGGAACATCAGCGGC
1915465 GGTTTATGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.19
Consensus pattern (41 bp):
TTCTCCAGAAACGCCGCTATAGACCGGAACATCAGCGGCAA
Found at i:1915761 original size:114 final size:113
Alignment explanation
Indices: 1915558--1915904 Score: 541
Period size: 113 Copynumber: 3.1 Consensus size: 113
1915548 GCTTAACGCC
* * *
1915558 AAACGCCGCTGAAGAACGGATTATTAGCGGCGTTTGGGCAAAAACCGCCACTAGTGTTCCCAAAT
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGC-AAAACCGCCACTAATGTTCCCAAAT
*
1915623 ATATGAAAACGGCGTTGTTCTGTGTTACTCTATTTGCGACGCTTTTTGTA
65 ATATGAAAACGGCGTCGTTCTGTGTTACTCTA-TTGCGACGCTTTTTGTA
*
1915673 AAACGCCGCTGAAGAATGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* * * *
1915738 TATGAAAACGTCGTCGTTCTGTGTTACTCCATTGCGGCGCTTTTTATA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGACGCTTTTTGTA
* * *
1915786 AAACGCCACTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* * *
1915851 TATAAAAACGGCGTCGTTCTGTGTGACTCTATTGCGTCGCTTTTTGTA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGACGCTTTTTGTA
1915899 AAACGC
1 AAACGC
1915905 TGCTAATGCT
Statistics
Matches: 213, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
113 124 0.58
114 53 0.25
115 36 0.17
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (113 bp):
AAACGCCGCTGAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGACGCTTTTTGTA
Found at i:1916014 original size:40 final size:41
Alignment explanation
Indices: 1915943--1916031 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 41
1915933 TTTATGTAGC
* *
1915943 GCCGCTAATGCTCGATATTTTGCGGCGTTTTTCGT-AAAAT
1 GCCGCTAATGCTCGATATTTAGCGGCATTTTTCGTCAAAAT
* * *
1915983 GCCGCTAATGCTCGAT-TATTAGTGGCATTTTTTGTCCAAAT
1 GCCGCTAATGCTCGATAT-TTAGCGGCATTTTTCGTCAAAAT
1916024 GCCGCTAA
1 GCCGCTAA
1916032 AAGCGCCGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.02
40 29 0.69
41 12 0.29
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (41 bp):
GCCGCTAATGCTCGATATTTAGCGGCATTTTTCGTCAAAAT
Found at i:1918154 original size:13 final size:13
Alignment explanation
Indices: 1918136--1918165 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1918126 GTTGGATTAT
*
1918136 GTATGCATGATTG
1 GTATGCATGACTG
1918149 GTATGCATGACTG
1 GTATGCATGACTG
1918162 GTAT
1 GTAT
1918166 ACTTTGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.37
Consensus pattern (13 bp):
GTATGCATGACTG
Found at i:1919620 original size:35 final size:36
Alignment explanation
Indices: 1919537--1919621 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 36
1919527 ATATGTGAAT
* * *
1919537 ATATATATGTCTATATATGCATTGTAAAATATACGAAAA
1 ATATATATG--TATATACGAATTATAAAATATAC-AAAA
*
1919576 ATATGTATGTATATACGAATTATAAAATATA-AAAA
1 ATATATATGTATATACGAATTATAAAATATACAAAA
*
1919611 CTATATATGTA
1 ATATATATGTA
1919622 AAGAAGGGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 13 0.32
37 19 0.47
39 8 0.20
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (36 bp):
ATATATATGTATATACGAATTATAAAATATACAAAA
Found at i:1922102 original size:16 final size:16
Alignment explanation
Indices: 1922083--1922115 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1922073 AATAGTCTAT
1922083 ATCTTTATAATTTTTA
1 ATCTTTATAATTTTTA
1922099 ATCTTTATAATTTTTA
1 ATCTTTATAATTTTTA
1922115 A
1 A
1922116 AGGATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
ATCTTTATAATTTTTA
Found at i:1922329 original size:2 final size:2
Alignment explanation
Indices: 1922248--1922320 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
1922238 GCCCCCTATC
* *
1922248 TA TA TC TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1922290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1922321 GCATATATAG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1924470 original size:24 final size:25
Alignment explanation
Indices: 1924439--1924492 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
1924429 ACATAAATCA
1924439 GATT-TCTTCTCCCAAT-TAAACTCT
1 GATTATCTTCTCCCAATCT-AACTCT
* *
1924463 G-TTATCTTTTCTCAATCTAACTCT
1 GATTATCTTCTCCCAATCTAACTCT
1924487 GATTAT
1 GATTAT
1924493 TCTAGGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 2 0.08
24 18 0.72
25 5 0.20
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.46
Consensus pattern (25 bp):
GATTATCTTCTCCCAATCTAACTCT
Found at i:1928518 original size:2 final size:2
Alignment explanation
Indices: 1928513--1928547 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1928503 TAAAAAATTG
1928513 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
1928548 GGGGCGAAGC
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:1932892 original size:25 final size:25
