Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 109 of 143
Found at i:33227226 original size:29 final size:29
Alignment explanation
Indices: 33227184--33227241 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
33227174 ATGAGTTTGA
33227184 AAGTTGATGTAATCTAATCCTATTTTAAT
1 AAGTTGATGTAATCTAATCCTATTTTAAT
33227213 AAGTTGATGTAATCTAATCCTATTTTAAT
1 AAGTTGATGTAATCTAATCCTATTTTAAT
33227242 TCCATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (29 bp):
AAGTTGATGTAATCTAATCCTATTTTAAT
Found at i:33228551 original size:61 final size:60
Alignment explanation
Indices: 33228437--33228611 Score: 212
Period size: 60 Copynumber: 2.9 Consensus size: 60
33228427 TTAATATAAC
* * *
33228437 ATTTGGTATCTGAACTTGATATTTTTTTCTTAATTTGGTATACTTAAACTTTTTCT-GACTC-A
1 ATTTGGTATCTGAACTTGATA-TTTTTTCCTAATTTGGTAT-C-TAAATTTTTTTTGGAC-CAA
* *
33228499 ATTTGGTA-CTTGAACTTGACACTTTTTCCTAATTTGGTATCTAAATTTTTTTTGGACCAA
1 ATTTGGTATC-TGAACTTGATATTTTTTCCTAATTTGGTATCTAAATTTTTTTTGGACCAA
** *
33228559 ATTTAATATCTGAACTTGATATTTTTTCCTAATTTGGTATCTAAGTTTTTTTT
1 ATTTGGTATCTGAACTTGATATTTTTTCCTAATTTGGTATCTAAATTTTTTTT
33228612 AGATTTAATT
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
59 11 0.11
60 51 0.52
61 19 0.19
62 18 0.18
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (60 bp):
ATTTGGTATCTGAACTTGATATTTTTTCCTAATTTGGTATCTAAATTTTTTTTGGACCAA
Found at i:33228871 original size:31 final size:31
Alignment explanation
Indices: 33228834--33228954 Score: 119
Period size: 31 Copynumber: 4.0 Consensus size: 31
33228824 CCCCAAAAAA
* *
33228834 TTTAAGTACCAATTTA-AAAAAAGGTGTCAAG
1 TTTAAGTACCAAATTAGAAAAAA-ATGTCAAG
33228865 TTTAAGTACCAAATTAGAAAAAAATGTCAAG
1 TTTAAGTACCAAATTAGAAAAAAATGTCAAG
** *
33228896 TTTAAGTACGGAATTA-AACCAAAAA----AAA
1 TTTAAGTACCAAATTAGAA--AAAAATGTCAAG
33228924 TTTAAGTACCAAATTAAGAAAAAAATGTCAA
1 TTTAAGTACCAAATT-AGAAAAAAATGTCAA
33228955 ATTCAAATGC
Statistics
Matches: 74, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
28 20 0.27
29 1 0.01
30 4 0.05
31 36 0.49
32 13 0.18
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (31 bp):
TTTAAGTACCAAATTAGAAAAAAATGTCAAG
Found at i:33228947 original size:28 final size:29
Alignment explanation
Indices: 33228865--33228949 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 29
33228855 AGGTGTCAAG
*
33228865 TTTAAGTACCAAATT-AGAAAAAAATGTCAAG
1 TTTAAGTACCAAATTAAGAAAAAAA--T-AAA
** *
33228896 TTTAAGTACGGAATTAA-ACCAAAAA-AAA
1 TTTAAGTACCAAATTAAGA-AAAAAATAAA
33228924 TTTAAGTACCAAATTAAGAAAAAAAT
1 TTTAAGTACCAAATTAAGAAAAAAAT
33228950 GTCAAATTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
28 22 0.51
29 1 0.02
31 14 0.33
32 6 0.14
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (29 bp):
TTTAAGTACCAAATTAAGAAAAAAATAAA
Found at i:33248607 original size:80 final size:80
Alignment explanation
Indices: 33248474--33248624 Score: 266
Period size: 80 Copynumber: 1.9 Consensus size: 80
33248464 ACCAAATTCA
* * * *
33248474 TCAATTCCTGACACCTAGTGCTTAGCGGATAAACCGCGATAAGTGAGCCCAGCTCTAGTTGGATT
1 TCAATTCATGACACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGATT
33248539 AACCAATGAAATCCG
66 AACCAATGAAATCCG
33248554 TCAATTCATGACACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGATT
1 TCAATTCATGACACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGATT
33248619 AACCAA
66 AACCAA
33248625 CGGTTCTGCG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (80 bp):
TCAATTCATGACACCCAGTGCCTAGCGGATAAACCGCAATAAGTGAGCCCAGCTCTAGTTGGATT
AACCAATGAAATCCG
Found at i:33251764 original size:22 final size:22
Alignment explanation
Indices: 33251738--33251782 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
33251728 CACAAAGAAA
*
33251738 AAACGTTTACGTGAAAGCGTTT
1 AAACGCTTACGTGAAAGCGTTT
*
33251760 AAACGCTTATGTGAAAGCGTTT
1 AAACGCTTACGTGAAAGCGTTT
33251782 A
1 A
33251783 TCTAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (22 bp):
AAACGCTTACGTGAAAGCGTTT
Found at i:33262207 original size:20 final size:20
Alignment explanation
Indices: 33262175--33262234 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
33262165 ATTTTGAAGT
*
33262175 GTTAAAATGATTTTGACTTG
1 GTTAAAATCATTTTGACTTG
* * *
33262195 GTTGAAATCATTTTGTCTTT
1 GTTAAAATCATTTTGACTTG
* *
33262215 TTTAAAATCATTTTAACTTG
1 GTTAAAATCATTTTGACTTG
33262235 ATTTTAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
GTTAAAATCATTTTGACTTG
Found at i:33265135 original size:23 final size:23
Alignment explanation
Indices: 33265109--33265153 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
33265099 AATAATTTTA
*
33265109 ATACTACGTTAGTTATGTTTATC
1 ATACCACGTTAGTTATGTTTATC
33265132 ATACCACGTTAGTTATGTTTAT
1 ATACCACGTTAGTTATGTTTAT
33265154 TGTAATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (23 bp):
ATACCACGTTAGTTATGTTTATC
Found at i:33274767 original size:18 final size:18
Alignment explanation
Indices: 33274744--33274780 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
33274734 TTTGTGATCA
33274744 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
33274762 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
33274780 A
1 A
33274781 TATGAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:33274769 original size:12 final size:12
Alignment explanation
Indices: 33274744--33274780 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
33274734 TTTGTGATCA
33274744 AAATTGAAAGTG
1 AAATTGAAAGTG
* *
33274756 AAAGTGAAATTG
1 AAATTGAAAGTG
33274768 AAATTGAAAGTG
1 AAATTGAAAGTG
33274780 A
1 A
33274781 TATGAATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:33277723 original size:20 final size:21
Alignment explanation
Indices: 33277680--33277723 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33277670 AATTTAGAAG
*
33277680 AAAACTTACTTTACTTTCATA
1 AAAACTTACTTGACTTTCATA
33277701 AAAACTTAC-TGACTTGTCA-A
1 AAAACTTACTTGACTT-TCATA
33277721 AAA
1 AAA
33277724 GCGATTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAACTTACTTGACTTTCATA
Found at i:33279660 original size:3 final size:3
Alignment explanation
Indices: 33279652--33279680 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
33279642 ATTTGCCCCA
33279652 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
33279681 ATCAGTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33281042 original size:15 final size:15
Alignment explanation
Indices: 33281022--33281054 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
33281012 AATCATTGGG
33281022 TTGAGCCTGAAAAGT
1 TTGAGCCTGAAAAGT
*
33281037 TTGAGCCTGAAAGGT
1 TTGAGCCTGAAAAGT
33281052 TTG
1 TTG
33281055 TCAACAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (15 bp):
TTGAGCCTGAAAAGT
Found at i:33286994 original size:28 final size:28
Alignment explanation
Indices: 33286944--33286997 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
33286934 ACCAATTTGA
* *
33286944 CAAAAAAAAATTAAGTATGAAAGTGATC
1 CAAAAAAAAATTAAGGATCAAAGTGATC
* *
33286972 CAAAAAAACATTAAGGGTCAAAGTGA
1 CAAAAAAAAATTAAGGATCAAAGTGA
33286998 CCTAACACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.56, C:0.09, G:0.17, T:0.19
Consensus pattern (28 bp):
CAAAAAAAAATTAAGGATCAAAGTGATC
Found at i:33288248 original size:31 final size:32
Alignment explanation
Indices: 33288190--33288259 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
33288180 TATTTAGAGG
* *
33288190 TTGATTAATATAAATCTTTGAAGAAATTAGGA
1 TTGATTAATACAAATCCTTGAAGAAATTAGGA
*
33288222 TTGATTAATACAAA-CCTTGAATAAATTAGGA
1 TTGATTAATACAAATCCTTGAAGAAATTAGGA
33288253 TTGATTA
1 TTGATTA
33288260 GAAATTTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (32 bp):
TTGATTAATACAAATCCTTGAAGAAATTAGGA
Found at i:33290333 original size:14 final size:14
Alignment explanation
Indices: 33290316--33290399 Score: 61
Period size: 14 Copynumber: 6.1 Consensus size: 14
33290306 TTTATTGTTC
33290316 TGTTACTATTTTAT
1 TGTTACTATTTTAT
33290330 TGTTACT-TTTATGAT
1 TGTTACTATTT-T-AT
* *
33290345 TATT-TTATTATTAT
1 TGTTACTATT-TTAT
*
33290359 T-TTACTATTAT-T
1 TGTTACTATTTTAT
*
33290371 TATTACTATTTTAT
1 TGTTACTATTTTAT
33290385 TGTTA-TATTTATAT
1 TGTTACTATTT-TAT
33290399 T
1 T
33290400 TATATTTGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
12 2 0.04
13 20 0.36
14 25 0.45
15 8 0.14
16 1 0.02
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (14 bp):
TGTTACTATTTTAT
Found at i:33290352 original size:23 final size:22
Alignment explanation
Indices: 33290322--33290383 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
33290312 GTTCTGTTAC
*
33290322 TATTTTATTGTTACTTTTA-TGAT
1 TATTTTATTATTA-TTTTACT-AT
33290345 TATTTTATTATTATTTTACTAT
1 TATTTTATTATTATTTTACTAT
*
33290367 TA-TTTATTACTATTTTA
1 TATTTTATTATTATTTTA
33290384 TTGTTATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.39
22 9 0.25
23 13 0.36
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (22 bp):
TATTTTATTATTATTTTACTAT
Found at i:33290385 original size:11 final size:11
Alignment explanation
Indices: 33290322--33290396 Score: 80
Period size: 11 Copynumber: 6.7 Consensus size: 11
33290312 GTTCTGTTAC
*
33290322 TATTTTATTGT
1 TATTTTATTAT
*
33290333 TACTTTTATGAT
1 TA-TTTTATTAT
33290345 TATTTTATTAT
1 TATTTTATTAT
*
33290356 TATTTTACTAT
1 TATTTTATTAT
*
33290367 TA-TTTATTAC
1 TATTTTATTAT
*
33290377 TATTTTATTGT
1 TATTTTATTAT
33290388 TATATTTAT
1 TAT-TTTAT
33290397 ATTTATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
10 8 0.15
11 31 0.58
12 14 0.26
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:33295102 original size:12 final size:12
Alignment explanation
Indices: 33295075--33295109 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
