Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 23
Found at i:4224147 original size:43 final size:44
Alignment explanation
Indices: 4224083--4224169 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
4224073 TCATGCATCA
* * *
4224083 AACAAAACTTTTACATGTAGGGGACAGCTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* *
4224127 AACAAAAC-TTTACATATAGGGGATAACTTTCTCTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
4224170 TCTAAATCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 30 0.79
44 8 0.21
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:4228439 original size:117 final size:118
Alignment explanation
Indices: 4228228--4228441 Score: 265
Period size: 117 Copynumber: 1.8 Consensus size: 118
4228218 ATCTTATTTT
*
4228228 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGGAGTTAGAGCTTTCAAAAA
1 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
*
4228293 TAAAATCGGAAAACTTTGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
66 TAAAATCGGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
* * * * *
4228346 GAAA-CTAAAATGGATTTTGAAAA-ACAAAATGAAAT-TTCGAAGAAGAATTTAGAGCTTTCAAA
1 GAAAGCTAAAAAGGACTTGGAAAATA-AAAATGAAATGTT-GAAAAAGAAGTTAGAGCTTTCAAA
* ** * *
4228408 GATAAAAT-TTAAAAGTATGGAAAAGGAAATTTTC
64 AATAAAATCGGAAAACT-TGGAAAAAGAAATTTTC
4228442 GATTTAGAAG
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
116 8 0.10
117 69 0.85
118 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (118 bp):
GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
TAAAATCGGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
Found at i:4228999 original size:20 final size:21
Alignment explanation
Indices: 4228966--4229005 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
4228956 TTTTAACATA
**
4228966 ATTGATATTCATTTT-AAACC
1 ATTGATATAAATTTTCAAACC
4228986 ATTGATATAAATTTTCAAAC
1 ATTGATATAAATTTTCAAAC
4229006 AATTTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATAAATTTTCAAACC
Found at i:4234306 original size:15 final size:15
Alignment explanation
Indices: 4234286--4234327 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
4234276 TTGTTTCAAC
*
4234286 ATTTTGGATTGTTTG
1 ATTTTGGATTGTTGG
4234301 ATTTTGTGGATTGTTGG
1 A-TTT-TGGATTGTTGG
4234318 ATTTTGGATT
1 ATTTTGGATT
4234328 TATGAATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:4234312 original size:17 final size:17
Alignment explanation
Indices: 4234290--4234323 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4234280 TTCAACATTT
*
4234290 TGGATTGTTTGATTTTG
1 TGGATTGTTGGATTTTG
4234307 TGGATTGTTGGATTTTG
1 TGGATTGTTGGATTTTG
4234324 GATTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTG
Found at i:4235912 original size:28 final size:29
Alignment explanation
Indices: 4235840--4235924 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 29
4235830 TTTGATAAAC
* *
4235840 AAATA-AAAATGAAAT-TTAAT-AT-CTA
1 AAATATAAAATAAAATATTAATAATAATA
*
4235865 AAA-ATAAAATAAAAAAATTAATAATAATA
1 AAATATAAAAT-AAAATATTAATAATAATA
4235894 AAATATAAAAT-AAATATT-ATAAGTAATA
1 AAATATAAAATAAAATATTAATAA-TAATA
4235922 AAA
1 AAA
4235925 ATTTTGAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
24 1 0.02
25 8 0.16
26 3 0.06
27 9 0.18
28 16 0.33
29 5 0.10
30 7 0.14
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (29 bp):
AAATATAAAATAAAATATTAATAATAATA
Found at i:4236578 original size:11 final size:11
Alignment explanation
Indices: 4236562--4236589 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4236552 TTCTCTAAAA
4236562 ATAATTAATAT
1 ATAATTAATAT
4236573 ATAATTAATAT
1 ATAATTAATAT
4236584 ATAATT
1 ATAATT
4236590 TATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATAATTAATAT
Found at i:4236824 original size:3 final size:3
Alignment explanation
Indices: 4236816--4236843 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4236806 ATATATATTT
4236816 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4236844 ATATATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4238295 original size:3 final size:3
Alignment explanation
Indices: 4238287--4238345 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
4238277 TAAAATTATT
* * *
4238287 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TTA TAA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4238334 TAA TAA TAA TAA
1 TAA TAA TAA TAA