Alignment explanation
Indices: 1932844--1932892 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1932834 TTTAAAATAC
* *
1932844 TTTTAAAATATTTTTATTTTTTTAA
1 TTTTAAAATATTTTTATATGTTTAA
1932869 TTTTAAAATAATTTTTA-ATGTTTA
1 TTTTAAAAT-ATTTTTATATGTTTA
1932893 TTAAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTTAAAATATTTTTATATGTTTAA
Found at i:1944142 original size:31 final size:30
Alignment explanation
Indices: 1944086--1944143 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
1944076 CCGCCCATAT
* *
1944086 TATTTTTTATTTTTTTAAATATTTATATTA
1 TATTTTTTATTATTTAAAATATTTATATTA
1944116 TATTATTTTATTATTTAATAAT-TTTATA
1 TATT-TTTTATTATTTAA-AATATTTATA
1944144 CATTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.17
31 17 0.71
32 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (30 bp):
TATTTTTTATTATTTAAAATATTTATATTA
Found at i:1948284 original size:22 final size:22
Alignment explanation
Indices: 1948259--1948312 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
1948249 TGTAGTGTCG
1948259 TTTTCTCGAAGCTATGTTGTTC
1 TTTTCTCGAAGCTATGTTGTTC
1948281 TTTTCTCGAAGCTATGTTGTTC
1 TTTTCTCGAAGCTATGTTGTTC
1948303 TTTTCTCGAA
1 TTTTCTCGAA
1948313 ACTACGATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.50
Consensus pattern (22 bp):
TTTTCTCGAAGCTATGTTGTTC
Found at i:1949681 original size:18 final size:18
Alignment explanation
Indices: 1949658--1949697 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1949648 CTGCACTAGA
1949658 GTATGAAACATGTGACAT
1 GTATGAAACATGTGACAT
1949676 GTATGAAACATGTGACAT
1 GTATGAAACATGTGACAT
1949694 GTAT
1 GTAT
1949698 TCAATCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (18 bp):
GTATGAAACATGTGACAT
Found at i:1953474 original size:22 final size:22
Alignment explanation
Indices: 1953449--1953494 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1953439 AAAATACTGA
* *
1953449 TTAAAACGTGTTGAATTGTTAT
1 TTAAAAAGTGTTAAATTGTTAT
1953471 TTAAAAAGTGTTAAATTGTTAT
1 TTAAAAAGTGTTAAATTGTTAT
1953493 TT
1 TT
1953495 TTTAACGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (22 bp):
TTAAAAAGTGTTAAATTGTTAT
Found at i:1962889 original size:26 final size:27
Alignment explanation
Indices: 1962851--1962901 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
1962841 AAAGTTGGTA
1962851 AAAAAAAATTTTG-GACCCTTAAAAGCT
1 AAAAAAAATTTTGAG-CCCTTAAAAGCT
1962878 AAAAAAAA-TTTGAGCCCTTAAAAG
1 AAAAAAAATTTTGAGCCCTTAAAAG
1962902 TTGGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (27 bp):
AAAAAAAATTTTGAGCCCTTAAAAGCT
Found at i:1965348 original size:101 final size:101
Alignment explanation
Indices: 1965170--1965400 Score: 372
Period size: 101 Copynumber: 2.3 Consensus size: 101
1965160 TTTACATTCG
*
1965170 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATAT
1 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATAT
* * *
1965235 AAACACTACCATGGTCCAACCATAGTCGTACGTTTA
66 AAACACGACCATGGTCCAACCATAGTAGTACGTTCA
* * *
1965271 TAGTGCCATAACCTAGTTATGGTCTTATGATTAGAATGCCATAGCCCAACTATGGTCTTACATAT
1 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATAT
* * *
1965336 AAACACGGCCATGGTCCAACCATGGTATTACGTTCA
66 AAACACGACCATGGTCCAACCATAGTAGTACGTTCA
1965372 TAGTGCCATAACCCAGTTATGGTCTTATC
1 TAGTGCCATAACCCAGTTATGGTCTTATC
1965401 CGTCAATTCA
Statistics
Matches: 118, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 118 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (101 bp):
TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATAT
AAACACGACCATGGTCCAACCATAGTAGTACGTTCA
Found at i:1968919 original size:30 final size:30
Alignment explanation
Indices: 1968879--1968936 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1968869 TCCGAGATTT
* *
1968879 GGGGCAAAAGTGTAAATATGTAAAAGTTTA
1 GGGGAAAAAGTGTAAATATGCAAAAGTTTA
1968909 GGGGAAAAAGTGTAAATATGCAAAAGTT
1 GGGGAAAAAGTGTAAATATGCAAAAGTT
1968937 CGAGTCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.45, C:0.03, G:0.28, T:0.24
Consensus pattern (30 bp):
GGGGAAAAAGTGTAAATATGCAAAAGTTTA
Found at i:1969406 original size:42 final size:42
Alignment explanation
Indices: 1969267--1969503 Score: 189
Period size: 41 Copynumber: 5.7 Consensus size: 42
1969257 CATTGAATGT
** * * *
1969267 AAGGGGTTGCTAAGTGCAGATTCC-CTGAATCACTGATCA-A
1 AAGGGGTTGCTAAGTGTTGATTCCACCGAATCATTGATTATA
** * * * * *
1969307 AGAGGGGTTGCTAAGTGCAGATTCC-CTGAATCACTAATCAAA
1 A-AGGGGTTGCTAAGTGTTGATTCCACCGAATCATTGATTATA
* *
1969349 AAGGGGTTGCTAAGTGTTGATTCC-CCGAATTATTGATTCTA
1 AAGGGGTTGCTAAGTGTTGATTCCACCGAATCATTGATTATA
* * * *
1969390 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGTTGATTCCACCGAATCATTGATTAT-A