33295065 ATATTTTTAA
*
33295075 AAAAAATTATAT
1 AAAAAATAATAT
33295087 -AAAAATAATAT
1 AAAAAATAATAT
33295098 AAAAAATAATAT
1 AAAAAATAATAT
33295110 GAGCGGGCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAAATAATAT
Found at i:33297054 original size:30 final size:29
Alignment explanation
Indices: 33296901--33297214 Score: 199
Period size: 30 Copynumber: 10.6 Consensus size: 29
33296891 AAGAATTCGA
* *
33296901 GGTCAAAATGCAAATTTGAAAAAGTTTAGGG
1 GGTCAAAATG-TAATTTTAAAAAGTTTA-GG
* *
33296932 GGTAAAAATGTAATTTTAGGAAAA-CTT-GG
1 GGTCAAAATGTAATTTTA--AAAAGTTTAGG
*
33296961 GGTCAAAATGCAATTTTAAAGAAGTTT-GG
1 GGTCAAAATGTAATTTTAAA-AAGTTTAGG
* * * * *
33296990 AGCCAAAATGTGATTTTTTATAAGTTTA-G
1 GGTCAAAATGT-AATTTTAAAAAGTTTAGG
*
33297019 GGTTAAAATGTAATTTTAAATAAGTTTAGG
1 GGTCAAAATGTAATTTTAAA-AAGTTTAGG
* * ** *
33297049 GGTTAAAATGCAATTTTAGGGAAGTTTAAG
1 GGTCAAAATGTAATTTTA-AAAAGTTTAGG
** *
33297079 GGTTGAAATGTAATTTTGGAAAAGTTTAGG
1 GGTCAAAATGTAATTTT-AAAAAGTTTAGG
* ** *
33297109 GGTCGAAATCAAATTTTGGAAAAGTTTA-G
1 GGTCAAAATGTAATTTT-AAAAAGTTTAGG
*
33297138 GGTCAAAATATAA-TTTAAGAGAAGTTTAGG
1 GGTCAAAATGTAATTTTAA-A-AAGTTTAGG
* * * * *
33297168 GGTTAAAATGTGATTTTTGAGAAGTTTAGA
1 GGTCAAAATGT-AATTTTAAAAAGTTTAGG
*
33297198 GGTCAAAATGTGATTTT
1 GGTCAAAATGTAATTTT
33297215 TGCAAAGCTT
Statistics
Matches: 223, Mismatches: 45, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
27 3 0.01
28 12 0.05
29 74 0.33
30 114 0.51
31 12 0.05
32 8 0.04
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (29 bp):
GGTCAAAATGTAATTTTAAAAAGTTTAGG
Found at i:33297214 original size:89 final size:89
Alignment explanation
Indices: 33296915--33297228 Score: 287
Period size: 89 Copynumber: 3.5 Consensus size: 89
33296905 AAAATGCAAA
* *
33296915 TTTGAAAAAGTTTAGGGGGTAAAAATGTAATTTTAGGAAAA-CTTGGGGTCAAAATGCAATTTTA
1 TTTG-AAAAGTTTA-GGGGTCAAAATGTAATTTT-GGAAAAGCTTAGGGTCAAAATGCAA-TTTA
* **
33296979 A-AGAAGTTT-GGAGCCAAAATGTGATT
62 AGAGAAGTTTAGGGGTTAAAATGTGATT
* * * * * * *
33297005 TTTTATAAGTTTA-GGGTTAAAATGTAATTTT-AAATAAGTTTAGGGGTTAAAATGCAATTTTAG
1 TTTGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAA-AAGCTTA-GGGTCAAAATGCAATTTAAG
* * * *
33297068 GGAAGTTTAAGGGTTGAAATGTAATT
64 AGAAGTTTAGGGGTTAAAATGTGATT
* * ** * **
33297094 TTGGAAAAGTTTAGGGGTCGAAATCAAATTTTGGAAAAGTTTAGGGTCAAAATATAATTTAAGAG
1 TTTGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGCTTAGGGTCAAAATGCAATTTAAGAG
33297159 AAGTTTAGGGGTTAAAATGTGATT
66 AAGTTTAGGGGTTAAAATGTGATT
* * * * *
33297183 TTTGAGAAGTTTAGAGGTCAAAATGTGATTTTTGCAAAGCTTAGGG
1 TTTGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGCTTAGGG
33297229 GCCTCTTAAG
Statistics
Matches: 176, Mismatches: 41, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
85 2 0.01
86 2 0.01
87 23 0.13
88 20 0.11
89 103 0.59
90 24 0.14
91 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.35
Consensus pattern (89 bp):
TTTGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGCTTAGGGTCAAAATGCAATTTAAGAG
AAGTTTAGGGGTTAAAATGTGATT
Found at i:33297964 original size:2 final size:2
Alignment explanation
Indices: 33297959--33297994 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
33297949 AAAAATAATG
*
33297959 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33297995 AGTATGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:33298970 original size:52 final size:53
Alignment explanation
Indices: 33298903--33299026 Score: 178
Period size: 52 Copynumber: 2.4 Consensus size: 53
33298893 ACGATTGACC
* * *
33298903 TAAATGCATTAATAACTAAATGTATCAAGTCTAATATGAATTTA-TAGGAAAT
1 TAAAAGCATTAATAACTAAATGTAGCAAGTCTAATATGAATTTATTAGAAAAT
* * *
33298955 TAAAAGCATTAATAACTAAATGTAGGAAGTCTGATGTGAATTTATTAGAAAAT
1 TAAAAGCATTAATAACTAAATGTAGCAAGTCTAATATGAATTTATTAGAAAAT
*
33299008 TAAAAGCATTAACAACTAA
1 TAAAAGCATTAATAACTAA
33299027 CACTATGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
52 39 0.61
53 25 0.39
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (53 bp):
TAAAAGCATTAATAACTAAATGTAGCAAGTCTAATATGAATTTATTAGAAAAT
Found at i:33302342 original size:16 final size:16
Alignment explanation
Indices: 33302323--33302368 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
33302313 ATTACAACCT
33302323 TATTCCATTACAGCTC
1 TATTCCATTACAGCTC
* *
33302339 TATTTCATTGCAGCTC
1 TATTCCATTACAGCTC
33302355 TATTCCATTACAGC
1 TATTCCATTACAGC
33302369 AAACCAAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.24, C:0.28, G:0.09, T:0.39
Consensus pattern (16 bp):
TATTCCATTACAGCTC
Found at i:33307046 original size:18 final size:18
Alignment explanation
Indices: 33307025--33307079 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
33307015 TCGTTCACAT
*
33307025 CCACGTCCTCGATCACGA
1 CCACGTCCTCGACCACGA
* *
33307043 CCACGACCAT-GACCACGG
1 CCACGTCC-TCGACCACGA
*
33307061 CCATGTCCTCGACCACGA
1 CCACGTCCTCGACCACGA
33307079 C
1 C
33307080 TACTAGTGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.13
Consensus pattern (18 bp):
CCACGTCCTCGACCACGA
Found at i:33307437 original size:6 final size:6
Alignment explanation
Indices: 33307426--33307503 Score: 57
Period size: 6 Copynumber: 13.0 Consensus size: 6
33307416 CGTCCTCGAT
* * * * * *
33307426 CACGAC CACGAC CATGAC CATGAC CATGTC CTCGAT CACGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
* * * * *
33307474 CATGAC CACGGC CATGTC CTCGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC
33307504 TACTAGTGTG
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.27, C:0.42, G:0.18, T:0.13
Consensus pattern (6 bp):
CACGAC
Found at i:33307444 original size:12 final size:12
Alignment explanation
Indices: 33307429--33307499 Score: 70
Period size: 12 Copynumber: 5.9 Consensus size: 12
33307419 CCTCGATCAC
33307429 GACCACGACCAT
1 GACCACGACCAT
*
33307441 GACCATGACCAT
1 GACCACGACCAT
* * * *
33307453 GTCCTCGATCAC
1 GACCACGACCAT
33307465 GACCACGACCAT
1 GACCACGACCAT
*
33307477 GACCACGGCCAT
1 GACCACGACCAT
* *
33307489 GTCCTCGACCA
1 GACCACGACCA
33307500 CGACTACTAG
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.27, C:0.41, G:0.18, T:0.14
Consensus pattern (12 bp):
GACCACGACCAT
Found at i:33307464 original size:36 final size:36
Alignment explanation
Indices: 33307417--33307503 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
33307407 TCAAATCCAC
*
33307417 GTCCTCGATCACGACCACGACCATGACCATGACCAT
1 GTCCTCGATCACGACCACGACCATGACCACGACCAT
*
33307453 GTCCTCGATCACGACCACGACCATGACCACGGCCAT
1 GTCCTCGATCACGACCACGACCATGACCACGACCAT
*
33307489 GTCCTCGACCACGAC
1 GTCCTCGATCACGAC
33307504 TACTAGTGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.25, C:0.41, G:0.18, T:0.15
Consensus pattern (36 bp):
GTCCTCGATCACGACCACGACCATGACCACGACCAT
Found at i:33307821 original size:424 final size:424
Alignment explanation
Indices: 33307029--33307836 Score: 1528
Period size: 424 Copynumber: 1.9 Consensus size: 424
33307019 TCACATCCAC
33307029 GTCCTCGATCACGACCACGACCATGACCACGGCCATGTCCTCGACCACGACTACTAGTGTGGCCT
1 GTCCTCGATCACGACCACGACCATGACCACGGCCATGTCCTCGACCACGACTACTAGTGTGGCCT
33307094 TTAACCTTTCTATTATATGATGTCACATTCACTTCAGGGAATGGAGTAGAACCAGTTGGTCGTGA
66 TTAACCTTTCTATTATATGATGTCACATTCACTTCAGGGAATGGAGTAGAACCAGTTGGTCGTGA
33307159 CTCATGATTTTTCATTAACAGCTCATTATTTTGCTCAGCCACAAGAAGACAAGATATTAATTCAG
131 CTCATGATTTTTCATTAACAGCTCATTATTTTGCTCAGCCACAAGAAGACAAGATATTAATTCAG
* *
33307224 AATTTTTGTTAAAACCTTTTTCACGATATTGTGTCTGCAAGACAACATTGTTTGCATGAAATGTG
196 AATATTTCTTAAAACCTTTTTCACGATATTGTGTCTGCAAGACAACATTGTTTGCATGAAATGTG
33307289 GAGTATTTTTTTGCTAACATATCTTCATCAGTTATGTTCTCTCCACATAATTTCAATTGAGAACT
261 GAGTATTTTTTTGCTAACATATCTTCATCAGTTATGTTCTCTCCACATAATTTCAATTGAGAACT
*
33307354 GATTCGAAACATAGCTGAATTGTATTCACTCACAGATTTAAAATATTGCAATCTCAAATCCACGT
326 GATTCGAAACATAGCTGAATTGTATTCACTCACAGACTTAAAATATTGCAATCTCAAATCCACGT
33307419 CCTCGATCACGACCACGACCATGACCATGACCAT
391 CCTCGATCACGACCACGACCATGACCATGACCAT
33307453 GTCCTCGATCACGACCACGACCATGACCACGGCCATGTCCTCGACCACGACTACTAGTGTGGCCT
1 GTCCTCGATCACGACCACGACCATGACCACGGCCATGTCCTCGACCACGACTACTAGTGTGGCCT
33307518 TTAACCTTTCTATTATATGATGTCACATTCACTTCAGGGAATGGAGTAGAACCAGTTGGTCGTGA
66 TTAACCTTTCTATTATATGATGTCACATTCACTTCAGGGAATGGAGTAGAACCAGTTGGTCGTGA
*
33307583 CTCATGATTTTTCATTAACAGCTCATTCTTTTGCTCAGCCACAAGAAGACAAGATATTAATTCAG
131 CTCATGATTTTTCATTAACAGCTCATTATTTTGCTCAGCCACAAGAAGACAAGATATTAATTCAG
33307648 AATATTTCTTAAAACCTTTTTCACGATATTGTGTCTGCAAGACAACATTGTTTGCATGAAATGTG
196 AATATTTCTTAAAACCTTTTTCACGATATTGTGTCTGCAAGACAACATTGTTTGCATGAAATGTG
* **
33307713 GTGTATGTTTTTT-CTAACATATCTTCATCAGTTATGTTCTCTCTTCATAATTTCAATTGAGAAC
261 GAGTAT-TTTTTTGCTAACATATCTTCATCAGTTATGTTCTCTCCACATAATTTCAATTGAGAAC
*
33307777 TGATTCGAAACATAGTTGAATTGTATTCACTCACAGACTTAAAATATTGCAATCTCAAAT
325 TGATTCGAAACATAGCTGAATTGTATTCACTCACAGACTTAAAATATTGCAATCTCAAAT
33307837 GCAGCCAGTC
Statistics
Matches: 375, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
424 369 0.98
425 6 0.02
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (424 bp):
GTCCTCGATCACGACCACGACCATGACCACGGCCATGTCCTCGACCACGACTACTAGTGTGGCCT
TTAACCTTTCTATTATATGATGTCACATTCACTTCAGGGAATGGAGTAGAACCAGTTGGTCGTGA
CTCATGATTTTTCATTAACAGCTCATTATTTTGCTCAGCCACAAGAAGACAAGATATTAATTCAG
AATATTTCTTAAAACCTTTTTCACGATATTGTGTCTGCAAGACAACATTGTTTGCATGAAATGTG
GAGTATTTTTTTGCTAACATATCTTCATCAGTTATGTTCTCTCCACATAATTTCAATTGAGAACT
GATTCGAAACATAGCTGAATTGTATTCACTCACAGACTTAAAATATTGCAATCTCAAATCCACGT
CCTCGATCACGACCACGACCATGACCATGACCAT
Found at i:33308785 original size:34 final size:34
Alignment explanation
Indices: 33308704--33308785 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
33308694 AGAATATGAA
*
33308704 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAGAG
1 AAGTTAAGGAAGATGGAAGATTAAAGATCAAGAG
* **
33308738 AGGTTAAAAAAGATGGAAGATTAAACG-TCAA-AGG
1 AAGTTAAGGAAGATGGAAGATTAAA-GATCAAGA-G
33308772 AAGTTAAGGAAGAT
1 AAGTTAAGGAAGAT
33308786 TCATTATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
33 1 0.03
34 37 0.95
35 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.29, T:0.18
Consensus pattern (34 bp):
AAGTTAAGGAAGATGGAAGATTAAAGATCAAGAG
Found at i:33311645 original size:53 final size:53
Alignment explanation
Indices: 33311577--33311694 Score: 182
Period size: 53 Copynumber: 2.2 Consensus size: 53
33311567 ACGATTGACC
* * *
33311577 TAAATGCATTAATAACTAAATGTACCAAGTCTAATATGAATTTATTAGGACAT
1 TAAAAGCATTAATAACTAAATGTACCAAGTCTAATATGAATTTATTAAGAAAT
** *
33311630 TAAAAGCATTAATAACTAAATGTAGGAAGTCTGATATGAATTTATTAAGAAAT
1 TAAAAGCATTAATAACTAAATGTACCAAGTCTAATATGAATTTATTAAGAAAT
33311683 TAAAAGCATTAA
1 TAAAAGCATTAA
33311695 CAATTAACAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (53 bp):
TAAAAGCATTAATAACTAAATGTACCAAGTCTAATATGAATTTATTAAGAAAT
Found at i:33314790 original size:20 final size:20
Alignment explanation
Indices: 33314765--33314865 Score: 70
Period size: 20 Copynumber: 5.2 Consensus size: 20
33314755 ATAATAATTA
33314765 TATTTAAAATATTATTAAAT
1 TATTTAAAATATTATTAAAT
** *
33314785 TATTTATTATTTTATTAAATT
1 TATTTAAAATATTATTAAA-T
33314806 GTATTT--AATA--A-T-AAT
1 -TATTTAAAATATTATTAAAT
*
33314821 TATGTTAAAATATAATTAAAT
1 TAT-TTAAAATATTATTAAAT
**
33314842 TATTTATTATACTTATTAAAT
1 TATTTAAAATA-TTATTAAAT
33314863 TAT
1 TAT
33314866 ATTTAATAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
14 3 0.05
15 3 0.05
16 2 0.03
17 5 0.08
18 1 0.02
19 1 0.02
20 25 0.40
21 18 0.29
22 5 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (20 bp):
TATTTAAAATATTATTAAAT
Found at i:33314887 original size:58 final size:57
Alignment explanation
Indices: 33314737--33314894 Score: 212
Period size: 58 Copynumber: 2.7 Consensus size: 57
33314727 ATTATAATTT
* *
33314737 TTATT-AATTCATAATTTAATAATAATTATATTTAAAATATTATTAAATTATTTATTATT
1 TTATTAAATT-AT-ATTTAATAATAATTATA-TTAAAATATAATTAAATTATTTATTATC
* *
33314796 TTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTATTTATTATAC
1 TTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTATTTATTAT-C
*
33314854 TTATTAAATTATATTTAATAATAA-TACTATTAAAATTTAAT
1 TTATTAAATTATATTTAATAATAATTA-TATTAAAATATAAT
33314895 AACAATAATC
Statistics
Matches: 89, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
57 28 0.31
58 51 0.57
59 6 0.07
60 4 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (57 bp):
TTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTATTTATTATC
Found at i:33315071 original size:16 final size:16
Alignment explanation
Indices: 33315050--33315105 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
33315040 TGAATTATTG
*
33315050 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
*
33315066 ATTACAGCTCAATTCC
1 ATTACAGCTCTATTCC
33315082 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
33315098 ATTACAGC
1 ATTACAGC
33315106 AAACCAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.32
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:33315784 original size:21 final size:20
Alignment explanation
Indices: 33315750--33315793 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
33315740 ATAATCACAC
*
33315750 TAAAAATAAT-AATTTTTAAA
1 TAAAAATATTAAATTTTT-AA
33315770 TAAAAATATTAAATTTTTAA
1 TAAAAATATTAAATTTTTAA
33315790 TAAA
1 TAAA
33315794 TATTAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATATTAAATTTTTAA
Found at i:33316240 original size:38 final size:38
Alignment explanation
Indices: 33316189--33316261 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
33316179 CGCAGCGGGA
*
33316189 CATCTCTTCAAGGCAATTGGTTAAACAGTCACGATGGG
1 CATCTCTTCAAGGCAATTGGTTAAACAATCACGATGGG
33316227 CATCTCTTCAAGGCAATTGGTTAAACAATCACGAT
1 CATCTCTTCAAGGCAATTGGTTAAACAATCACGAT
33316262 CACTATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (38 bp):
CATCTCTTCAAGGCAATTGGTTAAACAATCACGATGGG
Found at i:33318342 original size:6 final size:6
Alignment explanation
Indices: 33318331--33318404 Score: 59
Period size: 6 Copynumber: 13.0 Consensus size: 6
33318321 TAAGATTTAT
* * * * *
33318331 TTTAAA TTTAAA TTT-AT TTTAAA TTCAAAA GTT-AT TTTAAG TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA
33318377 TTTAAA -TT-AA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
33318405 ATAAATAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
4 2 0.04
5 15 0.28
6 32 0.60
7 4 0.08
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:33318367 original size:18 final size:17
Alignment explanation
Indices: 33318327--33318370 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
33318317 ATTTTAAGAT
* *
33318327 TTATTTTAAATTTAAAT
1 TTATTTTAAATTAAAAG
33318344 TTATTTTAAATTCAAAAG
1 TTATTTTAAATT-AAAAG
33318362 TTATTTTAA
1 TTATTTTAA
33318371 GTTTAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTATTTTAAATTAAAAG
Found at i:33318386 original size:10 final size:11
Alignment explanation
Indices: 33318319--33318404 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
33318309 CTAAACTCAT
*
33318319 TTTAAGATTTAT
1 TTTAA-ATTTAA
33318331 TTTAAATTTAAA
1 TTTAAATTT-AA
*
33318343 TTT-ATTTTAAA
1 TTTAAATTT-AA
* * *
33318354 TTCAAAAGTTAT
1 TT-TAAATTTAA
*
33318366 TTTAAGTTTAA
1 TTTAAATTTAA
33318377 TTTAAA-TTAA
1 TTTAAATTTAA
33318387 TTTAAATTTAAA
1 TTTAAATTT-AA
33318399 TTTAAA
1 TTTAAA
33318405 ATAAATAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
10 10 0.17
11 25 0.43
12 20 0.34
13 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:33320361 original size:30 final size:29
Alignment explanation
Indices: 33320304--33320436 Score: 133
Period size: 29 Copynumber: 4.5 Consensus size: 29
33320294 TAAACTTCTT
* * *
33320304 AAAAATTACACTTTTACCCCTGAACTCCC
1 AAAAATCACATTTTTACTCCTGAACTCCC
*
33320333 AAAAAGTCACATTTTTTC-CCTCGAACTCCC
1 AAAAA-TCACATTTTTACTCCT-GAACTCCC
** * *
33320363 AAAAAATCACATTTTCGCTCCCGAACTTCC
1 -AAAAATCACATTTTTACTCCTGAACTCCC
*
33320393 AAAAATCACATTTTTACTCCTGAACTTCC
1 AAAAATCACATTTTTACTCCTGAACTCCC
* *
33320422 AAAAATTATATTTTT
1 AAAAATCACATTTTT
33320437 GCCCTTGAAC
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
29 47 0.53
30 34 0.39
31 7 0.08
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAAATCACATTTTTACTCCTGAACTCCC
Found at i:33320434 original size:29 final size:29
Alignment explanation
Indices: 33320175--33320436 Score: 183
Period size: 30 Copynumber: 8.8 Consensus size: 29
33320165 AAGGTCCTTA
* *
33320175 AACTATCCAAAAACTACATTTTTAC-CCTTA
1 AACT-TCCAAAAATTACATTTTTACTCC-TG
* *
33320205 AACTTCTCAAAAAATTACATTTTAACTCC-A
1 AACTTC-C-AAAAATTACATTTTTACTCCTG
* *
33320235 AACTTCTCAAAAATTAGATTTTTGCCTCC-G
1 AACTTC-CAAAAATTACATTTTT-ACTCCTG
* *
33320265 AACTTCTCAAAAATTACACTTTTGAC-CCTTA
1 AACTTC-CAAAAATTACA-TTTTTACTCC-TG
* * *
33320296 AACTTCTTAAAAATTACACTTTTACCCCTG
1 AACTTC-CAAAAATTACATTTTTACTCCTG
* * *
33320326 AACTCCCAAAAAGTCACATTTTTTC-CCTCG
1 AACTTCCAAAAA-TTACATTTTTACTCCT-G
* * ** *
33320356 AACTCCCAAAAAATCACATTTTCGCTCCCG
1 AACTTCC-AAAAATTACATTTTTACTCCTG
*
33320386 AACTTCCAAAAATCACATTTTTACTCCTG
1 AACTTCCAAAAATTACATTTTTACTCCTG
*
33320415 AACTTCCAAAAATTATATTTTT
1 AACTTCCAAAAATTACATTTTT
33320437 GCCCTTGAAC
Statistics
Matches: 192, Mismatches: 28, Indels: 25
0.78 0.11 0.10
Matches are distributed among these distances:
29 64 0.33
30 81 0.42
31 45 0.23
32 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACTCCTG
Found at i:33320445 original size:29 final size:29
Alignment explanation
Indices: 33320170--33320468 Score: 171
Period size: 30 Copynumber: 10.1 Consensus size: 29
33320160 CCCAGAAGGT
* * *
33320170 CCTTAAACTATCCAAAAACTACATTTTTAC
1 CCTTGAACT-TCCAAAAATTACATTTTTGC
* **
33320200 CCTTAAACTTCTCAAAAAATTACATTTTAAC
1 CCTTGAACTTC-C-AAAAATTACATTTTTGC
* *
33320231 TCC--AAACTTCTCAAAAATTAGATTTTTG-
1 -CCTTGAACTTC-CAAAAATTACATTTTTGC
* *
33320259 CCTCCGAACTTCTCAAAAATTACACTTTTGAC
1 CCT-TGAACTTC-CAAAAATTACATTTTTG-C
* * * *
33320291 CCTTAAACTTCTTAAAAATTACACTTTTAC
1 CCTTGAACTTC-CAAAAATTACATTTTTGC
* * * *
33320321 CCCTGAACTCCCAAAAAGTCACATTTTTTC
1 CCTTGAACTTCCAAAAA-TTACATTTTTGC
* * * *
33320351 CCTCGAACTCCCAAAAAATCACATTTTCGC
1 CCTTGAACTTCC-AAAAATTACATTTTTGC
* * *
33320381 TCC-CGAACTTCCAAAAATCACATTTTTAC
1 -CCTTGAACTTCCAAAAATTACATTTTTGC
*
33320410 TCC-TGAACTTCCAAAAATTATATTTTTGC
1 -CCTTGAACTTCCAAAAATTACATTTTTGC
* *
33320439 CCTTGAACAT-CTAAAATTACCA-TTTTGC
1 CCTTGAACTTCCAAAAATTA-CATTTTTGC
33320467 CC
1 CC
33320469 CCAATTTTCC
Statistics
Matches: 223, Mismatches: 33, Indels: 28
0.79 0.12 0.10
Matches are distributed among these distances:
27 2 0.01
28 18 0.08
29 67 0.30
30 87 0.39
31 44 0.20
32 5 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
CCTTGAACTTCCAAAAATTACATTTTTGC
Found at i:33320519 original size:29 final size:29
Alignment explanation
Indices: 33320487--33320557 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 29
33320477 CCAAAAAGTC
*
33320487 ACATTTTCAACCTCAAACTTTTCAAAATT
1 ACATTTTCAACCTCAAACTCTTCAAAATT
*
33320516 ACATTTT-AACCCCAAACTCTTCAAAATT
1 ACATTTTCAACCTCAAACTCTTCAAAATT
* *
33320544 TCATTTTCGACCTC
1 ACATTTTCAACCTC
33320558 GTTTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 25 0.69
29 11 0.31
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (29 bp):
ACATTTTCAACCTCAAACTCTTCAAAATT
Found at i:33323203 original size:18 final size:18
Alignment explanation
Indices: 33323178--33323235 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
33323168 TAATTTTTTT
33323178 AAAA-ATTTTAAAAAATA
