Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008011.1 Hibiscus syriacus cultivar Beakdansim tig00110474_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1648842
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1357558 original size:41 final size:41
Alignment explanation
Indices: 1357469--1357988 Score: 388
Period size: 41 Copynumber: 12.7 Consensus size: 41
1357459 CAAAATAGTA
* * * *
1357469 ACTTTAGCGGCGTTTTTATACAAAACGCCGCGACAA-AGTAGT
1 ACTTTAGTGGCGTTTTTATAC-AAACGCCGCTA-AAGACTCGT
* * * *
1357511 ACTTTAGCGGTGTTTTTATAAAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* * * ** * ** * **
1357552 ATTTTAGTGACGCTTTGGTACAAATGTTGCTATAGACTTAT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* * *
1357593 ACGTTAGTGGCGTTTTT-T--AAACGCCGCTATAGACTCAT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* * * * *
1357631 ACGTTAGTGGCATTTTTATACAAATGTCGCTAAAGACTAGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* * * **
1357672 ACTTTAGTGACGTTTTTATATAAACGCCGCTATAGACTATT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
** * * *
1357713 GTTTTAGTGGCGTTTCTATATAAACGTCG-TAAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCT-AAAGACTCGT
* * *
1357754 ACTTTAGCGGCGTTCTTATACAAACGCCGCTAAAAACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
** * *
1357795 GTTTTACTGGCGTTTTTATACAAACGCCGCTGAAGACT-GAT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCG-T
** * * * **
1357836 GTTTTAGTAGCATTTTTATATAAACGCCATTAAAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
* * *
1357877 ACTTTAGTGGCGTTTTTATATAAACGCCGCTATAGACTCTT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
** * *
1357918 GTTTTAGTGGCATTTTCTTATAAAAACGCCGCTAAAGACTCGT
1 ACTTTAGTGGC-GTTT-TTATACAAACGCCGCTAAAGACTCGT
* *
1357961 -GTTTCAGTGGCGTTTTTATGCAAACGCC
1 ACTTT-AGTGGCGTTTTTATACAAACGCC
1357989 ACAAGTTTAC
Statistics
Matches: 377, Mismatches: 90, Indels: 23
0.77 0.18 0.05
Matches are distributed among these distances:
38 32 0.08
39 1 0.00
40 4 0.01
41 281 0.75
42 30 0.08
43 29 0.08
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGT
Found at i:1357627 original size:79 final size:82
Alignment explanation
Indices: 1357522--1357709 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 82
1357512 CTTTAGCGGT
* * ** * * * *
1357522 GTTTTTATAAAAACGCCGCTATAGACTCGTATTTTAGTGACGCTTTGGTACAAATGTTGCTATAG
1 GTTTTTATATAAACGCCGCTATAGACTCATACGTTAGTGACACTTTGATACAAATGTCGCTAAAG
*
1357587 ACTTA-TACGTTAGTGGC
66 AC-TAGTACGTTAGTGAC
* * *
1357604 G-TTTT-T-TAAACGCCGCTATAGACTCATACGTTAGTGGCATTTTTATACAAATGTCGCTAAAG
1 GTTTTTATATAAACGCCGCTATAGACTCATACGTTAGTGACACTTTGATACAAATGTCGCTAAAG
*
1357666 ACTAGTACTTTAGTGAC
66 ACTAGTACGTTAGTGAC
1357683 GTTTTTATATAAACGCCGCTATAGACT
1 GTTTTTATATAAACGCCGCTATAGACT
1357710 ATTGTTTTAG
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.02
79 58 0.65
80 5 0.06
81 5 0.06
82 19 0.21
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (82 bp):
GTTTTTATATAAACGCCGCTATAGACTCATACGTTAGTGACACTTTGATACAAATGTCGCTAAAG
ACTAGTACGTTAGTGAC
Found at i:1358940 original size:41 final size:40
Alignment explanation
Indices: 1358856--1358940 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 40
1358846 TAGATAAGGT
* * *
1358856 GGGGAAGTTCCTTTACGTTTGTGTCTTATTGCCCGCCGGG
1 GGGGAAGTTCCTTTACATTTGTGTCTTATTGCCCACCGCG
1358896 GGGGAGAGTTCCTTTACATTTGTGTCTTATTGCCACACC-CG
1 GGGGA-AGTTCCTTTACATTTGTGTCTTATTGCC-CACCGCG
1358937 GGGG
1 GGGG
1358941 GGTTGTGTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 5 0.12
41 32 0.80
42 3 0.08
ACGTcount: A:0.13, C:0.22, G:0.32, T:0.33
Consensus pattern (40 bp):
GGGGAAGTTCCTTTACATTTGTGTCTTATTGCCCACCGCG
Found at i:1360283 original size:65 final size:66
Alignment explanation
Indices: 1360209--1360357 Score: 221
Period size: 65 Copynumber: 2.3 Consensus size: 66
1360199 ACCCATTCAA
* * *
1360209 GGGGAACCGATGCCCCCTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATA-CCCCA
1360273 -G
65 GG
*
1360274 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCA-
1360339 GG
65 GG
*
1360341 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1360358 ATGAGGAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
65 32 0.42
66 27 0.36
67 17 0.22
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.15
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAG
G
Found at i:1361037 original size:23 final size:23
Alignment explanation
Indices: 1360970--1361029 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
1360960 ATCATTATAT
*
1360970 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
*
1360993 GGCACTTCGGTACAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
*
1361016 GGTACTTCGGTGCA
1 GGCACTTCGGTGCA
1361030 TTTATACGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:1363030 original size:16 final size:16
Alignment explanation
Indices: 1363009--1363043 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1362999 AATTAGTATT
1363009 GGTACTGATTGATCCG
1 GGTACTGATTGATCCG
*
1363025 GGTACTGATTGATCTG
1 GGTACTGATTGATCCG
1363041 GGT
1 GGT
1363044 TATAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.34, T:0.34
Consensus pattern (16 bp):
GGTACTGATTGATCCG
Found at i:1367128 original size:21 final size:21
Alignment explanation
Indices: 1367086--1367128 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1367076 TTTTCGGGCT
* * *
1367086 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1367107 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1367128 A
1 A
1367129 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1367188 original size:66 final size:67
Alignment explanation
Indices: 1367108--1367257 Score: 241
Period size: 67 Copynumber: 2.3 Consensus size: 67
1367098 ACCCATTCAA
* *
1367108 GGGGAACCGATACCCCCTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATA-CCCCA
1367172 -GG
65 GGG
*
1367174 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAG
1367239 GG
66 GG
*
1367241 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1367258 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
66 33 0.42
67 45 0.58
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAG
GG
Found at i:1367936 original size:23 final size:23
Alignment explanation
Indices: 1367869--1367928 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
1367859 ATCATTATAT
* *
1367869 GGCACTACGGTGCAATTCTATGG
1 GGCACTTCGGTGCAATTCTACGG
1367892 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
1367915 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1367929 TTTATACGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:1371066 original size:43 final size:43
Alignment explanation
Indices: 1371017--1371223 Score: 254
Period size: 43 Copynumber: 4.8 Consensus size: 43
1371007 TTTTGGATAC
1371017 AAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTATTCCAA
1 AAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTATTCCAA
* * * *
1371060 AAACGCCGTTATAGATCTCGACATTTTACGGTGTTTATTCCAA
1 AAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTATTCCAA
* * * *
1371103 AAATGACACTATAGATAT-GACCTTTTGCGGCGTTTATTCCAA
1 AAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTATTCCAA
** * * *
1371145 AAACGCCATTATAGATCTCGATCTTTTGCGGCGTTTGTTACAA
1 AAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTATTCCAA
* * * *
1371188 AAACGCCGCTATAGATATTGACCTATGGCGGCGTTT
1 AAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTT
1371224 TTGGTTCTCA
Statistics
Matches: 137, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 35 0.26
43 102 0.74
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (43 bp):
AAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTATTCCAA
Found at i:1371133 original size:85 final size:85
Alignment explanation
Indices: 1371025--1371223 Score: 265
Period size: 85 Copynumber: 2.3 Consensus size: 85
1371015 ACAAACGCCG
* *
1371025 CTATAGATCTCGACCTTTTGCGGCGTTTATTCCAAAAACGCCGTTATAGATCTCGA-CATTTTAC
1 CTATAGATAT-GACCTTTTGCGGCGTTTATTCCAAAAACGCCATTATAGATCTCGATC-TTTTAC
* * *
1371089 GGTGTTTATTCCAAAAATGACA
64 GGCGTTTATTACAAAAACGACA
*
1371111 CTATAGATATGACCTTTTGCGGCGTTTATTCCAAAAACGCCATTATAGATCTCGATCTTTTGCGG
1 CTATAGATATGACCTTTTGCGGCGTTTATTCCAAAAACGCCATTATAGATCTCGATCTTTTACGG
* * *
1371176 CGTTTGTTACAAAAACGCCG
66 CGTTTATTACAAAAACGACA
* *
1371196 CTATAGATATTGACCTATGGCGGCGTTT