* * * * *
1969434 AAGGGGTTGATATGTGTTGATTCC-CCGTATCACTGAATAT-
1 AAGGGGTTGCTAAGTGTTGATTCCACCGAATCATTGATTATA
1969474 AAGGTGGTTGCTAAGTGTTGATTCCACCGA
1 AAGG-GGTTGCTAAGTGTTGATTCCACCGA
1969504 GTAACGGTTA
Statistics
Matches: 165, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
40 5 0.03
41 90 0.55
42 36 0.22
43 29 0.18
44 5 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (42 bp):
AAGGGGTTGCTAAGTGTTGATTCCACCGAATCATTGATTATA
Found at i:1969498 original size:84 final size:85
Alignment explanation
Indices: 1969348--1969502 Score: 231
Period size: 85 Copynumber: 1.8 Consensus size: 85
1969338 CACTAATCAA
* * * * *
1969348 AAAGGGGTTGCTAAGTGTTGATTCCCCGAATTATTGATTCTAAAGGTGGTTGCTAAGTGCTGATT
1 AAAGGGGTTGATAAGTGTTGATTCCCCGAATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATT
1969413 CCACCGTATCCTTGATTGTG
66 CCACCGTATCCTTGATTGTG
* * *
1969433 AAAGGGGTTGATATGTGTTGATTCCCCGTATCACTGAATAT-AAGGTGGTTGCTAAGTGTTGATT
1 AAAGGGGTTGATAAGTGTTGATTCCCCGAATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATT
1969497 CCACCG
66 CCACCG
1969503 AGTAACGGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
84 28 0.45
85 34 0.55
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.34
Consensus pattern (85 bp):
AAAGGGGTTGATAAGTGTTGATTCCCCGAATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATT
CCACCGTATCCTTGATTGTG
Found at i:1972218 original size:43 final size:43
Alignment explanation
Indices: 1972133--1972250 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
1972123 TGAGATTACA
* * *
1972133 TGTAAGACCATATCTAGGATA-TGGCATCGATATGAGACTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGACTTCG
* *
1972175 TGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGACTTCG
* *
1972218 TGTAAGACTATGGCTGGG-CTATTGGCATCGATA
1 TGTAAGACCATGTCTGGGAC-ATTGGCATCGATA
1972251 CAATATTACA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 19 0.28
43 48 0.72
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGACTTCG
Found at i:1972278 original size:43 final size:41
Alignment explanation
Indices: 1972127--1972287 Score: 126
Period size: 43 Copynumber: 3.8 Consensus size: 41
1972117 GGTTACTGAG
* * *
1972127 ATTACATGTAAGACCATATCTAGGATATGGCATCGATATGAG
1 ATTACATGTAAGACCATATCTGGGATATGGCATCGATA-AAT
* * * **
1972169 ACTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGATATGT
1 A-TTACATGTAAGACCATATCTGGGATA-TGGCATCGATAAAT
* * * ** *
1972211 GATTTCGTGTAAGACTATGGCTGGGCTATTGGCATCGATACAAT
1 -ATTACATGTAAGACCATATCTGGGATA-TGGCATCGATA-AAT
*
1972255 ATTACATGTAATACCATATCTGGGATATGGCAT
1 ATTACATGTAAGACCATATCTGGGATATGGCAT
1972288 TGTTACGGTA
Statistics
Matches: 94, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
42 28 0.30
43 65 0.69
44 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (41 bp):
ATTACATGTAAGACCATATCTGGGATATGGCATCGATAAAT
Found at i:1973421 original size:30 final size:30
Alignment explanation
Indices: 1973352--1973432 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
1973342 GATATACGGG
* * *
1973352 AATA-AGTTGCTCGCACGAGCTGACAGTAT
1 AATAGAGTTGCTCACACAAGCTAACAGTAT
** * *
1973381 ACCAGGGTTGCTCACACAAGCTAACATTAT
1 AATAGAGTTGCTCACACAAGCTAACAGTAT
1973411 AATAGAGTTGCTCACACAAGCT
1 AATAGAGTTGCTCACACAAGCT
1973433 GGTATTATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 2 0.05
30 39 0.95
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (30 bp):
AATAGAGTTGCTCACACAAGCTAACAGTAT
Found at i:1977503 original size:2 final size:2
Alignment explanation
Indices: 1977496--1977523 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1977486 TTATTTACCA
1977496 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
1977524 TAAGTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1985449 original size:11 final size:11
Alignment explanation
Indices: 1985433--1985461 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1985423 TTTAATTTTT
1985433 TAATTTTAAAA
1 TAATTTTAAAA
1985444 TAATTTTAAAA
1 TAATTTTAAAA
1985455 TAATTTT
1 TAATTTT
1985462 TTATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:1991346 original size:16 final size:16
Alignment explanation
Indices: 1991325--1991371 Score: 69
Period size: 15 Copynumber: 2.9 Consensus size: 16
1991315 GGACCAACCT
1991325 TATTAATTAATTTTAC
1 TATTAATTAATTTTAC
*
1991341 TATTAAATTAATTTT-T
1 TATT-AATTAATTTTAC
1991357 TATTAATTAATTTTA
1 TATTAATTAATTTTA
1991372 GAGATAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.36
16 8 0.29
17 10 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTAATTAATTTTAC
Found at i:2002310 original size:16 final size:15
Alignment explanation