1 AAAATATTTTAAAAAATA
*
33323195 AAAATATTTTAAAATAT-
1 AAAATATTTTAAAAAATA
*
33323212 AAAATA--TAAAAAATATA
1 AAAATATTTTAAAAA-ATA
33323229 AAAATAT
1 AAAATAT
33323236 ATTTTTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 5 0.15
16 2 0.06
17 16 0.47
18 11 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATTTTAAAAAATA
Found at i:33328373 original size:40 final size:41
Alignment explanation
Indices: 33328301--33328378 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
33328291 GGTTTCCCAT
33328301 AAGCGCCACTAATGCTCTGACCTTTAGCGGCGTTTATGAGG
1 AAGCGCCACTAATGCTCTGACCTTTAGCGGCGTTTATGAGG
* * *
33328342 AAGCGCCACTATTGCT-TTACCTTTTGCGGCGTTTATG
1 AAGCGCCACTAATGCTCTGACCTTTAGCGGCGTTTATG
33328379 GAAAAAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 19 0.56
41 15 0.44
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (41 bp):
AAGCGCCACTAATGCTCTGACCTTTAGCGGCGTTTATGAGG
Found at i:33328873 original size:18 final size:18
Alignment explanation
Indices: 33328843--33328877 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33328833 TATTATGTCA
33328843 ATAAATAATTAAAAAATT
1 ATAAATAATTAAAAAATT
33328861 ATAAA-AATATAAAAAAT
1 ATAAATAAT-TAAAAAAT
33328878 ATTAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATAATTAAAAAATT
Found at i:33328887 original size:21 final size:19
Alignment explanation
Indices: 33328853--33328893 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
33328843 ATAAATAATT
33328853 AAAAAATTATAAAAATATA
1 AAAAAATTATAAAAATATA
*
33328872 AAAAATATTAATAAAATTATA
1 AAAAA-ATT-ATAAAAATATA
33328893 A
1 A
33328894 TTTCAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 11 0.58
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATTATAAAAATATA
Found at i:33332417 original size:11 final size:12
Alignment explanation
Indices: 33332370--33332457 Score: 58
Period size: 11 Copynumber: 7.6 Consensus size: 12
33332360 ATTGAGCCCA
33332370 AATTTTAAATTTT
1 AATTTTAAA-TTT
33332383 AATTTT-AATTT
1 AATTTTAAATTT
* *
33332394 AAGTTTGAATTT
1 AATTTTAAATTT
33332406 -ATTTTAAATTT
1 AATTTTAAATTT
** *
33332417 AAACTT-ATTTT
1 AATTTTAAATTT
* *
33332428 AAGTTTGAATTT
1 AATTTTAAATTT
*
33332440 -ACTTTAAATTT
1 AATTTTAAATTT
*
33332451 AAATTTA
1 AATTTTA
33332458 TTTTAAAATA
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
11 34 0.58
12 19 0.32
13 6 0.10
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (12 bp):
AATTTTAAATTT
Found at i:33332419 original size:6 final size:6
Alignment explanation
Indices: 33332373--33332457 Score: 59
Period size: 6 Copynumber: 14.7 Consensus size: 6
33332363 GAGCCCAAAT
* * * * *
33332373 TTTAAA TTTTAA TTTTAA TTTAAG TTTGAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
33332420 CTT-AT TTTAAG TTTGAA TTT-AC TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
33332458 TTTTAAAATA
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
5 11 0.18
6 50 0.82
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:33332472 original size:17 final size:17
Alignment explanation
Indices: 33332371--33332464 Score: 107
Period size: 17 Copynumber: 5.5 Consensus size: 17
33332361 TTGAGCCCAA
*
33332371 ATTTTAAATTTTAATTTT
1 ATTTTAAA-TTTAAATTT
* * *
33332389 AATTTAAGTTTGAATTT
1 ATTTTAAATTTAAATTT
*
33332406 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
33332423 ATTTTAAGTTTGAATTT
1 ATTTTAAATTTAAATTT
*
33332440 ACTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
33332457 ATTTTAAA
1 ATTTTAAA
33332465 ATAAAATTAA
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
17 55 0.90
18 6 0.10
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:33335497 original size:29 final size:29
Alignment explanation
Indices: 33335465--33335772 Score: 277
Period size: 29 Copynumber: 10.6 Consensus size: 29
33335455 AATCGGGATC
* * *
33335465 AAAAATGGAGTTTTTAGACGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
33335494 -AAAATGGTAATTTTTAGAAGTTTCGGGGT
1 AAAAATGG-AATTTTTGGAAGTTTGGGGGT
* * * *
33335523 TAAAATGGAATTTTTGAAAG-TTCGAGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
33335551 AAAATAAT--AATTTTTGGAAGTTTCGAGGT
1 -AAA-AATGGAATTTTTGGAAGTTTGGGGGT
* *
33335580 CAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * **
33335609 -GAAATGTAATTTTTGGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
*
33335637 CAAAAATGGAATTTTTGGAAGTTCGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * **
33335667 -GAAATGTAATTTTTGGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * * *
33335695 AAAAATGTAATTTTTAGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTT-GGGGGT
33335725 AAAAATGGAATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
*
33335754 AAAAAATGTAATTTTTGGA
1 -AAAAATGGAATTTTTGGA
33335773 TATTTTAGGA
Statistics
Matches: 231, Mismatches: 36, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
27 3 0.01
28 73 0.32
29 80 0.35
30 75 0.32
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGGT
Found at i:33335562 original size:28 final size:27
Alignment explanation
Indices: 33335491--33335772 Score: 222
Period size: 30 Copynumber: 9.7 Consensus size: 27
33335481 GACGTTTGGG
* *
33335491 GGTAAAATGGTAATTTTTAGAAGTTTCGG
1 GGTAAAAT-GTAATTTTTGGAAG-TTCGA
* *
33335520 GGTTAAAATGGAATTTTTGAAAGTTCGA
1 GG-TAAAATGTAATTTTTGGAAGTTCGA
*
33335548 GGTAAAATAATAATTTTTGGAAGTTTCGA
1 GGTAAAAT-GTAATTTTTGGAAG-TTCGA
* *
33335577 GGTCAAAATGGAATTTTTGGAAGTTCGGG
1 GGT-AAAATGTAATTTTTGGAAGTTC-GA
* **
33335606 GGTGAAATGTAATTTTTGGAAGTTTTA
1 GGTAAAATGTAATTTTTGGAAGTTCGA
* *
33335633 GGGTCAAAAATGGAATTTTTGGAAGTTCGGG
1 -GGT--AAAATGTAATTTTTGGAAGTTC-GA
* **
33335664 GGTGAAATGTAATTTTTGGAAGTTTTA
1 GGTAAAATGTAATTTTTGGAAGTTCGA
*
33335691 GGGTAAAAATGTAATTTTTAGAAGTTTCGA
1 -GGT-AAAATGTAATTTTTGGAAG-TTCGA
* * *
33335721 GGTTAAAAATGGAATTTTTGGAAGTTTGGG
1 GG-T-AAAATGTAATTTTTGGAAG-TTCGA
33335751 GGTAAAAAATGTAATTTTTGGA
1 GGT--AAAATGTAATTTTTGGA
33335773 TATTTTAGGA
Statistics
Matches: 205, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
27 6 0.03
28 64 0.31
29 57 0.28
30 78 0.38
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.37
Consensus pattern (27 bp):
GGTAAAATGTAATTTTTGGAAGTTCGA
Found at i:33335571 original size:57 final size:57
Alignment explanation
Indices: 33335432--33335770 Score: 299
Period size: 57 Copynumber: 5.8 Consensus size: 57
33335422 GATATCTGCT
* *** * * * * *
33335432 GGTAAAATGGTAATTTTTAGAAAAATCGGGATCAAAAATGGAGTTTTT-AGACGTTTGGG
1 GGTAAAAT-GTAATTTTTGGAAGTTTCGGGGT-AAAAATGGAATTTTTGA-AAGTTCGGA
* *
33335491 GGTAAAATGGTAATTTTTAGAAGTTTCGGGGTTAAAATGGAATTTTTGAAAGTTC-GA
1 GGTAAAAT-GTAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTGAAAGTTCGGA
* * * * *
33335548 GGTAAAATAATAATTTTTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAGTTCGGG
1 GGTAAAAT-GTAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTGAAAGTTCGGA
* ** * *
33335606 GGTGAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGGG
1 GGTAAAATGTAATTTTTGGAAGTTTCGGGGT-AAAAATGGAATTTTTGAAAGTTCGGA
* ** *
33335664 GGTGAAATGTAATTTTTGGAAGTTTTAGGGTAAAAATGTAATTTTT-AGAAGTTTC-GA
1 GGTAAAATGTAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTGA-AAG-TTCGGA
* * *
33335721 GGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAAATGTAATTTTTG
1 GG-T-AAAATGTAATTTTTGGAAGTTTCGGGGT-AAAAATGGAATTTTTG
33335771 GATATTTTAG
Statistics
Matches: 242, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
57 89 0.37
58 85 0.35
59 53 0.22
60 15 0.06
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.36
Consensus pattern (57 bp):
GGTAAAATGTAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTGAAAGTTCGGA
Found at i:33335662 original size:58 final size:58
Alignment explanation
Indices: 33335463--33335772 Score: 333
Period size: 58 Copynumber: 5.3 Consensus size: 58
33335453 AAAATCGGGA
* * * * * **
33335463 TCAAAAATGGAGTTTTTAGACGTTTGGGGGTAAAATGGTAATTTTTAGAAGTTTCGGGG
1 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAT-GTAATTTTTGGAAGTTTTAGGG
* * * * *
33335522 T-TAAAATGGAATTTTTGAAAGTTC-GAGGTAAAATAATAATTTTTGGAAG-TTTCGAGG
1 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAT-GTAATTTTTGGAAGTTTTAG-GG
*
33335579 TC-AAAATGGAATTTTTGGAAGTTCGGGGGTGAAATGTAATTTTTGGAAGTTTTAGGG
1 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGTAATTTTTGGAAGTTTTAGGG
*
33335636 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTGAAATGTAATTTTTGGAAGTTTTAGGG
1 TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGTAATTTTTGGAAGTTTTAGGG
* * * * * **
33335694 T-AAAAATGTAATTTTTAGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGG
1 TCAAAAATGGAATTTTTGGAAG-TTCGGGGGT-AAAATGTAATTTTTGGAAGTTTTAGGG
* *
33335753 TAAAAAATGTAATTTTTGGA
1 TCAAAAATGGAATTTTTGGA
33335773 TATTTTAGGA
Statistics
Matches: 217, Mismatches: 26, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
56 3 0.01
57 80 0.37
58 92 0.42
59 25 0.12
60 17 0.08
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (58 bp):
TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGTAATTTTTGGAAGTTTTAGGG
Found at i:33337562 original size:17 final size:17
Alignment explanation
Indices: 33337537--33337632 Score: 93
Period size: 17 Copynumber: 5.6 Consensus size: 17
33337527 TTTAATTTTC
*
33337537 AATTCAAAATAAATTCA
1 AATTTAAAATAAATTCA
*
33337554 AATTTAAAATAAATTTAA
1 AATTTAAAATAAA-TTCA
*** * *
33337572 AACCCAAAATGATTTCA
1 AATTTAAAATAAATTCA
*
33337589 AATTTAAAATAAATTCG
1 AATTTAAAATAAATTCA
*
33337606 AATTTAAAATAAATTAA
1 AATTTAAAATAAATTCA
*
33337623 AATTTTAAAT
1 AATTTAAAAT
33337633 TAAAAGTTGA
Statistics
Matches: 61, Mismatches: 17, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
17 50 0.82
18 11 0.18