1 CTATAGATA-TGACCTTTTGCGGCGTTT
1371224 TTGGTTCTCA
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
85 74 0.74
86 26 0.26
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (85 bp):
CTATAGATATGACCTTTTGCGGCGTTTATTCCAAAAACGCCATTATAGATCTCGATCTTTTACGG
CGTTTATTACAAAAACGACA
Found at i:1377960 original size:324 final size:323
Alignment explanation
Indices: 1377369--1377972 Score: 1165
Period size: 324 Copynumber: 1.9 Consensus size: 323
1377359 TTGAAGCATG
1377369 TGAATTTTGGTAACTTTCTACTTTGTGCATTCCATGACTAACTGTCTTCTATGTAGACTAAGAGG
1 TGAATTTTGGTAACTTTCTACTTTGTGCATTCCATGACTAACTGTCTTCTATGTAGACTAAGAGG
*
1377434 TCTTCTAAAACCATTTTTTTTGTTGCTTTGGCATATTGAGAAGCAATGACTCTGGAAATCAAACC
66 TCTTCTAAAACCATTTTTTTTATTGCTTTGGCATATTGAGAAGCAATGACTCTGGAAATCAAACC
1377499 TCTTTTTTTCTCTAAACATTTTTCTCCCCCCTGTTTTTGTCACATAATGTGAGTTAAATATGTTG
131 TCTTTTTTTCTCTAAACATTTTTCTCCCCCCTGTTTTTGTCACATAATGTGAGTTAAATATGTTG
1377564 AAGTGTTGGAGGTCTGCGTACCCTTGTGTGTCTGCCTCTATGTTCTATTTATGTTGTAAATTGAA
196 AAGTGTTGGAGGTCTGCGTACCCTTGTGTGTCTGCCTCTATGTTCTATTTATGTTGTAAATTGAA
*
1377629 GTGTAGTTATCAATAATTTGGATATTTAACCATTAGCCAACATATTTTTAATCCTTTCTGTTA
261 ATGTAGTTATCAATAATTTGGATATTTAACCATTAGCCAACATATTTTTAATCCTTTCTGTTA
1377692 TGAATTTTGGTAACTTTCTACTTTGTGCATTCCATGACTAACTGTCTTCTATGTAGACTAAGAGG
1 TGAATTTTGGTAACTTTCTACTTTGTGCATTCCATGACTAACTGTCTTCTATGTAGACTAAGAGG
1377757 TCTTCTAAAACCA-TTTTTTTATTGCTTTGGCATATTGAGAAGCAATGACTCTGGAAATCAAACC
66 TCTTCTAAAACCATTTTTTTTATTGCTTTGGCATATTGAGAAGCAATGACTCTGGAAATCAAACC
1377821 TCTTTTTTTTTCTCTAAACATTTTTCTCCCCCCTGTTTTTGTCACATAATGTGAGTTAAATATGT
131 TC--TTTTTTTCTCTAAACATTTTTCTCCCCCCTGTTTTTGTCACATAATGTGAGTTAAATATGT
1377886 TGAAGTGTTGGAGGTCTGCGTACCCTTGTGTGTCTGCCTCTATGTTCTATTTATGTTGTAAATTG
194 TGAAGTGTTGGAGGTCTGCGTACCCTTGTGTGTCTGCCTCTATGTTCTATTTATGTTGTAAATTG
1377951 AAATGTAGTTATCAATAATTTG
259 AAATGTAGTTATCAATAATTTG
1377973 TTCATGGACA
Statistics
Matches: 277, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
322 52 0.19
323 78 0.28
324 147 0.53
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.42
Consensus pattern (323 bp):
TGAATTTTGGTAACTTTCTACTTTGTGCATTCCATGACTAACTGTCTTCTATGTAGACTAAGAGG
TCTTCTAAAACCATTTTTTTTATTGCTTTGGCATATTGAGAAGCAATGACTCTGGAAATCAAACC
TCTTTTTTTCTCTAAACATTTTTCTCCCCCCTGTTTTTGTCACATAATGTGAGTTAAATATGTTG
AAGTGTTGGAGGTCTGCGTACCCTTGTGTGTCTGCCTCTATGTTCTATTTATGTTGTAAATTGAA
ATGTAGTTATCAATAATTTGGATATTTAACCATTAGCCAACATATTTTTAATCCTTTCTGTTA
Found at i:1382371 original size:29 final size:29
Alignment explanation
Indices: 1382324--1382382 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
1382314 CTAGTTCATC
1382324 TGATAAATCAGCCATAAAGTTAACTACAA
1 TGATAAATCAGCCATAAAGTTAACTACAA
*
1382353 TGATGAATCAGCC-TGAAAGTTAACTACAA
1 TGATAAATCAGCCAT-AAAGTTAACTACAA
1382382 T
1 T
1382383 CACTATCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (29 bp):
TGATAAATCAGCCATAAAGTTAACTACAA
Found at i:1392103 original size:21 final size:21
Alignment explanation
Indices: 1392073--1392130 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1392063 AGTGCCCAAC
1392073 AATAACAAAACCGATAGAAAA
1 AATAACAAAACCGATAGAAAA
*
1392094 AATAATAAAACCGATAGAAAA
1 AATAACAAAACCGATAGAAAA
1392115 AATAACAAAACCGATA
1 AATAACAAAACCGATA
1392131 AAACGCCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.12
Consensus pattern (21 bp):
AATAACAAAACCGATAGAAAA
Found at i:1400410 original size:21 final size:21
Alignment explanation
Indices: 1400386--1400427 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1400376 TACATAAAAT
*
1400386 GATAAAAACATTAATGTTTTA
1 GATAAAAACAATAATGTTTTA
*
1400407 GATAAAAATAATAATGTTTTA
1 GATAAAAACAATAATGTTTTA
1400428 ATTAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (21 bp):
GATAAAAACAATAATGTTTTA
Found at i:1407964 original size:60 final size:59
Alignment explanation
Indices: 1407872--1408048 Score: 205
Period size: 60 Copynumber: 3.0 Consensus size: 59
1407862 ATATGTACAC
* * ** *
1407872 AAACTATAACCCTCATT-TAAATTAGTTCTTAAACTTTTGAATATTAAAATTTCATCTT
1 AAACTATGACCCTCATTATAAATTAGATCTTAAACTTTTGAATATTCTAATTTCATCCT
* * * *
1407930 AAAACTATGACTCTGATTATAAATTAGATCTTAAACTTTTAAACATTCTAATTTCATCCCT
1 -AAACTATGACCCTCATTATAAATTAGATCTTAAACTTTTGAATATTCTAATTTCAT-CCT
* * *
1407991 AAATTATGACCCTCTTTATAAATTA-ATCCTCAAACTTTTGAATATTCTAATTTCATCC
1 AAACTATGACCCTCATTATAAATTAGAT-CTTAAACTTTTGAATATTCTAATTTCATCC
1408049 CCAAATTCAT
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 18 0.18
60 79 0.80
61 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (59 bp):
AAACTATGACCCTCATTATAAATTAGATCTTAAACTTTTGAATATTCTAATTTCATCCT
Found at i:1408287 original size:29 final size:29
Alignment explanation
Indices: 1408179--1408287 Score: 69
Period size: 29 Copynumber: 3.8 Consensus size: 29
1408169 TATACATATA
* *
1408179 GTTT-GGGATCAAATTAAAATATTTAAAA
1 GTTTAGGGACCAAATTAAAATATTTAAAG
* * * * * *
1408207 GTTTAAGAACTAATTTAAAATGATGGTCAAG
1 GTTTAGGGACCAAATTAAAAT-AT-TTAAAG
* ** *
1408238 TTTTA-GGATGAAATTGAAATATTTAAAG
1 GTTTAGGGACCAAATTAAAATATTTAAAG
*
1408266 GTTTAGGGACCAATTTAAAATA
1 GTTTAGGGACCAAATTAAAATA
1408288 AGGGTCATAC
Statistics
Matches: 56, Mismatches: 21, Indels: 7
0.67 0.25 0.08
Matches are distributed among these distances:
28 12 0.21
29 25 0.45
30 12 0.21
31 7 0.12
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (29 bp):
GTTTAGGGACCAAATTAAAATATTTAAAG
Found at i:1411270 original size:29 final size:30
Alignment explanation
Indices: 1411229--1411300 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1411219 AAACTTTCAC
1411229 ACAACAATCCTCTCAA-CCGAAAACATCAA
1 ACAACAATCCTCTCAATCCGAAAACATCAA
* * *
1411258 ACAACAATCCTCTCAATCCGTAAATATCAC
1 ACAACAATCCTCTCAATCCGAAAACATCAA
* *
1411288 CCGACAATCCTCT
1 ACAACAATCCTCT
1411301 TATATTTGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 16 0.43
30 21 0.57
ACGTcount: A:0.40, C:0.36, G:0.04, T:0.19
Consensus pattern (30 bp):
ACAACAATCCTCTCAATCCGAAAACATCAA
Found at i:1411358 original size:13 final size:13
Alignment explanation
Indices: 1411340--1411368 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1411330 TTCGTTGTAA
1411340 AATAATTTTTTAT
1 AATAATTTTTTAT
1411353 AATAATTTTTTAT
1 AATAATTTTTTAT
1411366 AAT
1 AAT
1411369 TATATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATAATTTTTTAT
Found at i:1419345 original size:2 final size:2
Alignment explanation
Indices: 1419338--1419392 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
1419328 CCATATAAAT
*
1419338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG 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
*
1419380 TA TG TA TA TA TA T
1 TA TA TA TA TA TA T
1419393 TGGCTACTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1421401 original size:2 final size:2
Alignment explanation
Indices: 1421396--1421420 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1421386 TTAGTCACAC
1421396 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1421421 GAAAATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1462970 original size:16 final size:16
Alignment explanation
Indices: 1462949--1462994 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1462939 TTTTTCAATT
1462949 TTAAATATATATTTGA
1 TTAAATATATATTTGA
* *
1462965 TTAAATTTA-ATTTTA
1 TTAAATATATATTTGA
*
1462980 ATAAATATATATTTG
1 TTAAATATATATTTG
1462995 GAAATTAGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (16 bp):
TTAAATATATATTTGA
Found at i:1473680 original size:21 final size:20
Alignment explanation
Indices: 1473645--1473692 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
1473635 CGATATACCA
*
1473645 GGTAAAAATATGATAAAACC
1 GGTAAAAAAATGATAAAACC
1473665 GGTAAGAAAAATGATAAAACC
1 GGTAA-AAAAATGATAAAACC
1473686 GGTAAAA
1 GGTAAAA
1473693 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (20 bp):
GGTAAAAAAATGATAAAACC
Found at i:1473836 original size:180 final size:182
Alignment explanation
Indices: 1473433--1473904 Score: 675
Period size: 182 Copynumber: 2.6 Consensus size: 182
1473423 GATCCAAATT
* * * *
1473433 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCAGTATTG-AAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCAGTA-AGAAAATGAT
* * * * * *
1473497 AAAATCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
1473562 CGTGAATTTAAAAGAGAAGCAGTTTTAAGTCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTTTAAGTCCTATAAAGTGTCGATACTTTTA