4238346 AACCGGGATA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4244275 original size:21 final size:21
Alignment explanation
Indices: 4244249--4244292 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
4244239 TGACTCAACT
4244249 CATATTATAAGAGTTGAAAAA
1 CATATTATAAGAGTTGAAAAA
4244270 CATATTATAAGAGTTGAAAAA
1 CATATTATAAGAGTTGAAAAA
4244291 CA
1 CA
4244293 CTTAATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (21 bp):
CATATTATAAGAGTTGAAAAA
Found at i:4246449 original size:45 final size:45
Alignment explanation
Indices: 4246385--4246583 Score: 149
Period size: 44 Copynumber: 4.5 Consensus size: 45
4246375 ACATATTTAC
4246385 CCTGTGCACAAAGCAGAGGAGCATGTA-AAAATGGTAAGGTCTTAT
1 CCTGTGCACAAAGCAGAGGAGCATG-AGAAAATGGTAAGGTCTTAT
*
4246430 CCTGTGCACACAA-CAGAGGAGCCTGAGAAAATGGTAAGGTCTTAT
1 CCTGTGCACA-AAGCAGAGGAGCATGAGAAAATGGTAAGGTCTTAT
* * * * ** * **
4246475 CAT-TGCACATAGCAAAAGAGTTTGCGGTAATGGTAAGGTCTTAT
1 CCTGTGCACAAAGCAGAGGAGCATGAGAAAATGGTAAGGTCTTAT
* * * * * **
4246519 CCT-TGCA-AATGACAAATGAACATGTGGTAATGGTAAGGTCTTAT
1 CCTGTGCACAAAG-CAGAGGAGCATGAGAAAATGGTAAGGTCTTAT
* * *
4246563 CCT-TACACATAGCAAAGGAGC
1 CCTGTGCACAAAGCAGAGGAGC
4246584 CTACGGTAAC
Statistics
Matches: 126, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
43 3 0.02
44 78 0.62
45 43 0.34
46 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (45 bp):
CCTGTGCACAAAGCAGAGGAGCATGAGAAAATGGTAAGGTCTTAT
Found at i:4246592 original size:44 final size:44
Alignment explanation
Indices: 4246414--4246598 Score: 167
Period size: 44 Copynumber: 4.2 Consensus size: 44
4246404 AGCATGTAAA
* * * **
4246414 AATGGTAAGGTCTTATCCTGTGCACACAACAGAGGAGCCTGA-GAA
1 AATGGTAAGGTCTTATCCT-TGCACATAGCAAAGGAGCCT-ACGGT
* * ** *
4246459 AATGGTAAGGTCTTATCATTGCACATAGCAAAAGAGTTTGCGGT
1 AATGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCCTACGGT
* * * * **
4246503 AATGGTAAGGTCTTATCCTTGCAAAT-GACAAATGAACATGTGGT
1 AATGGTAAGGTCTTATCCTTGCACATAG-CAAAGGAGCCTACGGT
*
4246547 AATGGTAAGGTCTTATCCTTACACATAGCAAAGGAGCCTACGGT
1 AATGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCCTACGGT
*
4246591 AACGGTAA
1 AATGGTAA
4246599 CTAATCATTT
Statistics
Matches: 112, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
43 1 0.01
44 92 0.82
45 19 0.17
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (44 bp):
AATGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCCTACGGT
Found at i:4259405 original size:23 final size:24
Alignment explanation
Indices: 4259373--4259424 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
4259363 GGAATCGATA
* * * *
4259373 CCCCTCTTGAAGGGGAACTGATTC
1 CCCCTCTTGAAAGAGAACCGACTC
4259397 CCCCT-TTGAAAGAGAACCGACTC
1 CCCCTCTTGAAAGAGAACCGACTC
4259420 CCCCT
1 CCCCT
4259425 GTAGGGGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (24 bp):
CCCCTCTTGAAAGAGAACCGACTC
Found at i:4264923 original size:19 final size:19
Alignment explanation
Indices: 4264899--4264935 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4264889 GGGTCAGCTG
*
4264899 GTTCAGACCGGTGTGGCCA
1 GTTCAGACCGGTCTGGCCA
4264918 GTTCAGACCGGTCTGGCC
1 GTTCAGACCGGTCTGGCC
4264936 GGTCAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.30, G:0.35, T:0.22
Consensus pattern (19 bp):
GTTCAGACCGGTCTGGCCA
Found at i:4269261 original size:18 final size:19
Alignment explanation
Indices: 4269238--4269280 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
4269228 AAAAAAATGA
*
4269238 TTTGTTTG-ATGCATTTAT
1 TTTGTTTGCATGCATTTAC
*
4269256 TTTG-TTGCATTCATTTAC
1 TTTGTTTGCATGCATTTAC
4269274 TTTGTTT
1 TTTGTTT
4269281 ATCTTGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 16 0.76
19 2 0.10
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (19 bp):
TTTGTTTGCATGCATTTAC
Found at i:4270258 original size:10 final size:10
Alignment explanation
Indices: 4270245--4270290 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
4270235 ATTTTTAAAG
4270245 TTCTTTACTT
1 TTCTTTACTT
4270255 TTCTTTA-TT
1 TTCTTTACTT
*
4270264 TTCTTTAAGTT
1 TTCTTT-ACTT
4270275 TTCTTTTAC-T
1 TTC-TTTACTT
4270285 TTCTTT
1 TTCTTT
4270291 TGAAAACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 11 0.34
10 12 0.38
11 6 0.19
12 3 0.09
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72
Consensus pattern (10 bp):
TTCTTTACTT
Found at i:4274561 original size:21 final size:21
Alignment explanation
Indices: 4274536--4274584 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