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:33337569 original size:35 final size:35
Alignment explanation
Indices: 33337530--33337632 Score: 102
Period size: 35 Copynumber: 3.0 Consensus size: 35
33337520 TAATAAATTT
33337530 AATTTTCAATTCAAAATAAATTCAAATTTAAAATA
1 AATTTTCAATTCAAAATAAATTCAAATTTAAAATA
** ** * *
33337565 AATTTAAAACCCAAAATGATTTCAAATTTAAAATA
1 AATTTTCAATTCAAAATAAATTCAAATTTAAAATA
* * *
33337600 AA--TTCGAATTTAAAATAAATTAAAATTTTAAAT
1 AATTTTC-AATTCAAAATAAATTCAAATTTAAAAT
33337633 TAAAAGTTGA
Statistics
Matches: 52, Mismatches: 15, Indels: 3
0.74 0.21 0.04
Matches are distributed among these distances:
33 1 0.02
34 20 0.38
35 31 0.60
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (35 bp):
AATTTTCAATTCAAAATAAATTCAAATTTAAAATA
Found at i:33344565 original size:2 final size:2
Alignment explanation
Indices: 33344558--33344586 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33344548 GAATAAGTTA
33344558 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 A
33344587 ATGCAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33346767 original size:3 final size:3
Alignment explanation
Indices: 33346759--33346790 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
33346749 TTTTACCTGG
33346759 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
33346791 AAACGTCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:33348357 original size:110 final size:110
Alignment explanation
Indices: 33348164--33348383 Score: 431
Period size: 110 Copynumber: 2.0 Consensus size: 110
33348154 TAAATCTTGA
33348164 AACCCCGAATCTCGAGGTTCGAGATTTAAGGTTTAAGGTTCGGATTTGGATTCGGGGTTAAGGTT
1 AACCCCGAATCTCGAGGTTCGAGATTTAAGGTTTAAGGTTCGGATTTGGATTCGGGGTTAAGGTT
33348229 TAGGTTTACGTTTAGAGTCAATGGTTTGGGATTTTAAGTTTTGGG
66 TAGGTTTACGTTTAGAGTCAATGGTTTGGGATTTTAAGTTTTGGG
*
33348274 AACCCCGAATCTCGAGGTTCGAGATTTAAGGTTTAAGGTTCGGGTTTGGATTCGGGGTTAAGGTT
1 AACCCCGAATCTCGAGGTTCGAGATTTAAGGTTTAAGGTTCGGATTTGGATTCGGGGTTAAGGTT
33348339 TAGGTTTACGTTTAGAGTCAATGGTTTGGGATTTTAAGTTTTGGG
66 TAGGTTTACGTTTAGAGTCAATGGTTTGGGATTTTAAGTTTTGGG
33348384 TTTAAGGTTT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.37
Consensus pattern (110 bp):
AACCCCGAATCTCGAGGTTCGAGATTTAAGGTTTAAGGTTCGGATTTGGATTCGGGGTTAAGGTT
TAGGTTTACGTTTAGAGTCAATGGTTTGGGATTTTAAGTTTTGGG
Found at i:33353204 original size:15 final size:15
Alignment explanation
Indices: 33353186--33353229 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
33353176 AATGACAAAT
*
33353186 ATTAAATTTATTTAA
1 ATTAAATTAATTTAA
*
33353201 ATTAAATTAAATTAA
1 ATTAAATTAATTTAA
*
33353216 ATT-AATTGATTTAA
1 ATTAAATTAATTTAA
33353230 TGACTCCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
ATTAAATTAATTTAA
Found at i:33353207 original size:5 final size:5
Alignment explanation
Indices: 33353186--33353220 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
33353176 AATGACAAAT
* *
33353186 ATTAA ATTTA TTTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
33353221 TTGATTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
ATTAA
Found at i:33353963 original size:55 final size:57
Alignment explanation
Indices: 33353903--33354016 Score: 133
Period size: 60 Copynumber: 2.0 Consensus size: 57
33353893 TTAAAAAATA
* *
33353903 AATAAA-T-AATTCTATTTCAGGATTTATTCTTGCCGTTCAACATAATTTAATCGAG
1 AATAAATTGAATTCTATTTCAGGATTTATTCTTGCCATTCAACAGAATTTAATCGAG
* * * *
33353958 AATAAATTGAGCAATTCTGTTTCGGGATTTATTCTTGCCATTTAACAGAATTTATTCGA
1 AATAAATT--G-AATTCTATTTCAGGATTTATTCTTGCCATTCAACAGAATTTAATCGA
33354017 TTTTGTTTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
55 6 0.12
56 1 0.02
60 41 0.85
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (57 bp):
AATAAATTGAATTCTATTTCAGGATTTATTCTTGCCATTCAACAGAATTTAATCGAG
Found at i:33354276 original size:31 final size:30
Alignment explanation
Indices: 33354231--33354321 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 30
33354221 GTTTATTATT
*
33354231 AATTGTGGCCTTAAATTGTGACAAAAACTTA
1 AATTGTGGCATTAAATTGTGAC-AAAACTTA
*
33354262 AATTTTGGCATTAAATTGTGAC----CTTA
1 AATTGTGGCATTAAATTGTGACAAAACTTA
*
33354288 AATTGTGGCTTTAAATTGTGACAAAAGCTTA
1 AATTGTGGCATTAAATTGTGACAAAA-CTTA
33354319 AAT
1 AAT
33354322 AATGTTTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
26 24 0.47
31 27 0.53
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (30 bp):
AATTGTGGCATTAAATTGTGACAAAACTTA
Found at i:33354277 original size:13 final size:13
Alignment explanation
Indices: 33354259--33354307 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
33354249 TGACAAAAAC
*
33354259 TTAAATTTTGGCA
1 TTAAATTGTGGCA
* *
33354272 TTAAATTGTGACC
1 TTAAATTGTGGCA
*
33354285 TTAAATTGTGGCT
1 TTAAATTGTGGCA
33354298 TTAAATTGTG
1 TTAAATTGTG
33354308 ACAAAAGCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (13 bp):
TTAAATTGTGGCA
Found at i:33354296 original size:26 final size:27
Alignment explanation
Indices: 33354231--33354310 Score: 90
Period size: 26 Copynumber: 2.9 Consensus size: 27
33354221 GTTTATTATT
*
33354231 AATTGTGGCCTTAAATTGTGACAAAAACTTA
1 AATTGTGGCATTAAATTGTGAC----ACTTA
*
33354262 AATTTTGGCATTAAATTGTGAC-CTTA
1 AATTGTGGCATTAAATTGTGACACTTA
*
33354288 AATTGTGGCTTTAAATTGTGACA
1 AATTGTGGCATTAAATTGTGACA
33354311 AAAGCTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 24 0.55
31 20 0.45
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (27 bp):
AATTGTGGCATTAAATTGTGACACTTA
Found at i:33357038 original size:15 final size:15
Alignment explanation
Indices: 33357020--33357050 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33357010 GCTGACATGG
33357020 ACGTGATGATGTGGC
1 ACGTGATGATGTGGC
33357035 ACGTGATGATGTGGC
1 ACGTGATGATGTGGC
33357050 A
1 A
33357051 GCTAACGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.39, T:0.26
Consensus pattern (15 bp):
ACGTGATGATGTGGC
Found at i:33357086 original size:26 final size:27
Alignment explanation
Indices: 33357026--33357086 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
33357016 ATGGACGTGA
**
33357026 TGATGTGGCACGTGATGATGTGGCAGC
1 TGATGTGGCACGTGATGACCTGGCAGC
* * *
33357053 TAACGTGG-ACGTGCTGACCTGGCAGC
1 TGATGTGGCACGTGATGACCTGGCAGC
33357079 TGATGTGG
1 TGATGTGG
33357087 TGGCTTAGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.18, C:0.18, G:0.39, T:0.25
Consensus pattern (27 bp):
TGATGTGGCACGTGATGACCTGGCAGC
Found at i:33357292 original size:17 final size:18
Alignment explanation
Indices: 33357208--33357295 Score: 76
Period size: 17 Copynumber: 5.1 Consensus size: 18
33357198 CTTTTAAATT
*
33357208 TAAATTGAAATATTTAAAA
1 TAAATTTAAA-ATTTAAAA
**
33357227 TAAATTT-AAATTCCAAA
1 TAAATTTAAAATTTAAAA
** *
33357244 TAAGCTT-AAATTTATAA
1 TAAATTTAAAATTTAAAA
33357261 TAAATTTAAAA-TTAAAA
1 TAAATTTAAAATTTAAAA
*
33357278 TGAA-TTAAAATTTAAAA
1 TAAATTTAAAATTTAAAA
33357295 T
1 T
33357296 CTAAAATTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
16 6 0.11
17 38 0.69
18 5 0.09
19 6 0.11
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAATTTAAAATTTAAAA
Found at i:33373624 original size:16 final size:16
Alignment explanation
Indices: 33373602--33373638 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
33373592 AATTTTATTT
33373602 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
33373619 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
33373634 TAATA
1 TAATA
33373639 TTTTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:33373685 original size:15 final size:15
Alignment explanation
Indices: 33373597--33373721 Score: 52
Period size: 13 Copynumber: 8.4 Consensus size: 15
33373587 AGTTCAATTT
33373597 TATTTTAATAAT-AA
1 TATTTTAATAATAAA
*
33373611 -ATTTTAAAAAT-AA
1 TATTTTAATAATAAA
33373624 TAATTTT-A-AAT-AA
1 T-ATTTTAATAATAAA
*
33373637 TATTTTTCACATGA-AAA
1 TA-TTTT-A-ATAATAAA
* *
33373654 TA-TTCAAT-ATTAA
1 TATTTTAATAATAAA
33373667 TATTTTAATAATAAA
1 TATTTTAATAATAAA
*
33373682 TATTTATTACAATTATAAA
1 TA-TT-TT--AATAATAAA
*
33373701 TATATTAATAATAAA
1 TATTTTAATAATAAA
*
33373716 TGTTTT
1 TATTTT
33373722 GCAATATAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 29
0.68 0.09 0.23
Matches are distributed among these distances:
12 2 0.02
13 28 0.33
14 7 0.08
15 25 0.29
16 3 0.04
17 9 0.11
18 1 0.01
19 10 0.12
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (15 bp):
TATTTTAATAATAAA
Found at i:33377068 original size:19 final size:18
Alignment explanation
Indices: 33377037--33377306 Score: 126
Period size: 19 Copynumber: 15.1 Consensus size: 18
33377027 TTTTAAACTA
* *
33377037 TTATATATATTATGTTTG
1 TTATGTATATTATGTATG
33377055 TTATGTACTATTATGTATG
1 TTATGTA-TATTATGTATG
33377074 -TATGT-TATGT-T-TACTG
1 TTATGTATAT-TATGTA-TG
*
33377090 TTATGTATATTATGTGCTG
1 TTATGTATATTATGT-ATG
33377109 TTATGT-TATGTATGTATG
1 TTATGTATAT-TATGTATG
*
33377127 TTATG--T-TTA-CTA--
1 TTATGTATATTATGTATG
**
33377139 TTATGTATATTATACATG
1 TTATGTATATTATGTATG
* *
33377157 TTATGTTTACTGTTATGTTTG
1 TTATG--TA-TATTATGTATG
* **
33377178 -TATGTATGTTATGTACAA
1 TTATGTATATTATGTA-TG
33377196 TTATGTATATTATGTATG
1 TTATGTATATTATGTATG
*
33377214 TATAATTGTATGTT-TGTTATG
1 T-T-A-TGTATATTATG-TATG
* *
33377235 TGT-TGTTTATAAT-TATG
1 T-TATGTATATTATGTATG
33377252 TT-TGTATATT-TGTATG
1 TTATGTATATTATGTATG
*
33377268 -TATGTTATGTTATGTACTG
1 TTATG-TATATTATGTA-TG
*
33377287 TTATGTATATTATGTTTG
1 TTATGTATATTATGTATG
33377305 TT
1 TT
33377307 TAATTGTATG
Statistics
Matches: 194, Mismatches: 27, Indels: 62
0.69 0.10 0.22
Matches are distributed among these distances:
12 5 0.03
14 3 0.02
15 9 0.05
16 21 0.11
17 26 0.13
18 46 0.24
19 51 0.26
20 13 0.07
21 20 0.10
ACGTcount: A:0.24, C:0.03, G:0.17, T:0.56