* *
1473615 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAAGAAAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCAGTAAG-AAAATGAT
* *
1473680 AAAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATA-TTTTATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
1473744 TGTGAATTTAAAAGAGAAGCAGTTTTTAG-CCTATAATGTGTCGATAC-TTTA
130 CGTGAATTTAAAAGAGAAGCAGTTTTAAGTCCTATAAAGTGTCGATACTTTTA
* * **
1473795 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAA-CATGTATCAAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCA-GTAAGAAAATGAT
* *
1473859 AAAACCGGTAAAATGATACCTGATATATTGAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1473905 CGTAAGTACG
Statistics
Matches: 261, Mismatches: 25, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
179 48 0.18
180 55 0.21
181 18 0.07
182 97 0.37
183 43 0.16
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCAGTAAGAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAAGTCCTATAAAGTGTCGATACTTTTA
Found at i:1473844 original size:20 final size:19
Alignment explanation
Indices: 1473816--1473871 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1473806 GATCCACAAC
*
1473816 GATATAACAGGTAAAAATAT
1 GATAAAACAGGTAAAAA-AT
* *
1473836 GATAAAACATGTATCAAAAT
1 GATAAAACAGGTA-AAAAAT
*
1473856 GATAAAACCGGTAAAA
1 GATAAAACAGGTAAAA
1473872 TGATACCTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.55, C:0.09, G:0.14, T:0.21
Consensus pattern (19 bp):
GATAAAACAGGTAAAAAAT
Found at i:1476118 original size:21 final size:21
Alignment explanation
Indices: 1476092--1476156 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1476082 AAGACAATCA
*
1476092 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
*
1476113 AGAGTCGAAAAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1476134 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1476155 AG
1 AG
1476157 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1476231 original size:33 final size:33
Alignment explanation
Indices: 1476189--1476254 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1476179 AAATAGATGG
*
1476189 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1476222 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1476255 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1478068 original size:19 final size:19
Alignment explanation
Indices: 1478044--1478092 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1478034 AATGTAGGGT
1478044 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1478063 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1478082 TAATTTTGTAT
1 TAATTTTGTAT
1478093 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1479030 original size:200 final size:200
Alignment explanation
Indices: 1478216--1479395 Score: 1931
Period size: 200 Copynumber: 5.9 Consensus size: 200
1478206 TGGCCAACAT
* *
1478216 GGTGCAACCATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAACTTCGAAAACCAAA
1 GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAA
1478281 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
66 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
1478346 TGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGAA
131 TGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGAA
*
1478411 AACAG
196 AACTG
* *
1478416 GGTGTAACCATAAAGTGTCGATCCATATAAAAAAAAGTGTCGATCCCAAAAACATCGAAAACCAA
1 GGTGCAACCATAAAGTGTCGATCCATAT-ATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAA
*
1478481 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATAAGAGAAT
65 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT
*
1478546 ATGTCTAAATAATGTGTCGATACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGA
130 ATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGA
*
1478611 AAACAG
195 AAACTG
*
1478617 GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAGCATCGAAAACCAAA
1 GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAA
*
1478682 AGTATAATGTAATATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGA
66 AG--T-A--T-A-ATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
* *
1478747 GAGAACATGTCTAAATAATTTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATG
124 GAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATG
*
1478812 AATGTAAAACAT-
189 AATGGAAAAC-TG
1478824 GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAA
1 GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAA
1478889 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
66 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
* * *
1478954 TGTCTAAATAATTTGTCGACAGTTTTTTAGTTTGTGTCGATACTTTTGGTCCAGAATGAATGGAA
131 TGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGAA
1479019 AACTG
196 AACTG
*
1479024 GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAATATCGAAAACCAAA
1 GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAA
*
1479089 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGAGAGAATA
66 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
* * *
1479154 TGTCTAAATAATGTGTCGACACTTTATTAGTTTGTGTCGATATTTTTTGTCCATAATGAATGGAA
131 TGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGAA
1479219 AACAT-
196 AAC-TG
* *
1479224 GGTGCAACCATAAAGTGTCGATCCATATATAGAAAA-TGTTGATCCTAAAAACATCGAAAACCAA
1 GGTGCAACCATAAAGTGTCGATCCATATATA-AAAAGTGTCGATCCCAAAAACATCGAAAACCAA
* *
1479288 AAGTACAATGTAATATGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATGAGAGAAT
65 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT
* * * *
1479353 -TGGTATATAAT-ATGTATCGACACTGTTTAATGTTT-TGTCGATA
130 AT-GTCTA-AATAATGTGTCGACACTTTTTTA-GTTTGTGTCGATA
1479396 CTAATTTAAA
Statistics
Matches: 924, Mismatches: 41, Indels: 30
0.93 0.04 0.03
Matches are distributed among these distances:
199 2 0.00
200 520 0.56
201 208 0.23
202 2 0.00
203 1 0.00
204 1 0.00
205 2 0.00
206 1 0.00
207 187 0.20
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (200 bp):
GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAA
AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
TGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGAA
AACTG
Found at i:1480880 original size:12 final size:12
Alignment explanation
Indices: 1480863--1480897 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1480853 GGTCAATGAA
1480863 GATGAAGCTGAC
1 GATGAAGCTGAC
*
1480875 GATGAAGATGAC
1 GATGAAGCTGAC
1480887 GATGAAGCTGA
1 GATGAAGCTGA
1480898 TGACGATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.17
Consensus pattern (12 bp):
GATGAAGCTGAC
Found at i:1480890 original size:24 final size:24
Alignment explanation
Indices: 1480858--1480915 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1480848 CAAGCGGTCA
*
1480858 ATGAAGATGAAGCTGACGATGAAG
1 ATGAAGATGAAGCTGACGACGAAG
* * *
1480882 ATGACGATGAAGCTGATGACGATG
1 ATGAAGATGAAGCTGACGACGAAG
*
1480906 ATGATGATGA
1 ATGAAGATGA
1480916 TCCAAACAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.33, T:0.21
Consensus pattern (24 bp):
ATGAAGATGAAGCTGACGACGAAG
Found at i:1480913 original size:15 final size:15
Alignment explanation
Indices: 1480875--1480915 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1480865 TGAAGCTGAC
*
1480875 GATGAAGATGACGAT
1 GATGATGATGACGAT
* *
1480890 GAAGCTGATGACGAT
1 GATGATGATGACGAT
1480905 GATGATGATGA
1 GATGATGATGA
1480916 TCCAAACAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.34, T:0.22
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:1482479 original size:183 final size:183
Alignment explanation
Indices: 1482117--1483606 Score: 2531
Period size: 183 Copynumber: 8.1 Consensus size: 183
1482107 ACAAAGTTTT
* * * *
1482117 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGGAAGAAAAATATGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* * * * * *
1482182 AAAAAAGTGTCG--ATTGAAAAAATATCGGAACTCATAATTATATTGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
*
1482245 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATATGTCTACAACCTATATCG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1482301 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* * * *
1482366 AAAAAAGTGTCGACATTTACACATCGGAATCCAGATTTATAATATAATAGATAATTTTATAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1482431 AACCGGTATAAATATACTGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1482484 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTG
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-
* * * *
1482548 TCAAAAAGTCTTGACATTTACAAATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
65 TAAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
*
1482613 TAACCGGTATAAATATACCGGTTTTATGAGCGAATATGTCTACAACCTATATCG
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1482667 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
1482732 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAAATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1482797 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCA
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1482850 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTG
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-
* *
1482914 TCAAAAAGTGTCGACATTTACAAATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
65 TAAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
* *
1482979 TAATCGGTATAAATATACCGGTTTTATGAGCGAATATGTCTACAACCTATATCG
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1483033 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
1483098 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* * *
1483163 AACCGGTATAAATATACCGATTTTATGAGTGAATATGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
1483216 ACACTTTCTAATATTGTGTCGGTACTTTATGCCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
1483281 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
1483346 AACCTGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1483399 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
1483464 AAAAAAGTGTCGACATTTACAAATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
**
1483529 AACATGTATAAATATACCGGTTTTATGAGCGAATAGGTCTTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTC-TACAACCTATATCG
1483583 ACACGTTT-TAATATTGTGTCGGTA
1 ACAC-TTTCTAATATTGTGTCGGTA
1483607 ATTGTAAGTA
Statistics
Matches: 1240, Mismatches: 58, Indels: 16
0.94 0.04 0.01
Matches are distributed among these distances:
182 8 0.01
183 1111 0.90
184 115 0.09
185 3 0.00
186 3 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1486480 original size:23 final size:23
Alignment explanation
Indices: 1486445--1486509 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
1486435 AATAGGTAAA
* *
1486445 AATATGATATAATAGGTAGCGTT
1 AATATAATGTAATAGGTAGCGTT
1486468 AATATAATGTAATAGGTAGCGTT
1 AATATAATGTAATAGGTAGCGTT
*
1486491 TATATAATGTAATAGGTAG
1 AATATAATGTAATAGGTAG
1486510 TGCTTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (23 bp):
AATATAATGTAATAGGTAGCGTT
Found at i:1486516 original size:23 final size:22
Alignment explanation
Indices: 1486454--1486518 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 22
1486444 AAATATGATA
1486454 TAATAGGTAGCGTTAATATAATG
1 TAATAGGTAGCGTT-ATATAATG
1486477 TAATAGGTAGCGTTTATATAATG
1 TAATAGGTAGCG-TTATATAATG
*
1486500 TAATAGGTAGTGCTTATAT
1 TAATAGGTAGCG-TTATAT
1486519 TGTAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
23 37 0.95
24 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (22 bp):
TAATAGGTAGCGTTATATAATG
Found at i:1492460 original size:21 final size:21
Alignment explanation
Indices: 1492421--1492462 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1492411 ATTCAAAAAG
1492421 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATT-CCCTGCTACA
1492443 GGGAACCGATAT-CCTGCTAC
1 GGGAACCGAT-TCCCTGCTAC
1492463 GGTACTGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 10 0.53
23 1 0.05
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (21 bp):
GGGAACCGATTCCCTGCTACA
Found at i:1493198 original size:24 final size:24
Alignment explanation
Indices: 1493171--1493250 Score: 96
Period size: 23 Copynumber: 3.4 Consensus size: 24
1493161 CAGCTCGTAT
1493171 AATTGCACCGAAGTGCCACGTAGA
1 AATTGCACCGAAGTGCCACGTAGA
*
1493195 AATTGTC-CCGAAG-GACCGCGTAGA
1 AATTG-CACCGAAGTG-CCACGTAGA
*
1493219 AA-TGCACCGAAGTGCCACATAG-
1 AATTGCACCGAAGTGCCACGTAGA
1493241 AATTGCACCG
1 AATTGCACCG
1493251 TAGTTCCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
22 3 0.06
23 22 0.46
24 22 0.46
25 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (24 bp):
AATTGCACCGAAGTGCCACGTAGA
Found at i:1495692 original size:29 final size:28
Alignment explanation
Indices: 1495660--1495745 Score: 82
Period size: 33 Copynumber: 2.9 Consensus size: 28
1495650 TGTGACATAC
1495660 AAAAATTATATACATGCATTTTAAAATT
1 AAAAATTATATACATGCATTTTAAAATT
* *
1495688 AAAAACCATGCATAATACATACATTTTAAAATT
1 -AAAA--AT-TAT-ATACATGCATTTTAAAATT
* *
1495721 AAAAATTATAAACCATGCATATTAA
1 AAAAATTATATA-CATGCATTTTAA
1495746 CATATAATGT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
28 2 0.04
29 16 0.35
30 2 0.04
31 2 0.04
32 6 0.13
33 18 0.39
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAAATTATATACATGCATTTTAAAATT
Found at i:1497578 original size:55 final size:54
Alignment explanation
Indices: 1497518--1498178 Score: 345
Period size: 51 Copynumber: 12.7 Consensus size: 54
1497508 TCAAATGGCG
* **
1497518 GGTCTGCTCCCTATTCTTTCATTGAGTATAAGACTCGAACAATCTTCATAAAAC
1 GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAAC
* * * * *
1497572 GTGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAAC
1 G-GTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATC-TTCATAAAAC
* * *
1497628 GGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCA-ATAAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAG-ACTCGAACAATCTTCATA-AAAC
* * *
1497683 AGGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCA-ACGAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC
* * * *
1497734 TAGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC
* * * *
1497785 TTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC
* * *
1497836 TTGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC
* * * *
1497887 TTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC
* * * *
1497938 TTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC
* * * *
1497989 TTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC
* * * *
1498040 TTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC
* * * *
1498091 TTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAAC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC
* * *
1498142 TTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC
1 -GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTC
1498179 AATCTTCAAC
Statistics
Matches: 573, Mismatches: 27, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
51 448 0.78
54 2 0.00
55 76 0.13
56 46 0.08
57 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (54 bp):
GGTCCGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAAC
Found at i:1497745 original size:51 final size:51
Alignment explanation
Indices: 1497630--1498188 Score: 974
Period size: 51 Copynumber: 10.9 Consensus size: 51
1497620 AATAAAACGG
* * * ** **
1497630 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
1497685 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
1497736 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1497787 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
1497838 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1497889 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1497940 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1497991 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1498042 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1498093 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1498144 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1498189 AAACGAATTT
Statistics
Matches: 490, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
51 459 0.94
55 31 0.06
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:1497912 original size:153 final size:153
Alignment explanation
Indices: 1497523--1498188 Score: 974
Period size: 153 Copynumber: 4.3 Consensus size: 153
1497513 TGGCGGGTCT
** * * * * *
1497523 GCTCCCTATTCTTTCATTGAGTATAAGACTCGAACAATCTTCATA-AAACGTGTCTGCTCTCTAT
1 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCCGCTCCCTAT
* * ** ** * *
1497587 TCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCCGCTCTCTATTCCTTCAGA
61 TCATTCAGAGAGTATAGGAC-T---CAATCTTCAA-CGAACTTGTCCGCTCCCTATTCATTCAGA
* ** **