Indices: 2002269--2002320 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2002259 CGGTTCGTTC
2002269 TAATAGAATAGAGATG
1 TAATA-AATAGAGATG
* *
2002285 CAATGAAATAGAGTTG
1 TAAT-AAATAGAGATG
*
2002301 TAATATAATAGAGCTG
1 TAATA-AATAGAGATG
2002317 TAAT
1 TAAT
2002321 CAATCTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (15 bp):
TAATAAATAGAGATG
Found at i:2002865 original size:52 final size:55
Alignment explanation
Indices: 2002752--2002853 Score: 124
Period size: 52 Copynumber: 1.9 Consensus size: 55
2002742 ATATTAAAAA
*
2002752 TAAT-TTAATAAATAAATAATAAATAATAAAATCATATTTTAATATTATTAAATC
1 TAATATTAATAAATAAATAATAAATAATAAAATCATATTTTAATATAATTAAATC
* **
2002806 TAA-ATTAAT-AA-AAATAATATATAATTTAAT-AGTATTTTAATATAATTA
1 TAATATTAATAAATAAATAATAAATAATAAAATCA-TATTTTAATATAATTA
2002854 TTTTAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
51 1 0.02
52 31 0.74
53 2 0.05
54 8 0.19
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (55 bp):
TAATATTAATAAATAAATAATAAATAATAAAATCATATTTTAATATAATTAAATC
Found at i:2005420 original size:42 final size:42
Alignment explanation
Indices: 2005373--2005458 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
2005363 ATTTCACGTG
*
2005373 AATAACAAAAACAAGGATGAGCTCATCAGGTATCGAGTTTCC
1 AATAACAAAAACAAGGATGAGCTCATCAAGTATCGAGTTTCC
*
2005415 AATAACAAAAATAAGGATGAGCTCATCAAGTATCGAGTTTCC
1 AATAACAAAAACAAGGATGAGCTCATCAAGTATCGAGTTTCC
2005457 AA
1 AA
2005459 ATATTTCATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (42 bp):
AATAACAAAAACAAGGATGAGCTCATCAAGTATCGAGTTTCC
Found at i:2005709 original size:25 final size:25
Alignment explanation
Indices: 2005681--2005816 Score: 130
Period size: 25 Copynumber: 5.5 Consensus size: 25
2005671 TTGAGCCTTG
*
2005681 TAACGGGAAGTTTATCCGAGCAATA
1 TAACGGGAAGCTTATCCGAGCAATA
** *
2005706 TAACACGAAGCTTATCCGGGCAATA
1 TAACGGGAAGCTTATCCGAGCAATA
* * * ** *
2005731 TAATGGGAAGCTCAT-TGAGCCTTG
1 TAACGGGAAGCTTATCCGAGCAATA
2005755 TAACGGGAAGCTTATCCGAGCAATA
1 TAACGGGAAGCTTATCCGAGCAATA
** *
2005780 TAACACGAAGCTTATCCGGGCAATA
1 TAACGGGAAGCTTATCCGAGCAATA
* *
2005805 TAATGGAAAGCT
1 TAACGGGAAGCT
2005817 CACAAAGAGT
Statistics
Matches: 84, Mismatches: 26, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
24 17 0.20
25 67 0.80
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (25 bp):
TAACGGGAAGCTTATCCGAGCAATA
Found at i:2005739 original size:74 final size:74
Alignment explanation
Indices: 2005655--2005818 Score: 310
Period size: 74 Copynumber: 2.2 Consensus size: 74
2005645 TCTCAAGCAC
*
2005655 TATAATGGGAAGCTCATTGAGCCTTGTAACGGGAAGTTTATCCGAGCAATATAACACGAAGCTTA
1 TATAATGGGAAGCTCATTGAGCCTTGTAACGGGAAGCTTATCCGAGCAATATAACACGAAGCTTA
2005720 TCCGGGCAA
66 TCCGGGCAA
2005729 TATAATGGGAAGCTCATTGAGCCTTGTAACGGGAAGCTTATCCGAGCAATATAACACGAAGCTTA
1 TATAATGGGAAGCTCATTGAGCCTTGTAACGGGAAGCTTATCCGAGCAATATAACACGAAGCTTA
2005794 TCCGGGCAA
66 TCCGGGCAA
*
2005803 TATAATGGAAAGCTCA
1 TATAATGGGAAGCTCA
2005819 CAAAGAGTCT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 88 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (74 bp):
TATAATGGGAAGCTCATTGAGCCTTGTAACGGGAAGCTTATCCGAGCAATATAACACGAAGCTTA
TCCGGGCAA
Found at i:2005831 original size:25 final size:24
Alignment explanation
Indices: 2005803--2005873 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
2005793 ATCCGGGCAA
*
2005803 TATAATGGAAAGCTCACAAAGAGTC
1 TATAACGGAAAGCTC-CAAAGAGTC
**
2005828 TATAACGGGTAGCTCCAAAGAG-C
1 TATAACGGAAAGCTCCAAAGAGTC
* **
2005851 AATTAACGGGTAGCTCCAAAGAG
1 TA-TAACGGAAAGCTCCAAAGAG
2005874 CAATTAACGG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
23 2 0.05
24 27 0.66
25 12 0.29
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (24 bp):
TATAACGGAAAGCTCCAAAGAGTC
Found at i:2005857 original size:24 final size:24
Alignment explanation
Indices: 2005813--2005884 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
2005803 TATAATGGAA
*
2005813 AGCTCACAAAGAGTCTA-TAACGGGT
1 AGCTC-CAAAGAG-CAATTAACGGGT
2005838 AGCTCCAAAGAGCAATTAACGGGT
1 AGCTCCAAAGAGCAATTAACGGGT
2005862 AGCTCCAAAGAGCAATTAACGGG
1 AGCTCCAAAGAGCAATTAACGGG
2005885 AAGCACCGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
23 2 0.04
24 38 0.84
25 5 0.11
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.17
Consensus pattern (24 bp):
AGCTCCAAAGAGCAATTAACGGGT
Found at i:2005984 original size:26 final size:25
Alignment explanation
Indices: 2005812--2005985 Score: 87
Period size: 24 Copynumber: 7.0 Consensus size: 25
2005802 ATATAATGGA
*
2005812 AAGCTCACAAAGAGTC-TATAACGGG
1 AAGCTCACAAAGAG-CATATAACGAG
* *
2005837 TAGCTC-CAAAGAGCA-ATTAACGGG
1 AAGCTCACAAAGAGCATA-TAACGAG
* *