Consensus pattern (18 bp):
TTATGTATATTATGTATG
Found at i:33377149 original size:9 final size:9
Alignment explanation
Indices: 33377035--33377212 Score: 64
Period size: 9 Copynumber: 19.1 Consensus size: 9
33377025 GTTTTTAAAC
*
33377035 TATTATATA
1 TATTATGTA
*
33377044 TATTATGTT
1 TATTATGTA
*
33377053 TGTTATGTA
1 TATTATGTA
33377062 CTATTATGTA
1 -TATTATGTA
*
33377072 T-GTATGT-
1 TATTATGTA
33377079 TATGT-T-TA
1 TAT-TATGTA
*
33377087 CTGTTATGTA
1 -TATTATGTA
*
33377097 TATTATGTGC
1 TATTATGT-A
*
33377107 TGTTATGT-
1 TATTATGTA
33377115 TATGTATGTA
1 TAT-TATGTA
*
33377125 TGTTATGTTTA
1 TATTATG--TA
33377136 CTATTATGTA
1 -TATTATGTA
**
33377146 TATTATACA
1 TATTATGTA
*
33377155 TGTTATGTTTA
1 TATTATG--TA
*
33377166 CTGTTATGT-
1 -TATTATGTA
33377175 T-TGTATGTA
1 TAT-TATGTA
*
33377184 TGTTATGTA
1 TATTATGTA
*
33377193 CAATTATGTA
1 -TATTATGTA
33377203 TATTATGTA
1 TATTATGTA
33377212 T
1 T
33377213 GTATAATTGT
Statistics
Matches: 127, Mismatches: 22, Indels: 40
0.67 0.12 0.21
Matches are distributed among these distances:
7 3 0.02
8 15 0.12
9 63 0.50
10 30 0.24
11 3 0.02
12 13 0.10
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (9 bp):
TATTATGTA
Found at i:33377158 original size:30 final size:30
Alignment explanation
Indices: 33377124--33377208 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
33377114 TTATGTATGT
33377124 ATGTTATGTTTACTATTATGTATATTATAC
1 ATGTTATGTTTACTATTATGTATATTATAC
* **
33377154 ATGTTATGTTTACTGTTATGT-T-TGTATGT
1 ATGTTATGTTTACTATTATGTATAT-TATAC
*
33377183 ATGTTATG--TACAATTATGTATATTAT
1 ATGTTATGTTTACTATTATGTATATTAT
33377209 GTATGTATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
27 9 0.19
28 5 0.11
29 13 0.28
30 20 0.43
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (30 bp):
ATGTTATGTTTACTATTATGTATATTATAC
Found at i:33377258 original size:42 final size:43
Alignment explanation
Indices: 33377201--33377336 Score: 157
Period size: 42 Copynumber: 3.0 Consensus size: 43
33377191 TACAATTATG
*
33377201 TATATTATGTATGTATAATTGTATGTTTGTTATGTGTTGTTTA
1 TATATTATGTTTGTATAATTGTATGTTTGTTATGTGTTGTTTA
* * *
33377244 TA-ATTATGTTTGTATATTTGTATGTATGTTATGTTATGTACTGTTATG
1 TATATTATGTTTGTATAATTGTATGTTTGTTATG---TGT--TGTT-TA
*
33377292 TATATTATGTTTGTTTAATTGTATGTTTGTTATGTGTTAGTTTA
1 TATATTATGTTTGTATAATTGTATGTTTGTTATGTGTT-GTTTA
33377336 T
1 T
33377337 GATTGTTTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
42 28 0.36
43 2 0.03
44 3 0.04
45 6 0.08
46 3 0.04
47 4 0.05
48 3 0.04
49 28 0.36
ACGTcount: A:0.22, C:0.01, G:0.18, T:0.59
Consensus pattern (43 bp):
TATATTATGTTTGTATAATTGTATGTTTGTTATGTGTTGTTTA
Found at i:33382011 original size:2 final size:2
Alignment explanation
Indices: 33382004--33382030 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33381994 CAAATTTCAT
33382004 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 T
33382031 CTTTCGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33384684 original size:24 final size:24
Alignment explanation
Indices: 33384656--33384718 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
33384646 AGAAATAATC
*
33384656 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
*
33384680 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
33384704 TTTAAGTCAAACTCT
1 TTTCAGTTAAACTCT
33384719 TATTAGTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:33386650 original size:24 final size:24
Alignment explanation
Indices: 33386617--33386663 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
33386607 AAAAATAATC
* *
33386617 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
33386641 TTTCAATTAAACTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
33386664 ATTTGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:33386676 original size:24 final size:24
Alignment explanation
Indices: 33386625--33386677 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
33386615 TCTTTCAGTT
* * *
33386625 AAACTTTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTATTTCAATC
* *
33386649 AAACTCTGTTTATTTATTTGAGTC
1 AAACTCTGTTTATTTATTTCAATC
33386673 AAACT
1 AAACT
33386678 TTTATTAGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTATTTATTTCAATC
Found at i:33388361 original size:2 final size:2
Alignment explanation
Indices: 33388354--33388383 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
33388344 ATCAATTACC
*
33388354 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33388384 GGAAAGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33406013 original size:25 final size:26
Alignment explanation
Indices: 33405985--33406033 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
33405975 CTAAAGTCTT
*
33405985 AAATA-AAAAATCTTAAAATCTAAGC
1 AAATATAAAAATCCTAAAATCTAAGC
*
33406010 AAATATAAAATTCCTAAAATCTAA
1 AAATATAAAAATCCTAAAATCTAA
33406034 TTTAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (26 bp):
AAATATAAAAATCCTAAAATCTAAGC
Found at i:33406422 original size:71 final size:72
Alignment explanation
Indices: 33406298--33406430 Score: 178
Period size: 71 Copynumber: 1.9 Consensus size: 72
33406288 GTGTGTTCAA
* ** * *
33406298 CTTGACAAGTTTTCTGCACAGGTGTTAAGAAAGTACGTTTAATTGAACGTG-TTTTTGAAAAGTG
1 CTTGACAAGTTTTCTGCACAGGTGTTAAGAAAATACGCCTAATTAAACATGTTTTTTGAAAAGTG
33406362 CATCTAG
66 CATCTAG
* * * *
33406369 CTTGACGAGTTTTCTGTACAGGTGTTAGGAAAATGCGCCTAATTAAACATGTTTTTTGAAAA
1 CTTGACAAGTTTTCTGCACAGGTGTTAAGAAAATACGCCTAATTAAACATGTTTTTTGAAAA
33406431 ACTCGTCTAG
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
71 42 0.81
72 10 0.19
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (72 bp):
CTTGACAAGTTTTCTGCACAGGTGTTAAGAAAATACGCCTAATTAAACATGTTTTTTGAAAAGTG
CATCTAG
Found at i:33419623 original size:14 final size:15
Alignment explanation
Indices: 33419604--33419633 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
33419594 AAGGTTAGTT
33419604 TGTAATTAT-TTTTA
1 TGTAATTATATTTTA
33419618 TGTAATTATATTTTA
1 TGTAATTATATTTTA
33419633 T
1 T
33419634 TTTATATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TGTAATTATATTTTA
Found at i:33431046 original size:28 final size:28
Alignment explanation
Indices: 33431014--33431099 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
33431004 GTAGGAGAAC
33431014 AACATAACAACTCTAAATTCAAATAATA
1 AACATAACAACTCTAAATTCAAATAATA
* * *
33431042 AACAT---AACTCAAAATT-AGGAGAAT-
1 AACATAACAACTCTAAATTCA-AATAATA
*
33431066 AACAAAACAACTCTAAATTCAAATAATA
1 AACATAACAACTCTAAATTCAAATAATA
33431094 AA-ATAA
1 AACATAA
33431100 TGTTTTAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
24 5 0.11
25 14 0.32
27 17 0.39
28 8 0.18
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.22
Consensus pattern (28 bp):
AACATAACAACTCTAAATTCAAATAATA
Found at i:33431052 original size:52 final size:51
Alignment explanation
Indices: 33430995--33431099 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 51
33430985 TAAAATACAA
*
33430995 AACTCAAAAGTAGGAGAACAACATAACAACTCTAAATTCAAATAATAAACAT
1 AACTCAAAAGTAGGAGAACAACAAAACAACTCTAAATTCAAATAATAAA-AT
* *
33431047 AACTCAAAATTAGGAGAATAACAAAACAACTCTAAATTCAAATAATAAAAT
1 AACTCAAAAGTAGGAGAACAACAAAACAACTCTAAATTCAAATAATAAAAT
33431098 AA
1 AA
33431100 TGTTTTAATC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
51 4 0.08
52 46 0.92
ACGTcount: A:0.58, C:0.15, G:0.07, T:0.20
Consensus pattern (51 bp):
AACTCAAAAGTAGGAGAACAACAAAACAACTCTAAATTCAAATAATAAAAT
Found at i:33431083 original size:27 final size:27
Alignment explanation
Indices: 33430995--33431084 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
33430985 TAAAATACAA
* * *
33430995 AACTCAAAAGTAGGAGAACAACATAAC
1 AACTCAAAATTAGGAGAATAACAAAAC
* * * *
33431022 AACTCTAAATT--CA-AATAATAAACAT
1 AACTCAAAATTAGGAGAATAACAAA-AC
33431047 AACTCAAAATTAGGAGAATAACAAAAC
1 AACTCAAAATTAGGAGAATAACAAAAC
*
33431074 AACTCTAAATT
1 AACTCAAAATT
33431085 CAAATAATAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
24 6 0.13
25 12 0.26
27 21 0.45
28 8 0.17
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.20
Consensus pattern (27 bp):
AACTCAAAATTAGGAGAATAACAAAAC
Found at i:33432780 original size:3 final size:3
Alignment explanation
Indices: 33432772--33432826 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
33432762 TGAGTTTGAG
* * * * *
33432772 TGT TGT TGT TGT TCT GGT GGT TGT TGC TGT TGT TGT TGT TGT TGT GGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
*
33432820 TAT TGT T
1 TGT TGT T
33432827 ATTGCTCATC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.02, C:0.04, G:0.35, T:0.60
Consensus pattern (3 bp):
TGT
Found at i:33436341 original size:58 final size:56
Alignment explanation
Indices: 33436279--33436412 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 56
33436269 AGACTCTTAG
* * * *
33436279 GGGTAAAATGGTAATTTTGGGAAAATTTGGGATTAAAAAT-GACA-TTTGAGACATCCGA
1 GGGTAAAATGGTAATTTT--AAAAAATCGAGATTAAAAATGGA-ATTTTG-GACATCCGA
* *
33436337 GGGTAAAACGGTAACTTTTAAAAAATCGAGATTAAAAATGGAATTTTTGGACATTCGA
1 GGGTAAAATGGTAA-TTTTAAAAAATCGAGATTAAAAATGGAA-TTTTGGACATCCGA
33436395 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
33436413 TGAAAGTTTG
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
57 21 0.32
58 36 0.55
59 8 0.12
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.31
Consensus pattern (56 bp):
GGGTAAAATGGTAATTTTAAAAAATCGAGATTAAAAATGGAATTTTGGACATCCGA
Found at i:33436427 original size:29 final size:30
Alignment explanation
Indices: 33436369--33436630 Score: 170
Period size: 29 Copynumber: 8.8 Consensus size: 30
33436359 AAATCGAGAT
* * *
33436369 TAAAAATGG-AATTTTTGGACA-TTCGAGGG
1 TAAAAATGGTAATTTTT-GAAAGTTTGGGGG