1497652 GAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCC
121 GAGTATAGGACTC----AATCTTCAACGAACTTGTCC
* * *
1497689 GCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTAGTCCGCTCCCTATTCCTT
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1497754 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGA
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGA
1497819 CTCAATCTTCAACGAACTTGTCC
131 CTCAATCTTCAACGAACTTGTCC
1497842 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1497907 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGA
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGA
1497972 CTCAATCTTCAACGAACTTGTCC
131 CTCAATCTTCAACGAACTTGTCC
*
1497995 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
1498060 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGA
66 CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGA
1498125 CTCAATCTTCAACGAACTTGTCC
131 CTCAATCTTCAACGAACTTGTCC
*
1498148 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAAC
1498189 AAACGAATTT
Statistics
Matches: 473, Mismatches: 26, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
153 359 0.76
157 35 0.07
158 9 0.02
161 2 0.00
162 41 0.09
166 27 0.06
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (153 bp):
GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATT
CAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGA
CTCAATCTTCAACGAACTTGTCC
Found at i:1499530 original size:19 final size:19
Alignment explanation
Indices: 1499508--1499602 Score: 60
Period size: 18 Copynumber: 5.2 Consensus size: 19
1499498 TGAACCCTCC
1499508 TTTTATTTCTCTTTTTCCA
1 TTTTATTTCTCTTTTTCCA
* *
1499527 --TT-TTTCTCTTTCT-CT
1 TTTTATTTCTCTTTTTCCA
*
1499542 TTTTATTTTTCTTTTT-CA
1 TTTTATTTCTCTTTTTCCA
* *
1499560 TTTTTTTTCTTCCCTTTTCCA
1 TTTTATTTC-T-CTTTTTCCA
*
1499581 TTTTTTCTTCT-TTTTTCC-
1 TTTTAT-TTCTCTTTTTCCA
1499599 TTTT
1 TTTT
1499603 CGTTTTTTCC
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
15 1 0.02
16 10 0.17
17 4 0.07
18 21 0.35
19 7 0.12
20 5 0.08
21 9 0.15
22 3 0.05
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATTTCTCTTTTTCCA
Found at i:1499565 original size:20 final size:20
Alignment explanation
Indices: 1499513--1499558 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1499503 CCTCCTTTTA
1499513 TTTCTCTTTTTCCATTTTTCTC
1 TTTCTCTTTTT--ATTTTTCTC
*
1499535 TTTCTCTTTTTATTTTTCTT
1 TTTCTCTTTTTATTTTTCTC
1499555 TTTC
1 TTTC
1499559 ATTTTTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.52
22 11 0.48
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTCTCTTTTTATTTTTCTC
Found at i:1499576 original size:21 final size:22
Alignment explanation
Indices: 1499552--1499592 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1499542 TTTTATTTTT
*
1499552 CTTTTTCATTTTTT-TTCTTCC
1 CTTTTCCATTTTTTCTTCTTCC
1499573 CTTTTCCATTTTTTCTTCTT
1 CTTTTCCATTTTTTCTTCTT
1499593 TTTTCCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (22 bp):
CTTTTCCATTTTTTCTTCTTCC
Found at i:1499584 original size:34 final size:34
Alignment explanation
Indices: 1499506--1499585 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
1499496 CTTGAACCCT
*
1499506 CCTTTT-ATTTCTCTTTTTCCATTTTTCTCTTTC
1 CCTTTTCATTTTTCTTTTTCCATTTTTCTCTTTC
* * *
1499539 TCTTTTTATTTTTCTTTTT-CATTTTT-TTTCTTC
1 CCTTTTCATTTTTCTTTTTCCATTTTTCTCT-TTC
1499572 CCTTTTCCATTTTT
1 CCTTTT-CATTTTT
1499586 TCTTCTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 2 0.05
33 20 0.51
34 17 0.44
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (34 bp):
CCTTTTCATTTTTCTTTTTCCATTTTTCTCTTTC
Found at i:1499585 original size:22 final size:21
Alignment explanation
Indices: 1499552--1499592 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1499542 TTTTATTTTT
* *
1499552 CTTTTTCATTTTTTTTCTTCC
1 CTTTTCCATTTTTCTTCTTCC
1499573 CTTTTCCATTTTTTCTTCTT
1 CTTTTCCA-TTTTTCTTCTT
1499593 TTTTCCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (21 bp):
CTTTTCCATTTTTCTTCTTCC
Found at i:1499621 original size:54 final size:54
Alignment explanation
Indices: 1499520--1499624 Score: 126
Period size: 54 Copynumber: 1.9 Consensus size: 54
1499510 TTATTTCTCT
* **
1499520 TTTTCCATTTTTCTCTTTCTCTTTTTATTTTTCTTTTTCATTTTTTTTCTTCCC
1 TTTTCCATTTTTCTCTTTCTCTTTTTACTTTTCTTTTTCATCATTTTTCTTCCC
*
1499574 TTTTCCATTTTT-TC-TTCT-TTTTTCCTTTTCGTTTTTTCCATCATTTTTCTT
1 TTTTCCATTTTTCTCTTTCTCTTTTTACTTTTC--TTTTT-CATCATTTTTCTT
1499625 TTTTCTCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
51 10 0.23
52 4 0.09
53 7 0.16
54 23 0.52
ACGTcount: A:0.06, C:0.22, G:0.01, T:0.71
Consensus pattern (54 bp):
TTTTCCATTTTTCTCTTTCTCTTTTTACTTTTCTTTTTCATCATTTTTCTTCCC
Found at i:1499627 original size:19 final size:17
Alignment explanation
Indices: 1499599--1499646 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
1499589 TCTTTTTTCC
1499599 TTTTCGTTTTTTCCATCAT
1 TTTTC-TTTTTTCC-TCAT
1499618 TTTTCTTTTTT-CTCAT
1 TTTTCTTTTTTCCTCAT
1499634 TTTCTCATTTTTT
1 TTT-TC-TTTTTT
1499647 TCTCTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.26
17 3 0.11
18 12 0.44
19 5 0.19
ACGTcount: A:0.08, C:0.19, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTCTTTTTTCCTCAT
Found at i:1510952 original size:29 final size:28
Alignment explanation
Indices: 1510920--1511005 Score: 82
Period size: 33 Copynumber: 2.9 Consensus size: 28
1510910 TGTGACATAC
1510920 AAAAATTATATACATGCATTTTAAAATT
1 AAAAATTATATACATGCATTTTAAAATT
* *
1510948 AAAAACCATGCATAATACATACATTTTAAAATT
1 -AAAA--AT-TAT-ATACATGCATTTTAAAATT
* *
1510981 AAAAATTATAAACCATGCATATTAA
1 AAAAATTATATA-CATGCATTTTAA
1511006 CATATAATGT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
28 2 0.04
29 16 0.35
30 2 0.04
31 2 0.04
32 6 0.13
33 18 0.39
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAAATTATATACATGCATTTTAAAATT
Found at i:1512724 original size:45 final size:45
Alignment explanation
Indices: 1512674--1512776 Score: 206
Period size: 45 Copynumber: 2.3 Consensus size: 45
1512664 TGCATTGGTA
1512674 GTGCATCGATGCACTCTTTTAAAATAAATACATCGAATGCAATTT
1 GTGCATCGATGCACTCTTTTAAAATAAATACATCGAATGCAATTT
1512719 GTGCATCGATGCACTCTTTTAAAATAAATACATCGAATGCAATTT
1 GTGCATCGATGCACTCTTTTAAAATAAATACATCGAATGCAATTT
1512764 GTGCATCGATGCA
1 GTGCATCGATGCA
1512777 TAAGTAGTGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (45 bp):
GTGCATCGATGCACTCTTTTAAAATAAATACATCGAATGCAATTT
Found at i:1512787 original size:64 final size:64
Alignment explanation
Indices: 1512719--1512929 Score: 257
Period size: 64 Copynumber: 3.3 Consensus size: 64
1512709 AATGCAATTT
**
1512719 GTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTGCATCGATGCATAAGT
1 GTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTTGTGCATCGATGCATAAGT
1512782 A
64 A
** *
1512783 GTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGCATCGATGCATAAGTCA
1 GTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGCATCGATGCATAAGT-A
* * * * * * *
1512848 -TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGCACCGATGCATCAGTA
1 GTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGCATCGATGCATAAGTA
*
1512911 GTGCATCGATGCATACCAT
1 GTGCATCGATGCATCCCAT
1512930 CATTAAAAGA
Statistics
Matches: 126, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
63 1 0.01
64 119 0.94
65 6 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGCATCGATGCATAAGTA
Found at i:1513901 original size:103 final size:103
Alignment explanation
Indices: 1513676--1513893 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1513666 GTCGAGGGTC
1513676 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1513741 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1513779 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1513844 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1513882 TATGTGGTCCTT
1 TATGTGGTCCTT
1513894 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1513943 original size:23 final size:23
Alignment explanation
Indices: 1513910--1513972 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1513900 ATTATTATAT
1513910 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1513933 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
1513956 GGCACTTCGATGCAATT
1 GGCACTACGGTGCAATT
1513973 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1518478 original size:64 final size:64
Alignment explanation