2005861 TAGCTC-CAAAGAGCA-ATTAACGGG
1 AAGCTCACAAAGAGCATA-TAACGAG
* * * *
2005885 AAGCAC-CGGATA-ACCATATAACGTG
1 AAGCTCAC--AAAGAGCATATAACGAG
* ** *
2005910 AAGTTCA-AGCGAGCA-CTAACGAG
1 AAGCTCACAAAGAGCATATAACGAG
*
2005933 AAGCTCACAAAGAGCATTTAATCGAG
1 AAGCTCACAAAGAGCATATAA-CGAG
*
2005959 AAGCTCACGAAGAGCCATATAACGAG
1 AAGCTCACAAAGAG-CATATAACGAG
2005985 A
1 A
2005986 CGCTTATAAG
Statistics
Matches: 119, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
23 15 0.13
24 52 0.44
25 21 0.18
26 25 0.21
27 6 0.05
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (25 bp):
AAGCTCACAAAGAGCATATAACGAG
Found at i:2014682 original size:23 final size:23
Alignment explanation
Indices: 2014647--2014715 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 23
2014637 TTTTGAACAA
* *
2014647 TTTAATTTT-TTCTTT-TTATTTC
1 TTTATTTTTCTTCTTTCTT-TTCC
2014669 TTTATTTTTCTTCTCTTCTTTTCC
1 TTTATTTTTCTTCT-TTCTTTTCC
2014693 TTTATTTTTCTCTCTTATCTTTT
1 TTTATTTTTCT-TCTT-TCTTTT
2014716 TCTTCATTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 8 0.20
23 4 0.10
24 17 0.43
25 11 0.28
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTATTTTTCTTCTTTCTTTTCC
Found at i:2017186 original size:32 final size:32
Alignment explanation
Indices: 2017150--2017214 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2017140 ACATGGATCC
*
2017150 TTTGTTCAATTATTGTAAATGTAAATTCTCTT
1 TTTGTTCAATCATTGTAAATGTAAATTCTCTT
*
2017182 TTTGTTCAATCATTGTCAATGTAAATTCTCTT
1 TTTGTTCAATCATTGTAAATGTAAATTCTCTT
2017214 T
1 T
2017215 CTCTTGCTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.52
Consensus pattern (32 bp):
TTTGTTCAATCATTGTAAATGTAAATTCTCTT
Found at i:2022844 original size:135 final size:137
Alignment explanation
Indices: 2022598--2022866 Score: 337
Period size: 135 Copynumber: 1.9 Consensus size: 137
2022588 GCGTGCTGGC
2022598 GTGTAGCATCGAGAAATGCCTTCTTTTTCTTGGGGGGAAGGGGTAGGCTGGCGACTTTTTGAGTG
1 GTGTAGCATCGAGAAATGCCTTCTTTTTCTTGGGGGGAA--GGTA-GC-GGCGACTTTTTGAGTG
** * * ** *
2022663 ATCCTCGTAAATGATATGGAAATCTTGTAAATGCTTGATCAAGGATGCTTATTTTTTGTGTCATG
62 ATCCTCGTAAATGATACAGAAATCGTGCAAATGCTTGATCAAGGATGCTTATAATTTGTCTCATG
2022728 TGTGCGTGCGT
127 TGTGCGTGCGT
* * * * *
2022739 GTGTAGCATCGAGAAATGTCTTCTTTTTCTTGAGGGGGTA-GT-G-GGTGAGTTTTTGCGTGATC
1 GTGTAGCATCGAGAAATGCCTTCTTTTTCTTG-GGGGGAAGGTAGCGGCGACTTTTTGAGTGATC
* * *
2022801 CTCGTAAATGGTACAGAAATCGTGCAAATGCTTGGTCACGGATGCTTATAATTTGTCTCATGTGT
65 CTCGTAAATGATACAGAAATCGTGCAAATGCTTGATCAAGGATGCTTATAATTTGTCTCATGTGT
2022866 G
130 G
2022867 TGCGCGGTGC
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
135 72 0.64
137 1 0.01
139 2 0.02
141 31 0.28
142 6 0.05
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (137 bp):
GTGTAGCATCGAGAAATGCCTTCTTTTTCTTGGGGGGAAGGTAGCGGCGACTTTTTGAGTGATCC
TCGTAAATGATACAGAAATCGTGCAAATGCTTGATCAAGGATGCTTATAATTTGTCTCATGTGTG
CGTGCGT
Found at i:2031667 original size:3 final size:3
Alignment explanation
Indices: 2031659--2031724 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
2031649 AGAAACGAAA
2031659 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2031707 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
2031725 TTATCCACTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2037249 original size:20 final size:20
Alignment explanation
Indices: 2037224--2037261 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2037214 TTGTCTAAAT
2037224 TTTCTTTCACTTTCTCTCAC
1 TTTCTTTCACTTTCTCTCAC
*
2037244 TTTCTTTCATTTTCTCTC
1 TTTCTTTCACTTTCTCTC
2037262 TCTGCTTTTT
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:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCTTTCACTTTCTCTCAC
Found at i:2048712 original size:24 final size:26
Alignment explanation
Indices: 2048658--2048712 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
2048648 CCATTAATGC
2048658 CTTTTTAGTAGTACTTAAAAATAACA
1 CTTTTTAGTAGTACTTAAAAATAACA
*
2048684 CTTTTTAGTAGTACTT-CAAA-AACA
1 CTTTTTAGTAGTACTTAAAAATAACA
2048708 CTTTT
1 CTTTT
2048713 GAAAGTGTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 9 0.32
25 3 0.11
26 16 0.57
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (26 bp):
CTTTTTAGTAGTACTTAAAAATAACA
Found at i:2048889 original size:30 final size:31
Alignment explanation
Indices: 2048855--2048913 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
2048845 GCTTAATTAT
2048855 AAATA-TATTAAAATTATTAATTA-AAATAAA
1 AAATATTATTAAAA-TATTAATTACAAATAAA
*
2048885 AAATATTTTTAAAATATTAATTACAAATA
1 AAATATTATTAAAATATTAATTACAAATA
2048914 TTTAATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
AAATATTATTAAAATATTAATTACAAATAAA