33436398 T-AAAATGGTAATTTTTGAAAGTTTGGGGG
1 TAAAAATGGTAATTTTTGAAAGTTTGGGGG
* * * *
33436427 TCAAAATGG-AGTTTTTGGACA-TTCGAGGGG
1 TAAAAATGGTAATTTTT-GAAAGTTTG-GGGG
* * *
33436457 TAAAGCA--GTAATTTTTAGAAAGTTTTGAGGT
1 TAAA-AATGGTAATTTTT-GAAAG-TTTGGGGG
* * *
33436488 TAAAAATAG-AATTTTTGGAAGTTTAGGGG
1 TAAAAATGGTAATTTTTGAAAGTTTGGGGG
* * *
33436517 T-AAAATGGTAATTTTTGGAAGTTTCGAGGT
1 TAAAAATGGTAATTTTTGAAAGTTT-GGGGG
*
33436547 TAAAAAT-GTAATTTTTGAAAGTTTAGGGG
1 TAAAAATGGTAATTTTTGAAAGTTTGGGGG
* *
33436576 TAAAAAT-GTAATTTTTAAAAGTTTTGGGG
1 TAAAAATGGTAATTTTTGAAAGTTTGGGGG
* *
33436605 TCAAAAAT-ATAATTTTAGAGAAGTTT
1 T-AAAAATGGTAATTTTTGA-AAGTTT
33436631 AGGGATCAAA
Statistics
Matches: 185, Mismatches: 32, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
28 16 0.09
29 76 0.41
30 64 0.35
31 25 0.14
32 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (30 bp):
TAAAAATGGTAATTTTTGAAAGTTTGGGGG
Found at i:33436435 original size:30 final size:28
Alignment explanation
Indices: 33436395--33436650 Score: 158
Period size: 30 Copynumber: 8.6 Consensus size: 28
33436385 GGACATTCGA
33436395 GGGTAAAATGGTAATTTTTGAAAGTTTGG
1 GGGTAAAAT-GTAATTTTTGAAAGTTTGG
* * * *
33436424 GGGTCAAAATGGAGTTTTTGGACA-TTCGAG
1 GGGT-AAAATGTAATTTTT-GAAAGTTTG-G
*
33436454 GGGTAAAGCA-GTAATTTTTAGAAAGTTTTGA
1 GGGTAAA--ATGTAATTTTT-GAAAG-TTTGG
* * *
33436485 GGTTAAAAATAG-AATTTTTGGAAGTTTAG
1 GGGT-AAAAT-GTAATTTTTGAAAGTTTGG
* *
33436514 GGGTAAAATGGTAATTTTTGGAAGTTTCGA
1 GGGTAAAAT-GTAATTTTTGAAAGTTT-GG
* *
33436544 GGTTAAAAATGTAATTTTTGAAAGTTTAG
1 GGGT-AAAATGTAATTTTTGAAAGTTTGG
* *
33436573 GGGTAAAAATGTAATTTTTAAAAGTTTTG
1 GGGT-AAAATGTAATTTTTGAAAGTTTGG
* * *
33436602 GGGTCAAAAATATAATTTTAGAGAAGTTTAG
1 GGGT--AAAATGTAATTTTTGA-AAGTTTGG
* *
33436633 GGATCAAAATATAATTTT
1 GGGT-AAAATGTAATTTT
33436651 GAGATAGTTT
Statistics
Matches: 181, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
28 6 0.03
29 68 0.38
30 74 0.41
31 26 0.14
32 7 0.04
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTGAAAGTTTGG
Found at i:33436523 original size:119 final size:118
Alignment explanation
Indices: 33436368--33436634 Score: 301
Period size: 119 Copynumber: 2.2 Consensus size: 118
33436358 AAAATCGAGA
* * * *
33436368 TTAAAAATGGAATTTTTGGACA--TTCGAGGGTAAAATGGTAATTTTTGAAAGTTT-GGGGGTCA
1 TTAAAAATAGAATTTTTGGA-AGTTTAG-GGGTAAAATGGTAATTTTTGAAAGTTTCGAGGGTAA
* * *
33436430 AAATGGAGTTTTTGGACA-TTCGAGGGGTAAAGCA-GTAATTTTTAGAAAGTTTTGAGG
64 AAATGGAATTTTT-GAAAGTT-GAGGGGTAAA-AATGTAATTTTTA-AAAGTTTTGAGG
* *
33436487 TTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTTAAAA
1 TTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGGTAAAA
* * *
33436552 ATGTAATTTTTGAAAGTTTAGGGGTAAAAATGTAATTTTTAAAAGTTTTGGGG
66 ATGGAATTTTTGAAAGTTGAGGGGTAAAAATGTAATTTTTAAAAGTTTTGAGG
* * *
33436605 TCAAAAATATAATTTTAGAGAAGTTTAGGG
1 TTAAAAATAGAATTTTTG-GAAGTTTAGGG
33436635 ATCAAAATAT
Statistics
Matches: 127, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
118 28 0.22
119 78 0.61
120 21 0.17
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (118 bp):
TTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGGTAAAA
ATGGAATTTTTGAAAGTTGAGGGGTAAAAATGTAATTTTTAAAAGTTTTGAGG
Found at i:33436553 original size:59 final size:59
Alignment explanation
Indices: 33436362--33436634 Score: 243
Period size: 59 Copynumber: 4.6 Consensus size: 59
33436352 TTTTAAAAAA
* * *
33436362 TCGAGATTAAAAATGGAATTTTTGGACA--TTCGAGGGTAAAATGGTAATTTTTGAAAGTT
1 TCGAGGTTAAAAATAGAATTTTTGGA-AGTTTAG-GGGTAAAATGGTAATTTTTGAAAGTT
* * * * * * ***
33436421 T-GGGGGTCAAAATGGAGTTTTTGGACA-TTCGAGGGGTAAAGCAGTAATTTTTAGAAAGTT
1 TCGAGGTTAAAAATAGAATTTTTGGA-AGTT-TAGGGGTAAAATGGTAATTTTT-GAAAGTT
* *
33436481 TTGAGGTTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGTT
1 TCGAGGTTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAAAGTT
* *
33436540 TCGAGGTTAAAAAT-GTAATTTTTGAAAGTTTAGGGGTAAAAAT-GTAATTTTTAAAAGTT
1 TCGAGGTTAAAAATAG-AATTTTTGGAAGTTTAGGGGT-AAAATGGTAATTTTTGAAAGTT
* * * * *
33436599 TTGGGGTCAAAAATATAATTTTAGAGAAGTTTAGGG
1 TCGAGGTTAAAAATAGAATTTTTG-GAAGTTTAGGG
33436635 ATCAAAATAT
Statistics
Matches: 175, Mismatches: 30, Indels: 17
0.79 0.14 0.08
Matches are distributed among these distances:
58 22 0.13
59 89 0.51
60 43 0.25
61 21 0.12
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (59 bp):
TCGAGGTTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAAAGTT
Found at i:33436660 original size:30 final size:28
Alignment explanation
Indices: 33436490--33436665 Score: 111
Period size: 29 Copynumber: 5.9 Consensus size: 28
33436480 TTTGAGGTTA
* * *
33436490 AAAATAGAATTTTTGGAAGTTTAGGGGT-
1 AAAATATAA-TTTTGAAAGTTTAGGGATC
* * * * *
33436518 AAAATGGTAATTTTTGGAAGTTTCGAGGTTA
1 AAAAT-ATAA-TTTTGAAAGTTTAG-GGATC
* * *
33436549 AAAATGTAATTTTTGAAAGTTTAGGGGTA
1 AAAATATAA-TTTTGAAAGTTTAGGGATC
* * * *
33436578 AAAATGTAATTTTTAAAAGTTTTGGGGTC
1 AAAATATAA-TTTTGAAAGTTTAGGGATC
33436607 AAAAATATAATTTTAGAGAAGTTTAGGGATC
1 -AAAATATAATTTT-GA-AAGTTTAGGGATC
33436638 AAAATATAATTTTGAGATAGTTTAGGGA
1 AAAATATAATTTTGA-A-AGTTTAGGGA
33436666 CCTTCAGGGT
Statistics
Matches: 127, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
28 5 0.04
29 54 0.43
30 52 0.41
31 16 0.13
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (28 bp):
AAAATATAATTTTGAAAGTTTAGGGATC
Found at i:33437442 original size:20 final size:21
Alignment explanation
Indices: 33437405--33437443 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
33437395 GTAAAAAAAA
* *
33437405 TTCTTCTTTAATGCCCTTTCT
1 TTCTTCTTTAAAGACCTTTCT
33437426 TTCTT-TTTAAAGACCTTT
1 TTCTTCTTTAAAGACCTTT
33437444 TCCCTCTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (21 bp):
TTCTTCTTTAAAGACCTTTCT
Found at i:33438570 original size:17 final size:17
Alignment explanation
Indices: 33438548--33438591 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
33438538 AATTTGAAAA
33438548 TAAATTTAAACTCAAAT
1 TAAATTTAAACTCAAAT
* *
33438565 TAAATTTAAATTTAAAT
1 TAAATTTAAACTCAAAT
*
33438582 TTAATTTAAA
1 TAAATTTAAA
33438592 ATTTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAACTCAAAT
Found at i:33438573 original size:6 final size:6
Alignment explanation
Indices: 33438517--33438591 Score: 61
Period size: 6 Copynumber: 13.0 Consensus size: 6
33438507 CTTTATATAT
* * * *
33438517 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTCAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
33438564 -TTAAA TTTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
33438592 ATTTTTAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 14 0.25
6 35 0.64
7 5 0.09
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:33438595 original size:12 final size:12
Alignment explanation
Indices: 33438517--33438591 Score: 61
Period size: 11 Copynumber: 6.5 Consensus size: 12
33438507 CTTTATATAT
33438517 TTTAAATTTATAA
1 TTTAAATTTA-AA
*
33438530 --TAATTTTAAA
1 TTTAAATTTAAA
*
33438540 TTTGAAA-ATAAA
1 TTT-AAATTTAAA
* *
33438552 TTTAAACTCAAA
1 TTTAAATTTAAA
33438564 -TTAAATTTAAA
1 TTTAAATTTAAA
33438575 TTTAAATTT-AA
1 TTTAAATTTAAA
33438586 TTTAAA
1 TTTAAA
33438592 ATTTTTAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
10 2 0.04
11 27 0.54
12 19 0.38
13 2 0.04
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:33439214 original size:3 final size:3
Alignment explanation
Indices: 33439208--33439262 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
33439198 GGTGGTGGTG
* * * *
33439208 GTT GTT GTT TTT GTT GTT GTT GTT ATT GTT ATT GTT GTT GTG GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
33439256 GTT GTT G
1 GTT GTT G
33439263 CTCATCAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.04, C:0.00, G:0.31, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:33439813 original size:15 final size:16
Alignment explanation
Indices: 33439793--33439829 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
33439783 AGATAAGAAT
33439793 AAAGAAAGAAA-AAAA
1 AAAGAAAGAAACAAAA
33439808 AAAGAAAGAAACAAAA
1 AAAGAAAGAAACAAAA
*
33439824 GAAGAA
1 AAAGAA
33439830 TAAAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAACAAAA
Found at i:33446391 original size:28 final size:28
Alignment explanation
Indices: 33446360--33446445 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
33446350 TTAGGAGTAT
33446360 AACATAACAACTCTAAATTCAAATAATA
1 AACATAACAACTCTAAATTCAAATAATA
* * *
33446388 AACAT---AACTCAAAATT-AGGAGAAT-
1 AACATAACAACTCTAAATTCA-AATAATA
*
33446412 AACAAAACAACTCTAAATTCAAATAATA
1 AACATAACAACTCTAAATTCAAATAATA
33446440 AA-ATAA
1 AACATAA
33446446 TATTTTAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
24 5 0.11
25 14 0.32
27 17 0.39
28 8 0.18
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.22
Consensus pattern (28 bp):
AACATAACAACTCTAAATTCAAATAATA
Found at i:33446406 original size:52 final size:51
Alignment explanation
Indices: 33446333--33446445 Score: 181
Period size: 52 Copynumber: 2.2 Consensus size: 51
33446323 TAAAAGATAA
* * * *
33446333 AATAAAAAAACTCAAATTTAGGAGTATAACATAACAACTCTAAATTCAAAT
1 AATAAAATAACTCAAAATTAGGAGAATAACAAAACAACTCTAAATTCAAAT
33446384 AATAAACATAACTCAAAATTAGGAGAATAACAAAACAACTCTAAATTCAAAT
1 AATAAA-ATAACTCAAAATTAGGAGAATAACAAAACAACTCTAAATTCAAAT
33446436 AATAAAATAA
1 AATAAAATAA
33446446 TATTTTAATC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
51 10 0.18
52 47 0.82
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.23
Consensus pattern (51 bp):
AATAAAATAACTCAAAATTAGGAGAATAACAAAACAACTCTAAATTCAAAT
Found at i:33446436 original size:24 final size:24
Alignment explanation
Indices: 33446358--33446442 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 24