Indices: 1518410--1518630 Score: 250
Period size: 64 Copynumber: 3.5 Consensus size: 64
1518400 TTGAAGGTGT
** **
1518410 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTTGTG
1518473 C
64 C
** ** *
1518474 ATCGATGCATAAGTAGTGCATCGATGTTTCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGC
* * * * *
1518538 ATCGATGCATAAGTTA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAAG-TAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGC
* *
1518602 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
1518631 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 2 0.02
64 123 0.93
65 7 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTTGTGC
Found at i:1519607 original size:103 final size:103
Alignment explanation
Indices: 1519382--1519599 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1519372 GTCGAGGGTC
1519382 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1519447 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1519485 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1519550 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1519588 TATGTGGTCCTT
1 TATGTGGTCCTT
1519600 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1519649 original size:23 final size:23
Alignment explanation
Indices: 1519616--1519678 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1519606 ATTATTATAT
*
1519616 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1519639 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
1519662 GGCACTTCGATGCAATT
1 GGCACTACGGTGCAATT
1519679 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1523639 original size:2 final size:2
Alignment explanation
Indices: 1523632--1523671 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1523622 CAAACTATCC
1523632 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
1523672 CAAAATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1526181 original size:24 final size:24
Alignment explanation
Indices: 1526154--1526233 Score: 87
Period size: 23 Copynumber: 3.4 Consensus size: 24
1526144 CAGCTCGTAT
1526154 AATTGCACCGAAGTGCCACGTAGA
1 AATTGCACCGAAGTGCCACGTAGA
**
1526178 AATTGTC-CCGAAG-GACTGCGTAGA
1 AATTG-CACCGAAGTG-CCACGTAGA
*
1526202 AA-TGCACCGAAGTGCCACATAG-
1 AATTGCACCGAAGTGCCACGTAGA
1526224 AATTGCACCG
1 AATTGCACCG
1526234 TAGTTCCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
22 3 0.07
23 21 0.46
24 21 0.46
25 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (24 bp):
AATTGCACCGAAGTGCCACGTAGA
Found at i:1544910 original size:34 final size:34
Alignment explanation
Indices: 1544860--1544938 Score: 108
Period size: 33 Copynumber: 2.3 Consensus size: 34
1544850 AATGGTAATA
*
1544860 AACAAAATTAACCAAAATACATTAACAA-AAAGTCC
1 AACAAAATTAACCAAAATAAATTAA-AATAAA-TCC
*
1544895 AACAAATTTAA-CAAAATAAATTAAAATAAATCC
1 AACAAAATTAACCAAAATAAATTAAAATAAATCC
1544928 AACAAAATTAA
1 AACAAAATTAA
1544939 TGAAATAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
33 15 0.38
34 15 0.38
35 10 0.25
ACGTcount: A:0.63, C:0.15, G:0.01, T:0.20
Consensus pattern (34 bp):
AACAAAATTAACCAAAATAAATTAAAATAAATCC
Found at i:1545471 original size:33 final size:33
Alignment explanation
Indices: 1545404--1545471 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
1545394 TCCTCCAGGA
* **
1545404 GGGGTCATAAAACTCTGTGACGGTGACGGTGGC
1 GGGGTCATAAAACTCGGTGACGGTGACGACGGC
*
1545437 GGGGTCATAAAA-TCAGGTGACGGTGGCGACGGC
1 GGGGTCATAAAACTC-GGTGACGGTGACGACGGC
1545470 GG
1 GG
1545472 CATCGGGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.22, C:0.18, G:0.43, T:0.18
Consensus pattern (33 bp):
GGGGTCATAAAACTCGGTGACGGTGACGACGGC
Found at i:1547267 original size:17 final size:16
Alignment explanation
Indices: 1547221--1547268 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1547211 TATGCAAAAA
* *
1547221 ATTAATTAAATAAAAT
1 ATTAAATAAATTAAAT
1547237 ATTAAA-AAATTTAAAT
1 ATTAAATAAA-TTAAAT
1547253 ACTTAAATAAATTAAA
1 A-TTAAATAAATTAAA
1547269 ACAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 10 0.37
18 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:1547283 original size:22 final size:23
Alignment explanation
Indices: 1547249--1547291 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1547239 TAAAAAATTT
1547249 AAATACTTAAATA-AATTAAAACA
1 AAATACTTAAATATAA-TAAAACA
1547272 AAATA-TTAAATATAATAAAA
1 AAATACTTAAATATAATAAAA
1547292 TATACTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATACTTAAATATAATAAAACA
Found at i:1547715 original size:2 final size:2
Alignment explanation
Indices: 1547669--1547700 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1547659 AAAACGCTTA
1547669 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
1547701 GAATTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1547800 original size:17 final size:18
Alignment explanation
Indices: 1547772--1547806 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1547762 ATTTGCTGCT
1547772 CTGTATTTTTTTTTCTCA
1 CTGTATTTTTTTTTCTCA
1547790 CTGTA-TTTTTTTTCTCA
1 CTGTATTTTTTTTTCTCA
1547807 AATAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.11, C:0.17, G:0.06, T:0.66
Consensus pattern (18 bp):
CTGTATTTTTTTTTCTCA
Found at i:1556548 original size:31 final size:28
Alignment explanation
Indices: 1556512--1556573 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 28
1556502 ATTAAATATA
1556512 TTTTATT-TTAATGTAAAAATATATATTTTAT
1 TTTTATTCTTAAT-TAAAAA-A-ATATTTT-T
*
1556543 TTTTATTCTTACTTAAAAAAATATTTTT
1 TTTTATTCTTAATTAAAAAAATATTTTT
1556571 TTT
1 TTT
1556574 AAATATCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.14
29 7 0.24
30 1 0.03
31 13 0.45
32 4 0.14
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTATTCTTAATTAAAAAAATATTTTT
Found at i:1556653 original size:26 final size:28
Alignment explanation
Indices: 1556604--1556666 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 28
1556594 TATTTAAATA
* * *
1556604 TTTTATTATTAATTTAATATATAT-TAC
1 TTTTATTATTAAATTAAAAAATATATAC
1556631 TTTTATT-TTAAATTAAAAAATATATAC
1 TTTTATTATTAAATTAAAAAATATATAC
*
1556658 TATT-TTATT
1 TTTTATTATT
1556667 CTTATCTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTATTATTAAATTAAAAAATATATAC
Found at i:1556690 original size:29 final size:28
Alignment explanation
Indices: 1556658--1556750 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 28
1556648 AAATATATAC
*
1556658 TATTTTATTCTTATCTTTACTTAAAAATA
1 TATTTTATTATTAT-TTTACTTAAAAATA
* * *
1556687 TATTTTATTATTATTGTAAATTAAAAACA
1 TATTTTATTATTATT-TTACTTAAAAATA
*
1556716 TGTTTTATTATTATTTTAACTTTTAAAAATA
1 TATTTTATTATTATTTT-AC--TTAAAAATA
1556747 TATT
1 TATT
1556751 AAAATATTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.04
29 38 0.75
31 11 0.22
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (28 bp):
TATTTTATTATTATTTTACTTAAAAATA
Found at i:1556730 original size:64 final size:60
Alignment explanation
Indices: 1556619--1556750 Score: 135
Period size: 64 Copynumber: 2.1 Consensus size: 60
1556609 TTATTAATTT
* * *
1556619 AATATATATTACTTTTATTTTAAATTAAAAAATATATACTATTTTATTCTTATCTTTACTTAAA
1 AATATATTTTACTTTTATTGTAAATTAAAAAATATATACTATTTTATT-TTAAC-TT--TTAAA
* *
1556683 AATATATTTTA-TTATTATTGTAAATTAAAAACATGT-T-TTATTATTATTTTAACTTTTAAA
1 AATATATTTTACTT-TTATTGTAAATTAAAAA-ATATATACTATT-TTATTTTAACTTTTAAA
1556743 AATATATT
1 AATATATT
1556751 AAAATATTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
60 13 0.22
62 2 0.03
63 10 0.17
64 32 0.53
65 3 0.05
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (60 bp):
AATATATTTTACTTTTATTGTAAATTAAAAAATATATACTATTTTATTTTAACTTTTAAA
Found at i:1556907 original size:29 final size:29
Alignment explanation
Indices: 1556875--1556931 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1556865 ACATTGAAAT
*
1556875 ATATTTAATAAATTAAGACAAAAATAAAA
1 ATATTTAATAAATTAAAACAAAAATAAAA
*
1556904 ATATTTAATAAGTTAAAACAAAAATAAA
1 ATATTTAATAAATTAAAACAAAAATAAA
1556932 GATAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (29 bp):
ATATTTAATAAATTAAAACAAAAATAAAA
Found at i:1558049 original size:30 final size:31
Alignment explanation
Indices: 1558009--1558070 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1557999 AATTTTTTAG
* *
1558009 TCAAAGAAAATAA-TAATTAAATGCTTAACA
1 TCAAACAAAATAACTAATTAAATGATTAACA
*
1558039 TCAAACAAAATAACTAATTAAATTATTAACA
1 TCAAACAAAATAACTAATTAAATGATTAACA