Found at i:2048965 original size:33 final size:35
Alignment explanation
Indices: 2048928--2049025 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 35
2048918 ATTGTTATAT
2048928 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTACTTAA
* *
2048961 TTAAAT-TTTATAA-ATAATTAATATTTATTACTTAA
1 TTAAATATTTAAAATATAATT--TATATATTACTTAA
*
2048996 --AAATATTTAAAATTTATATTTCATATATTA
1 TTAAATATTTAAAATATA-ATTT-ATATATTA
2049026 AAATATTAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.15
35 12 0.23
36 3 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTACTTAA
Found at i:2049015 original size:30 final size:30
Alignment explanation
Indices: 2048976--2049032 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2048966 TTTTATAAAT
2048976 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
2049006 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
2049033 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:2049312 original size:101 final size:100
Alignment explanation
Indices: 2049138--2049342 Score: 340
Period size: 101 Copynumber: 2.0 Consensus size: 100
2049128 TAACATGTCT
2049138 AAAATTGACATTTTATTTCTCAAAAAACTTTTTGAAAGCAATGCTAAACATTCAAATTTTAAAAC
1 AAAATTGACATTTTATTTCTCAAAAAACTTTTTGAAAGCAATGCTAAACATTCAAATTTTAAAAC
*
2049203 AAACTTCTCAAAAGCACTTTTAAACAACACTTTTC
66 AAACTTCTCAAAAGCACTTTTAAACAACAATTTTC
*
2049238 AAAATTGACATTTTATTTCTCAAAATCACTTTTT-AACAGCAATGCTAAACATTCAAATTTTAAA
1 AAAATTGACATTTTATTTCTCAAAA-AACTTTTTGAA-AGCAATGCTAAACATTCAAATTTTAAA
* **
2049302 ACAAGCTTCTCAAAAGCACTTTTTTACAACAATTTTC
64 ACAAACTTCTCAAAAGCACTTTTAAACAACAATTTTC
2049339 AAAA
1 AAAA
2049343 GCCCTGTCAA
Statistics
Matches: 98, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
100 27 0.28
101 71 0.72
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (100 bp):
AAAATTGACATTTTATTTCTCAAAAAACTTTTTGAAAGCAATGCTAAACATTCAAATTTTAAAAC
AAACTTCTCAAAAGCACTTTTAAACAACAATTTTC
Found at i:2052771 original size:33 final size:35
Alignment explanation
Indices: 2052734--2052830 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
2052724 ATGGTTATAT
2052734 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
2052767 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
2052802 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
2052831 AAAATATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.16
35 11 0.22
36 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:2057029 original size:2 final size:2
Alignment explanation
Indices: 2057022--2057057 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2057012 TTTTGGCTTT
2057022 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2057058 AAACTTTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2060148 original size:19 final size:19
Alignment explanation
Indices: 2060126--2060182 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2060116 AATCACTTTT
2060126 TTAAAAATAATAAAAATTA
1 TTAAAAATAATAAAAATTA
*
2060145 TTAAAAATTAT-AAAATT-
1 TTAAAAATAATAAAAATTA
**
2060162 TTATTTAATAATAAAAATTA
1 TTA-AAAATAATAAAAATTA
2060182 T
1 T
2060183 AATAATATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 3 0.10
18 11 0.35
19 16 0.52
20 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAAATAATAAAAATTA
Found at i:2085426 original size:37 final size:40
Alignment explanation
Indices: 2085348--2085429 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 40
2085338 AACACATTAA
*
2085348 ATTTTATTTATATTAAAAACACTACTATAACTATAACAAAT
1 ATTTTATTTATATTAAAAACACTAC-ATAAATATAACAAAT
* * *
2085389 ATTTTA-TTATATTAAAAA-ATTA-ATAAATATGATAAAT
1 ATTTTATTTATATTAAAAACACTACATAAATATAACAAAT
2085426 ATTT
1 ATTT
2085430 ATTGCATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 16 0.43
39 3 0.08
40 12 0.32
41 6 0.16
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (40 bp):
ATTTTATTTATATTAAAAACACTACATAAATATAACAAAT
Found at i:2086475 original size:29 final size:29
Alignment explanation
Indices: 2086440--2086504 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
2086430 ATCTAAATTC
* **
2086440 AAAATAATTCGAAAAAAATAATTAAATCT
1 AAAATAATTCGAAAAAAATAACTAAAAAT
* *
2086469 AAAATAATTCTAACAAAATAACTAAAAAT
1 AAAATAATTCGAAAAAAATAACTAAAAAT
2086498 AAAATAA
1 AAAATAA
2086505 AATTCACCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.66, C:0.08, G:0.02, T:0.25
Consensus pattern (29 bp):
AAAATAATTCGAAAAAAATAACTAAAAAT
Found at i:2086488 original size:14 final size:14
Alignment explanation
Indices: 2086439--2086489 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2086429 CATCTAAATT
2086439 CAAAATAATTCGAAA
1 CAAAATAATTC-AAA
2086454 -AAAATAATT-AAA
1 CAAAATAATTCAAA
*