33446348 ATTTAGGAGT
*
33446358 ATAACATAACAACTCTAAATTCAA
1 ATAACAAAACAACTCTAAATTCAA
* * * *
33446382 ATAATAAACATAACTCAAAATTAGGAGA
1 ATAACAAA-ACAACTCTAAATT--CA-A
33446410 ATAACAAAACAACTCTAAATTCAA
1 ATAACAAAACAACTCTAAATTCAA
*
33446434 ATAATAAAA
1 ATAACAAAA
33446443 TAATATTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
24 15 0.32
25 12 0.26
27 12 0.26
28 8 0.17
ACGTcount: A:0.59, C:0.15, G:0.04, T:0.22
Consensus pattern (24 bp):
ATAACAAAACAACTCTAAATTCAA
Found at i:33448107 original size:3 final size:3
Alignment explanation
Indices: 33448094--33448145 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
33448084 TGAGTTTGAG
* * * * * *
33448094 TGT TAT TGT TGT TGT GGT GGT TGT TGC TGT TGT TGT TCT TGT TGT GGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
33448142 TGT T
1 TGT T
33448146 ATTATTGCTC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.02, C:0.04, G:0.35, T:0.60
Consensus pattern (3 bp):
TGT
Found at i:33453449 original size:21 final size:21
Alignment explanation
Indices: 33453423--33453477 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
33453413 TAGAGGTAAG
**
33453423 ACTTGTATCGGTAGAGGAGTC
1 ACTTGTATCGGTAGAACAGTC
* * *
33453444 ATTTGTTTCGGTAGAACCGTC
1 ACTTGTATCGGTAGAACAGTC
33453465 ACTTGTATCGGTA
1 ACTTGTATCGGTA
33453478 CAAATCTGCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:33454880 original size:19 final size:17
Alignment explanation
Indices: 33454832--33454881 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
33454822 TTTGTCTCAC
33454832 ATTAAAAAAATAATTTAA
1 ATTAAAAAAAT-ATTTAA
* *
33454850 ATTATAACAATATTTCAAA
1 ATTAAAAAAATATTT--AA
33454869 ATTAAAAAAATAT
1 ATTAAAAAAATAT
33454882 AAGAAGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 9 0.35
19 13 0.50
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAAAAAATATTTAA
Found at i:33458918 original size:16 final size:18
Alignment explanation
Indices: 33458887--33458923 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
33458877 TCATAATCCG
*
33458887 TTTCATCTCAATTCT-AT
1 TTTCATATCAATTCTAAT
33458904 TTTCATATC-ATTCTAAT
1 TTTCATATCAATTCTAAT
33458921 TTT
1 TTT
33458924 TAGTTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.24, C:0.19, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTCATATCAATTCTAAT
Found at i:33465132 original size:25 final size:23
Alignment explanation
Indices: 33465085--33465132 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
33465075 TTATCCTAAA
*
33465085 TTATTATACTATTTTAATAATTT
1 TTATTATACTATTTAAATAATTT
*
33465108 TTATTATATCATATTTAAATTATTT
1 TTATTATA-C-TATTTAAATAATTT
33465133 ATATATCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 12 0.57
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATTATACTATTTAAATAATTT
Found at i:33466289 original size:12 final size:12
Alignment explanation
Indices: 33466274--33466298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33466264 ATGAGTTTGA
33466274 GTTGTTGTTTTT
1 GTTGTTGTTTTT
33466286 GTTGTTGTTTTT
1 GTTGTTGTTTTT
33466298 G
1 G
33466299 CTCATCAATT
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:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (12 bp):
GTTGTTGTTTTT
Found at i:33479259 original size:19 final size:21
Alignment explanation
Indices: 33479223--33479265 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
33479213 TTTAAAATTC
* *
33479223 AAAATTGTTTATTATTGAA-A
1 AAAATTATTTAATATTGAACA
33479243 AAAATTATTTAAT-TTGAACA
1 AAAATTATTTAATATTGAACA
33479263 AAA
1 AAA
33479266 GTTCAATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAATTATTTAATATTGAACA
Found at i:33479446 original size:20 final size:20
Alignment explanation
Indices: 33479411--33479455 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
33479401 TCAATAAAAA
33479411 ATATA-AAAATATTTAT-TT
1 ATATATAAAATATTTATATT
*
33479429 ATATATAAATTATATTATATT
1 ATATATAAAATAT-TTATATT
33479450 AT-TATA
1 ATATATA
33479456 TTTATAAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 6 0.26
20 8 0.35
21 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATAAAATATTTATATT
Found at i:33481342 original size:2 final size:2
Alignment explanation
Indices: 33481337--33481363 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33481327 TAAAAAAAAC
33481337 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 T
33481364 TAGATATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33491028 original size:19 final size:18
Alignment explanation
Indices: 33491004--33491074 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 18
33490994 CAATATTTAT
*
33491004 TTAATATTTTCATAACTTA
1 TTAATATTTTTATAA-TTA
33491023 TTAATAATATTTTATAA-TA
1 TTAAT-AT-TTTTATAATTA
33491042 TTAAATAGTTTTTATAATTA
1 TT-AATA-TTTTTATAATTA
*
33491062 TTAAAATTTTTAT
1 TTAATATTTTTAT
33491075 GATATATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.16
19 21 0.47
20 10 0.22
21 7 0.16
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (18 bp):
TTAATATTTTTATAATTA
Found at i:33491063 original size:20 final size:19
Alignment explanation
Indices: 33491000--33491074 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
33490990 ATTACAATAT
* *
33491000 TTATTTAATATTTTCATAA
1 TTATTAAATATTTTTATAA
33491019 CTTATT-AATAATATTTTATAA
1 -TTATTAAAT-AT-TTTTATAA
33491040 -TATTAAATAGTTTTTATAA
1 TTATTAAATA-TTTTTATAA
33491059 TTATTAAA-ATTTTTAT
1 TTATTAAATATTTTTAT
33491075 GATATATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
18 7 0.14
19 17 0.35
20 18 0.37
21 7 0.14
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (19 bp):
TTATTAAATATTTTTATAA
Found at i:33491064 original size:39 final size:37
Alignment explanation
Indices: 33491001--33491079 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 37
33490991 TTACAATATT
*
33491001 TATTTAATATTTTCATAACTTATTAATAATATTTTATAA
1 TATTAAATATTTTCATAACTTATTAA-AAT-TTTTATAA
* *
33491040 TATTAAATAGTTTTTATAA-TTATTAAAATTTTTATGA
1 TATTAAATA-TTTTCATAACTTATTAAAATTTTTATAA
33491077 TAT
1 TAT
33491080 ATAATAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 10 0.28
38 3 0.08
39 15 0.42
40 8 0.22
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (37 bp):
TATTAAATATTTTCATAACTTATTAAAATTTTTATAA
Found at i:33492625 original size:15 final size:15
Alignment explanation
Indices: 33492578--33492626 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
33492568 TTAAAAAAAA
*
33492578 TATTTTTAT-TATAT
1 TATTTTTATATTTAT
* *
33492592 TATTTTAATATTTAA
1 TATTTTTATATTTAT
*
33492607 TATTTTTATATTTTT
1 TATTTTTATATTTAT
33492622 TATTT
1 TATTT
33492627 ATTGAAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 8 0.29
15 20 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTTATATTTAT
Found at i:33492629 original size:26 final size:26
Alignment explanation
Indices: 33492581--33492647 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
33492571 AAAAAAATAT
*
33492581 TTTTATTATATTATTTTAATATT-TAA
1 TTTT-TTATATTATTTTAATATTGAAA
*
33492607 TATTTTTATATT-TTTTATTTATTGAAA
1 T-TTTTTATATTATTTTA-ATATTGAAA
33492634 TTTTTTATA-TATTT
1 TTTTTTATATTATTT
33492648 ATCTTAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
25 6 0.17
26 23 0.66
27 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (26 bp):
TTTTTTATATTATTTTAATATTGAAA
Found at i:33493427 original size:13 final size:13
Alignment explanation
Indices: 33493405--33493462 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
33493395 AAATTGAAGG
33493405 AAAAAG-GAAAGA
1 AAAAAGAGAAAGA
33493417 AAAAAGAGAAAGA
1 AAAAAGAGAAAGA
*
33493430 AAGAAAGAAGAAGGA
1 AA-AAAG-AGAAAGA
* * *
33493445 AGAATGAGAAGGA
1 AAAAAGAGAAAGA
33493458 AAAAA
1 AAAAA
33493463 AAGGTAATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
12 6 0.16
13 18 0.47
14 7 0.18
15 7 0.18
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.02
Consensus pattern (13 bp):
AAAAAGAGAAAGA
Found at i:33493650 original size:12 final size:12
Alignment explanation
Indices: 33493633--33493657 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33493623 TTAAGTTTGG
33493633 TTAATTTTAAAA
1 TTAATTTTAAAA
33493645 TTAATTTTAAAA
1 TTAATTTTAAAA
33493657 T
1 T
33493658 ATTTTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTAAAA
Found at i:33494355 original size:16 final size:16
Alignment explanation
Indices: 33494310--33494359 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
33494300 TAAACCTAGC
*
33494310 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
33494326 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
33494340 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
33494356 TAAT
1 TAAT
33494360 ATTTCCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:33495741 original size:43 final size:43
Alignment explanation
Indices: 33495659--33495743 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
33495649 ATTAACATGT
* * *
33495659 TAAATTATATTACTTGACTCATGTTAATATGGTTGCATGTTAC
1 TAAACTATATTACTTGACTCATATTAATATGATTGCATGTTAC
* *
33495702 TAAACTATATTACTTTACTCTTATTAATAT-ATTGACATGTTA
1 TAAACTATATTACTTGACTCATATTAATATGATTG-CATGTTA
33495744 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (43 bp):
TAAACTATATTACTTGACTCATATTAATATGATTGCATGTTAC
Found at i:33496398 original size:21 final size:21
Alignment explanation
Indices: 33496372--33496416 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
33496362 GAGTAACCGT
*
33496372 AATACTTTACTCCTCTC-GGGC
1 AATACTCTACTCCTC-CGGGGC
33496393 AATACTCTACTCCTCCGGGGC
1 AATACTCTACTCCTCCGGGGC
33496414 AAT
1 AAT
33496417 TGGACCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (21 bp):
AATACTCTACTCCTCCGGGGC
Done.