1558070 T
1 T
1558071 ATCAACATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.29
Consensus pattern (31 bp):
TCAAACAAAATAACTAATTAAATGATTAACA
Found at i:1558707 original size:17 final size:18
Alignment explanation
Indices: 1558664--1558706 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1558654 ATTTAATACG
*
1558664 TATCATTTTATTGTATAT
1 TATCTTTTTATTGTATAT
*
1558682 TATCTTTTTATTTTA-AT
1 TATCTTTTTATTGTATAT
1558699 TAT-TTTTT
1 TATCTTTTT
1558707 TTTCAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 5 0.22
17 5 0.22
18 13 0.57
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (18 bp):
TATCTTTTTATTGTATAT
Found at i:1579769 original size:108 final size:108
Alignment explanation
Indices: 1579580--1579833 Score: 321
Period size: 108 Copynumber: 2.4 Consensus size: 108
1579570 AAATATGAAA
* * * *
1579580 ATAACTAAAT-AGTTTAATTACTTATTTTATTATTAATATTATCAACATATTATGTAGCGCCTAA
1 ATAACAAAATAAG-TTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGTAGCGCCTAA
* * * * *
1579644 AATGTTACTAAAATTTAAGTTGATAGGGCCTTAGAAATCTCACT
65 AATGCTACCAAAATTTAAGCTGATAGGGCATTAGAAATCTCACG
* * * *
1579688 ATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGTTGTGCTTAAT
1 ATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGTAGCGCCTAAA
* *
1579753 ATGCTACCAAACTTTAAGCTGATAGGGCATTCGAAATCTCACG
66 ATGCTACCAAAATTTAAGCTGATAGGGCATTAGAAATCTCACG
* * * *
1579796 ACAACAAAATATGTTAAATACGTATTTTGTTATAAATA
1 ATAACAAAATAAGTTAATTACTTATTTTGTTATAAATA
1579834 AATAACATAC
Statistics
Matches: 126, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
108 124 0.98
109 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (108 bp):
ATAACAAAATAAGTTAATTACTTATTTTGTTATAAATATTATCAACATATTAGGTAGCGCCTAAA
ATGCTACCAAAATTTAAGCTGATAGGGCATTAGAAATCTCACG
Found at i:1580098 original size:21 final size:20
Alignment explanation
Indices: 1580074--1580140 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
1580064 CTTAAACTCC
1580074 GTATCGATACTTAGTGTAGAT
1 GTATCGATACTTAGTGTA-AT
* *
1580095 GTATGGA-AATTA-T-TAA-
1 GTATCGATACTTAGTGTAAT
*
1580111 -TACCGATACTTAGTGTATAT
1 GTATCGATACTTAGTGTA-AT
1580131 GTATCGATAC
1 GTATCGATAC
1580141 GTATTCATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
15 4 0.12
16 4 0.12
17 2 0.06
18 4 0.12
19 2 0.06
20 4 0.12
21 14 0.41
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.37
Consensus pattern (20 bp):
GTATCGATACTTAGTGTAAT
Found at i:1580825 original size:77 final size:77
Alignment explanation
Indices: 1580727--1580921 Score: 295
Period size: 76 Copynumber: 2.5 Consensus size: 77
1580717 AAATAAATGA
* *
1580727 TAGGTAGTTTACCGTAATAGGTAGCGCTTATTTTATTTTAAC-GTGTTACATTATTATTATACCT
1 TAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATTTTAACAGT-TTACATTATTATTATACCT
1580791 TTAAACAAACCAG
65 TTAAACAAACCAG
* *
1580804 TGGGTAGTTTAACGTAATAGGTAGCGCCTATTTTA-TTTCACAGTTTACATTATTATTATACCTT
1 TAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATTTTAACAGTTTACATTATTATTATACCTT
* *
1580868 TAAACGAACCGG
66 TAAACAAACCAG
* *
1580880 TAGGTAGTTTAACGTAATAGGTATCACCTATTTTATTTTAAC
1 TAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATTTTAAC
1580922 CGGTTAAGTA
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
76 67 0.63
77 39 0.37
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (77 bp):
TAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATTTTAACAGTTTACATTATTATTATACCTT
TAAACAAACCAG
Found at i:1580955 original size:100 final size:100
Alignment explanation
Indices: 1580837--1581127 Score: 431
Period size: 100 Copynumber: 2.9 Consensus size: 100
1580827 GCGCCTATTT
* * * * * * *
1580837 TATTTCACAGTTTACATTATTATTATACCTTTAAACGAACCGGTAGGTAGTTTAACGTAATAGGT
1 TATTTCACCGGTTACATTAATATTATACATTTAAACAAACCGATAGGTAGTTTAACGTAATATGT
* **
1580902 ATCACCTATTTTATTTTAACCGGTTAAGTAGT-AGA
66 AGCGTCTATTTTATTTTAACCGGTTAAGTAGTGA-A
* *
1580937 TATTTTACCGGTTACATTAATATTATACATTTAAACAAACCGATAGGTAGTTTAACATAATATGT
1 TATTTCACCGGTTACATTAATATTATACATTTAAACAAACCGATAGGTAGTTTAACGTAATATGT
* *
1581002 AGCGTTTATTTTATTTTAACCGGTTAAGTTGTGAA
66 AGCGTCTATTTTATTTTAACCGGTTAAGTAGTGAA
*
1581037 TATTTCACCGGTTACATTAATATTATACATTTCAACAAACCGATAGGTAGTTTAACGTAATATGT
1 TATTTCACCGGTTACATTAATATTATACATTTAAACAAACCGATAGGTAGTTTAACGTAATATGT
1581102 AGCGTCTATTTTATTTTAACCGGTTA
66 AGCGTCTATTTTATTTTAACCGGTTA
1581128 CATTATTATT
Statistics
Matches: 172, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
100 171 0.99
101 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (100 bp):
TATTTCACCGGTTACATTAATATTATACATTTAAACAAACCGATAGGTAGTTTAACGTAATATGT
AGCGTCTATTTTATTTTAACCGGTTAAGTAGTGAA
Found at i:1581168 original size:80 final size:79
Alignment explanation
Indices: 1581043--1581283 Score: 282
Period size: 76 Copynumber: 3.1 Consensus size: 79
1581033 TGAATATTTC
* * * *
1581043 ACCGGTTACATTA-A-TATTATACATTTCAACAAACCGATAGGTAGTTTAACGTAATATGTAGCG
1 ACCGGTTACATTATATTATTATACATTTAAACAAACAGATAGCTAGTTTAACGTAATATGTTGCG
1581106 -TCTATTTTATTTTA
66 CT-TATTTTATTTTA
* *
1581120 ACCGGTTACATTATTATTATTATACATTTAAACAAACAGGTAGCTAGTTTAACTTAATATGTTGC
1 ACCGGTTACATTA-TATTATTATACATTTAAACAAACAGATAGCTAGTTTAACGTAATATGTTGC
*
1581185 GCTTATTTTA-TTTC
65 GCTTATTTTATTTTA
* * * * *
1581199 ACCGTTTACA--ATATAATTATA-ACTTTAAATAAATTA-ATAGCTAGTTTAACGTAATAAGTTG
1 ACCGGTTACATTATATTATTATACA-TTTAAACAAA-CAGATAGCTAGTTTAACGTAATATGTTG
1581260 CGCTTATTTTATTTTA
64 CGCTTATTTTATTTTA
1581276 ACCGGTTA
1 ACCGGTTA
1581284 AATTGTAAAT
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
75 1 0.01
76 51 0.36
77 25 0.18
79 13 0.09
80 50 0.35
81 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (79 bp):
ACCGGTTACATTATATTATTATACATTTAAACAAACAGATAGCTAGTTTAACGTAATATGTTGCG
CTTATTTTATTTTA
Found at i:1581254 original size:76 final size:79
Alignment explanation
Indices: 1581037--1581283 Score: 276
Period size: 80 Copynumber: 3.2 Consensus size: 79
1581027 AAGTTGTGAA
* * * *
1581037 TATTTCACCGGTTAC-AT-TAA-TATTATACATTTCAACAAACCGATAGGTAGTTTAACGTAATA
1 TATTTAACCGGTTACAATATAATTATTATACATTTAAACAAACAGATAGCTAGTTTAACGTAATA
*
1581099 TGTAGCG-TCTATTT
66 TGTTGCGCT-TATTT
* * * *
1581113 TATTTTAACCGGTTACATTATTATTATTATACATTTAAACAAACAGGTAGCTAGTTTAACTTAAT
1 TA-TTTAACCGGTTACAATATAATTATTATACATTTAAACAAACAGATAGCTAGTTTAACGTAAT
1581178 ATGTTGCGCTTATTT
65 ATGTTGCGCTTATTT
* * * *
1581193 TATTTCACCGTTTACAATATAATTA-TA-AC-TTTAAATAAATTA-ATAGCTAGTTTAACGTAAT
1 TATTTAACCGGTTACAATATAATTATTATACATTTAAACAAA-CAGATAGCTAGTTTAACGTAAT
*
1581254 AAGTTGCGCTTATTT
65 ATGTTGCGCTTATTT
1581269 TATTTTAACCGGTTA
1 TA-TTTAACCGGTTA
1581284 AATTGTAAAT
Statistics
Matches: 144, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
76 44 0.31
77 25 0.17
78 3 0.02
79 21 0.15
80 50 0.35
81 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (79 bp):
TATTTAACCGGTTACAATATAATTATTATACATTTAAACAAACAGATAGCTAGTTTAACGTAATA
TGTTGCGCTTATTT
Found at i:1581282 original size:356 final size:352
Alignment explanation
Indices: 1580572--1581375 Score: 1053
Period size: 356 Copynumber: 2.3 Consensus size: 352
1580562 ATTTCAAACA
*
1580572 GTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAAGTAGTT
1 GTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGGTAGTT
* * *
1580637 TAGCGTAATAGGTAACAG-TTATTTTATTTTAACCGGTTAAATTGTAAATATTTTACTGTTCACA
66 TAACGTAATAGGTAAC-GTTTATTTTATTTTAACCGGTTAAATTGTAAATATTTCACGGTTCACA
* * *
1580701 TTAATATTATACAATTAAATAAATGATAGGTAGTTTACCGTAATAGGTAGCGCTTATTTTATTTT
130 TTAATATTATACAATTAAACAAACGATAGGTAGTTTAACGTAATAGGTAGCGCTTATTTTATTTT
* * *
1580766 AACGTGTTACATTATTATTATACCTTTAAACAAACCAGTGGGTAGTTTAACGTAATAGGTAGCGC
195 AACGTGTTACATTATTATTATACATTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGTAGCGC
* * * * ** *
1580831 CTATTTTATTTCACAGTTTACATTATTATTATACCTTTAAACGAACCGGTAGGTAGTTTAACGTA
260 CTATTTTATTTCACAGTTTACAATATAATTATAACTTTAAACAAACCAATAGCTAGTTTAACGTA
*
1580896 ATAGGTATCACCTATTTTATTTTAACCG
325 ATAAGTATCACCTATTTTATTTTAACCG
* * * * * *
1580924 GTTAAGTAGTAGATATTTTACCGGTTACATTAATATTATACATTTAAACAAACCGATAGGTAGTT
1 GTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGGTAGTT
* * * * *
1580989 TAACATAATATGTAGCGTTTATTTTATTTTAACCGGTTAAGTTGTGAATATTTCACCGGTT-ACA
66 TAACGTAATAGGTAACGTTTATTTTATTTTAACCGGTTAAATTGTAAATATTTCA-CGGTTCACA
* * *
1581053 TTAATATTATACATTTCAACAAACCGATAGGTAGTTTAACGTAATATGTAGCG-TCTATTTTATT