2086466 TCTAAAATAATTCTAA
1 -C-AAAATAATTCAAA
2086482 CAAAATAA
1 CAAAATAA
2086490 CTAAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
12 3 0.10
14 16 0.52
15 10 0.32
16 2 0.06
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (14 bp):
CAAAATAATTCAAA
Found at i:2093239 original size:30 final size:30
Alignment explanation
Indices: 2093203--2093265 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2093193 ACTTATTTTA
*
2093203 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
2093233 TTGTTAATTTTATTATTATTTTAGAGTCAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
2093263 TTG
1 TTG
2093266 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:2097023 original size:119 final size:119
Alignment explanation
Indices: 2096872--2097113 Score: 430
Period size: 119 Copynumber: 2.0 Consensus size: 119
2096862 TTTTAAAATT
* * *
2096872 TTAAACGAGAAAAAGGCCTCCGCAGTCCCTCTCAATTTCTAAATTGAGAAGATTTGTCTCTTTAA
1 TTAAACGAGAAAAAGGCCTCCGCAGTCCCTCTCAATTTCAAAATTGAGAAGATTTGTCCCTCTAA
*
2096937 AAAATCAAAGTAAATTAATTCTTGTCAATTTTGAAAGTGAGCAATTAAGAATAA
66 AAAATCAAAGCAAATTAATTCTTGTCAATTTTGAAAGTGAGCAATTAAGAATAA
*
2096991 TTAAACGAGAAAAAGGTCTCCGCAGTCCCTCTCAATTTCAAAATTGAGAAGATTTGTCCCTCTAA
1 TTAAACGAGAAAAAGGCCTCCGCAGTCCCTCTCAATTTCAAAATTGAGAAGATTTGTCCCTCTAA
*
2097056 AAAATCAAAGCAATTTAATTCTTGTCAATTTTGAAAGTGAGCAATTAAGAATAA
66 AAAATCAAAGCAAATTAATTCTTGTCAATTTTGAAAGTGAGCAATTAAGAATAA
2097110 TTAA
1 TTAA
2097114 TCAAGACGTT
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 117 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (119 bp):
TTAAACGAGAAAAAGGCCTCCGCAGTCCCTCTCAATTTCAAAATTGAGAAGATTTGTCCCTCTAA
AAAATCAAAGCAAATTAATTCTTGTCAATTTTGAAAGTGAGCAATTAAGAATAA
Found at i:2110015 original size:17 final size:17
Alignment explanation
Indices: 2109985--2110018 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2109975 TTGGATGAAC
*
2109985 TTATATTATAATTTTAT
1 TTATAATATAATTTTAT
*
2110002 TTATAATATTATTTTAT
1 TTATAATATAATTTTAT
2110019 ATCTTGCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATAATATAATTTTAT
Found at i:2110530 original size:20 final size:20
Alignment explanation
Indices: 2110483--2110520 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2110473 TTAATAATGT
2110483 TAAAATT-TTAATTTTAACC
1 TAAAATTCTTAATTTTAACC
2110502 TAAAATTCTTAATTTTAAC
1 TAAAATTCTTAATTTTAAC
2110521 TTAATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAATTCTTAATTTTAACC
Found at i:2111153 original size:33 final size:33
Alignment explanation
Indices: 2111083--2111155 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
2111073 AAACAATACT
* *
2111083 AACAAAATAATATTAACATAATAGTAAAATGAT
1 AACAAAATAATATTAAAATAATAGTAAAATGAC
2111116 AACAAAATAATGA-TAAAATAATAAG-AAAATTG-C
1 AACAAAATAAT-ATTAAAATAAT-AGTAAAA-TGAC
2111149 AACAAAA
1 AACAAAA
2111156 CAGTAAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
33 30 0.86
34 5 0.14
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (33 bp):
AACAAAATAATATTAAAATAATAGTAAAATGAC
Found at i:2121133 original size:21 final size:21
Alignment explanation
Indices: 2121107--2121149 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
2121097 ATAAATCAGT
2121107 TCTTTTAAAA-AAGTAGAATAA
1 TCTTTTAAAAGAA-TAGAATAA
2121128 TCTTTTAAAAGAATAGAATAA
1 TCTTTTAAAAGAATAGAATAA
2121149 T
1 T
2121150 TTAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (21 bp):
TCTTTTAAAAGAATAGAATAA
Found at i:2122346 original size:22 final size:22
Alignment explanation
Indices: 2122293--2122335 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2122283 CCCCAGTTTT
2122293 TACTGGTTTAGTCCGTTCTTTG
1 TACTGGTTTAGTCCGTTCTTTG
2122315 TACTGGTTTAGTCCGTTCTTT
1 TACTGGTTTAGTCCGTTCTTT
2122336 TGTCGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (22 bp):
TACTGGTTTAGTCCGTTCTTTG
Found at i:2128721 original size:22 final size:22
Alignment explanation
Indices: 2128696--2128741 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2128686 AAAAAGATAC
*
2128696 AAATA-AAATAATATTTAATTAA
1 AAATACAAATAATA-TTAAATAA
2128718 AAATACAAATAATATTAAATAA
1 AAATACAAATAATATTAAATAA
2128740 AA
1 AA
2128742 TATCGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATACAAATAATATTAAATAA
Found at i:2132224 original size:5 final size:5
Alignment explanation
Indices: 2132214--2132241 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2132204 GCATTCGATG
2132214 GAATC GAATC GAATC GAATC GAATC GAA
1 GAATC GAATC GAATC GAATC GAATC GAA
2132242 AATTTTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (5 bp):
GAATC
Found at i:2132339 original size:5 final size:5
Alignment explanation