130 TTAATATTATACAATTAAACAAA-CGATAGGTAGTTTAACGTAATAGGTAGCGCT-TATTTTATT
* *
1581117 TTAACCG-GTTACATTATTATTATTATACATTTAAACAAA-CAGGTAGCTAGTTTAACTTAATAT
193 TTAA-CGTGTTAC---ATTATTATTATACATTTAAACAAACCA-GTAGCTAGTTTAACGTAATAG
* * * * **
1581180 GTTGCGCTTATTTTATTTCACCGTTTACAATATAATTATAACTTTAAATAAATTAATAGCTAGTT
253 GTAGCGCCTATTTTATTTCACAGTTTACAATATAATTATAACTTTAAACAAACCAATAGCTAGTT
* *
1581245 TAACGTAATAAGT-TGCGCTTATTTTATTTTAACCG
318 TAACGTAATAAGTAT-CACCTATTTTATTTTAACCG
* * *
1581280 GTTAAATTGTAAATATTTTAACGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTT
1 GTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGGTAGTT
* *
1581345 TAACGTAATAGGTATCGTCTATTTTATTTTA
66 TAACGTAATAGGTAACGTTTATTTTATTTTA
1581376 CCGTTTACAT
Statistics
Matches: 387, Mismatches: 55, Indels: 16
0.84 0.12 0.03
Matches are distributed among these distances:
351 1 0.00
352 128 0.33
353 48 0.12
354 2 0.01
355 3 0.01
356 205 0.53
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (352 bp):
GTTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGGTAGTT
TAACGTAATAGGTAACGTTTATTTTATTTTAACCGGTTAAATTGTAAATATTTCACGGTTCACAT
TAATATTATACAATTAAACAAACGATAGGTAGTTTAACGTAATAGGTAGCGCTTATTTTATTTTA
ACGTGTTACATTATTATTATACATTTAAACAAACCAGTAGCTAGTTTAACGTAATAGGTAGCGCC
TATTTTATTTCACAGTTTACAATATAATTATAACTTTAAACAAACCAATAGCTAGTTTAACGTAA
TAAGTATCACCTATTTTATTTTAACCG
Found at i:1581346 original size:176 final size:176
Alignment explanation
Indices: 1581132--1581449 Score: 460
Period size: 176 Copynumber: 1.8 Consensus size: 176
1581122 CGGTTACATT
* *
1581132 ATTATTATTATACATTTAAACAAACAGGTAGCTAGTTTAACTTAATATGT-TGCG-CTTATTTTA
1 ATTATTATTATACATTTAAACAAACAGGTAGCTAGTTTAACGTAATAGGTAT-CGTC-TATTTTA
* *
1581195 TTTCACCGTTTACAATATAATTATAACTTTAAATAAATTAATAGCTAGTTTAACGTAATAAGTTG
64 TTTCACCGTTTACAATATAATTATAACTTTAAACAAATCAATAGCTAGTTTAACGTAATAAGTTG
* *
1581260 CGCTTATTTTATTTTAACCGGTTAAATTGTAAATATTTTAACGTTTAC
129 AGCCTATTTTATTTTAACCGGTTAAATTGTAAATATTTTAACGTTTAC
* *
1581308 ATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGTATCGTCTATTTTATT
1 ATTATTATTATACATTTAAACAAACAGGTAGCTAGTTTAACGTAATAGGTATCGTCTATTTTATT
* * * * ** * *
1581373 TTACCGTTTACATTATTATTATACCTTTAAACAAATCGGTAGTTAGTTTAACGTAATAGGTTGAG
66 TCACCGTTTACAATATAATTATAACTTTAAACAAATCAATAGCTAGTTTAACGTAATAAGTTGAG
1581438 CCTATTTTATTT
131 CCTATTTTATTT
1581450 CACCGTTTAC
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
176 122 0.98
177 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.43
Consensus pattern (176 bp):
ATTATTATTATACATTTAAACAAACAGGTAGCTAGTTTAACGTAATAGGTATCGTCTATTTTATT
TCACCGTTTACAATATAATTATAACTTTAAACAAATCAATAGCTAGTTTAACGTAATAAGTTGAG
CCTATTTTATTTTAACCGGTTAAATTGTAAATATTTTAACGTTTAC
Found at i:1581392 original size:76 final size:75
Alignment explanation
Indices: 1581293--1581527 Score: 364
Period size: 76 Copynumber: 3.1 Consensus size: 75
1581283 AAATTGTAAA
* *
1581293 TATTTTAACGTTTACATTATTATTATACCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGTTAGTTTAACGTAATAGGT
1581358 AT-CGTCTATTT
66 -TGCG-CTATTT
*
1581369 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAATCGGTAGTTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGTTAGTTTAACGTAATAGGT
*
1581434 TGAGCCTATTT
66 TGCG-CTATTT
* **
1581445 TATTTCACCGTTTACATTATTATTATACCTTTAAACAAACTAGTAGTTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGTTAGTTTAACGTAATAGGT
1581510 TGCGCTTATTT
66 TGCGC-TATTT
1581521 TATTTTA
1 TATTTTA
1581528 ACAGGTTATG
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
75 2 0.01
76 144 0.99
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.44
Consensus pattern (75 bp):
TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAGTTAGTTTAACGTAATAGGT
TGCGCTATTT
Found at i:1581951 original size:69 final size:70
Alignment explanation
Indices: 1581818--1581978 Score: 193
Period size: 69 Copynumber: 2.3 Consensus size: 70
1581808 ATTTTCTATC
* * * * * *
1581818 TATTTTTTAAATTCGAAAATATTGATATTTGTGGAGAAATATTGAAACTTTATGGCATTCTCATT
1 TATTTTTTAAATTCGAAAGTATCGATATTTGTAGAAAAATATTGAAACTTTACGGCATTATCATT
1581883 TTTCA
66 TTTCA
* * * *
1581888 T-TTTTTTAAATTTGAAAGTATCGATATTTGTAGAAAAATATTGATATTTTGCGGTC-TTATCAT
1 TATTTTTTAAATTCGAAAGTATCGATATTTGTAGAAAAATATTGAAACTTTACGG-CATTATCAT
1581951 TTTTCA
65 TTTTCA
1581957 TATCTTTTT-AATTCGAAAGTAT
1 TAT-TTTTTAAATTCGAAAGTAT
1581979 TTATACTTGC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
69 57 0.74
70 15 0.19
71 5 0.06
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (70 bp):
TATTTTTTAAATTCGAAAGTATCGATATTTGTAGAAAAATATTGAAACTTTACGGCATTATCATT
TTTCA
Found at i:1583132 original size:24 final size:25
Alignment explanation
Indices: 1583096--1583142 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1583086 TATATATATA
1583096 TATATTAATAA-TTTAAATTTTATT
1 TATATTAATAATTTTAAATTTTATT
1583120 TATA-TAATGAATTTTAAATTTTA
1 TATATTAAT-AATTTTAAATTTTA
1583143 AGGATTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TATATTAATAATTTTAAATTTTATT
Found at i:1597991 original size:2 final size:2
Alignment explanation
Indices: 1597984--1598033 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1597974 TCTTACAATA
1597984 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
1598026 AT AT AT AT
1 AT AT AT AT
1598034 GAGTATTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1604082 original size:2 final size:2
Alignment explanation
Indices: 1604075--1604124 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1604065 AATTCTATCA
1604075 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
1604117 AT AT AT AT
1 AT AT AT AT
1604125 TAATTTAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1604846 original size:37 final size:36
Alignment explanation
Indices: 1604771--1604846 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1604761 TTTTTATATT
*
1604771 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1604807 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1604844 TTT
1 TTT
1604847 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1605028 original size:20 final size:20
Alignment explanation
Indices: 1604992--1605029 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1604982 ATCCTATTCC
**
1604992 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1605012 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1605030 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1618613 original size:14 final size:12
Alignment explanation
Indices: 1618582--1618606 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1618572 TATAAATAAA
1618582 TATATAAAATTT
1 TATATAAAATTT
1618594 TATATAAAATTT
1 TATATAAAATTT
1618606 T
1 T
1618607 CTCTATATTA
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):
TATATAAAATTT
Found at i:1627903 original size:3 final size:3
Alignment explanation
Indices: 1627895--1627919 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1627885 TCATCGTCGG
1627895 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1627920 ATTTCCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1635324 original size:20 final size:21
Alignment explanation
Indices: 1635270--1635332 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1635260 GATTCCCATG
1635270 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1635294 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1635314 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1635333 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1639186 original size:22 final size:21
Alignment explanation
Indices: 1639144--1639183 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1639134 GAGTTTGTTT
*
1639144 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1639165 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1639184 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1642282 original size:35 final size:35
Alignment explanation
Indices: 1642236--1642306 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1642226 TATGCCTTCC
1642236 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
1 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
1642271 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
1 ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
1642306 A
1 A
1642307 TCATCTGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (35 bp):
ACGGTGGTTGACGCTTCACATCATAAATCATCTCA
Done.