Indices: 2132331--2132356 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2132321 GAGATGAAAT
2132331 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
2132357 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:2133041 original size:30 final size:31
Alignment explanation
Indices: 2133002--2133061 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
2132992 AGAGGTGGGA
*
2133002 TGGGAAGGGAATAAAAGTTTTAGG-GGAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGTGGAAAAG
*
2133033 TGGG-AGGGAGTAAAAATTTTGGTGGAAAA
1 TGGGAAGGGAATAAAAATTTTGGTGGAAAA
2133062 TAAAAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.08
30 20 0.77
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGTGGAAAAG
Found at i:2133685 original size:27 final size:29
Alignment explanation
Indices: 2133645--2133704 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
2133635 GTACAATTAA
*
2133645 TTTTATATGATTAATTATA-ATTTTTATT
1 TTTTATATGATTAATTAGATATTTTTATT
*
2133673 TTTTATAT-TTTAATTAGATATTTTTATT
1 TTTTATATGATTAATTAGATATTTTTATT
2133701 TTTT
1 TTTT
2133705 TAAGTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (29 bp):
TTTTATATGATTAATTAGATATTTTTATT
Found at i:2133712 original size:28 final size:27
Alignment explanation
Indices: 2133645--2133715 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
2133635 GTACAATTAA
* *
2133645 TTTTATATGATTAATTATAATTTTTATT
1 TTTTATA-GTTTAATTAGAATTTTTATT
*
2133673 TTTTATATTTTAATTAGATATTTTTATT
1 TTTTATAGTTTAATTAGA-ATTTTTATT
2133701 TTTT-TAAGTTTAATT
1 TTTTAT-AGTTTAATT
2133716 TATAAAGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.24
28 28 0.76
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (27 bp):
TTTTATAGTTTAATTAGAATTTTTATT
Found at i:2135219 original size:2 final size:2
Alignment explanation
Indices: 2135208--2135240 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2135198 TAACATATTT
2135208 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2135241 GTGAACAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2137562 original size:10 final size:11
Alignment explanation
Indices: 2137521--2137562 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
2137511 CCGATGTAAT
2137521 TAAATTATTAG
1 TAAATTATTAG
*
2137532 TAAATTTATATAT
1 TAAA-TTAT-TAG
2137545 TAAATTATTAG
1 TAAATTATTAG
2137556 T-AATTAT
1 TAAATTAT
2137563 ATCCGATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 6 0.22
11 7 0.26
12 8 0.30
13 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (11 bp):
TAAATTATTAG
Found at i:2138414 original size:25 final size:24
Alignment explanation
Indices: 2138370--2138425 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
2138360 ATTCCATAAA
2138370 TTAAAAATAAAAAAGACTAA-ATT
1 TTAAAAATAAAAAAGACTAACATT
* * *
2138393 TTAAATATACAAAAAGTTCTAACCTT
1 TTAAAAATA-AAAAAG-ACTAACATT
2138419 TTAAAAA
1 TTAAAAA
2138426 AATATAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 8 0.31
24 6 0.23
25 4 0.15
26 8 0.31
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (24 bp):
TTAAAAATAAAAAAGACTAACATT
Found at i:2139149 original size:31 final size:33
Alignment explanation
Indices: 2139084--2139151 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
2139074 TAAAAAATTC
*
2139084 ATTTGGACTCTTTTTCAAAAAATTGATAACCAA
1 ATTTGGACTCTTTTTCAAAAAATTGAGAACCAA
* * *
2139117 ATTT-GACTCTTTTT-AAAATATTGAGGATCAA
1 ATTTGGACTCTTTTTCAAAAAATTGAGAACCAA
2139148 ATTT
1 ATTT
2139152 AACTAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 17 0.55
32 10 0.32
33 4 0.13
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (33 bp):
ATTTGGACTCTTTTTCAAAAAATTGAGAACCAA
Found at i:2140451 original size:110 final size:108
Alignment explanation
Indices: 2140247--2140458 Score: 336
Period size: 110 Copynumber: 1.9 Consensus size: 108
2140237 TGCACAAAAA
* *
2140247 TCCACCCAACATGTTTCCCACATCTTTTTTTCATTAATTTATTTTGTTTTTATTTTATTAATTAA
1 TCCACCCAACATGTCTCCCACATCTTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTAA
* **
2140312 TAATGTTAAATTTTATAAAAATATTTCATTTACCACTAGATGTG
66 TAAAGTTAAATTTTATAAAAATAAATCATTTA-CACTAGATGTG
*
2140356 TCCACCCAACATGTCTCTCACATCTTTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTA
1 TCCACCCAACATGTCTCCCACATC-TTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTA
2140421 ATAAAAGTTAAATTTTATAAAAA-AAATCATTTACACTA
65 AT-AAAGTTAAATTTTATAAAAATAAATCATTTACACTA
2140459 AAGGTGCCAA
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
109 27 0.28
110 49 0.52
111 19 0.20
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (108 bp):
TCCACCCAACATGTCTCCCACATCTTTTTTTCATTAATTTATTTTGTTTTTATCTTATTAATTAA
TAAAGTTAAATTTTATAAAAATAAATCATTTACACTAGATGTG
Done.