4274526 CTAAAATAAT
*
4274536 AAAAATATT-ATTTTTATTCAA
1 AAAAATATTGA-TTTAATTCAA
*
4274557 AAAAATATTGATTTAATTGAA
1 AAAAATATTGATTTAATTCAA
4274578 AAAAATA
1 AAAAATA
4274585 ATATATAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (21 bp):
AAAAATATTGATTTAATTCAA
Found at i:4277142 original size:36 final size:36
Alignment explanation
Indices: 4277087--4277223 Score: 220
Period size: 36 Copynumber: 3.8 Consensus size: 36
4277077 ATTTATCCAT
* *
4277087 TATCAGCTTTGATATATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
**
4277123 TATCATTTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
4277159 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
4277195 TATCAGCTTTGGTACATTTGTGTATCAAT
1 TATCAGCTTTGGTACATTCGTGTATCAAT
4277224 ATCTAGAACC
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 92 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:4277851 original size:14 final size:14
Alignment explanation
Indices: 4277832--4277864 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4277822 TAGAACTATT
4277832 TTAGTTTA-TTTTA
1 TTAGTTTAGTTTTA
4277845 CTTAGTTTAGTTTTA
1 -TTAGTTTAGTTTTA
4277860 TTAGT
1 TTAGT
4277865 ATATATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (14 bp):
TTAGTTTAGTTTTA
Found at i:4284160 original size:23 final size:22
Alignment explanation
Indices: 4284084--4284152 Score: 88
Period size: 23 Copynumber: 3.2 Consensus size: 22
4284074 GAGGGCATCA
*
4284084 GTTCCC-T-CAAGGGGGAATCA
1 GTTCCCATGCAAGGGGGAATCG
*
4284104 GTTCCCATTCAAAGGGGGAATCG
1 GTTCCCATGC-AAGGGGGAATCG
*
4284127 GTTCCCATGCAAGGGGGTATCG
1 GTTCCCATGCAAGGGGGAATCG
4284149 GTTC
1 GTTC
4284153 TTCCTGCACT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 6 0.14
21 1 0.02
22 16 0.37
23 20 0.47
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (22 bp):
GTTCCCATGCAAGGGGGAATCG
Found at i:4288238 original size:117 final size:117
Alignment explanation
Indices: 4288018--4288238 Score: 277
Period size: 117 Copynumber: 1.9 Consensus size: 117
4288008 CTTTCAAATC
* * *
4288018 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCTTCAACATTT
* *
4288083 CATTTTGATTTTCAAAATACATTTTTGTTTCTAGAAGAAACTTGTTTAATTT
66 CATTTTGATTTTCAAAATACATTTTAGTTTCTAAAAGAAACTTGTTTAATTT
* * * * *
4288135 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTCGTTTTTAAAAGCTCTAACTCATT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCT-TCAACAT
* **
4288198 TTCATTTTGATTTTCTAAATATGTTTTAGCTTTC-AAAAGAA
64 TTCATTTTGATTTTCAAAATACATTTTAG-TTTCTAAAAGAA
4288239 GATCATTTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 2 0.02
117 82 0.93
118 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATACATTTTAGTTTCTAAAAGAAACTTGTTTAATTT
Found at i:4300870 original size:21 final size:21
Alignment explanation
Indices: 4300844--4300883 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4300834 CCCCCTTTGA
*
4300844 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
4300865 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
4300884 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:4305128 original size:24 final size:24
Alignment explanation
Indices: 4305100--4305146 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
4305090 TCGAAAGTTT
4305100 AAGAATTCACAATTTGTGACTTAA
1 AAGAATTCACAATTTGTGACTTAA
*
4305124 AAGAATTCACAATTTGTGGCTTA
1 AAGAATTCACAATTTGTGACTTA
4305147 TTTGTGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (24 bp):
AAGAATTCACAATTTGTGACTTAA
Found at i:4305772 original size:36 final size:36
Alignment explanation
Indices: 4305732--4305822 Score: 173
Period size: 36 Copynumber: 2.5 Consensus size: 36
4305722 TCACCTTTGA
4305732 TACATTCGTGTATCAATGTTATCATATCAGCTTTTC
1 TACATTCGTGTATCAATGTTATCATATCAGCTTTTC
*
4305768 TACATTCGTGTATCAATGTTATCATATCAGCTTTTG
1 TACATTCGTGTATCAATGTTATCATATCAGCTTTTC
4305804 TACATTCGTGTATCAATGT
1 TACATTCGTGTATCAATGT
4305823 CCAACACCGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (36 bp):
TACATTCGTGTATCAATGTTATCATATCAGCTTTTC
Found at i:4307772 original size:14 final size:14
Alignment explanation
Indices: 4307753--4307785 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4307743 TAGAATTATT
4307753 TTAGTTTA-TTTTA
1 TTAGTTTAGTTTTA
4307766 CTTAGTTTAGTTTTA
1 -TTAGTTTAGTTTTA
4307781 TTAGT
1 TTAGT
4307786 ATCTATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (14 bp):
TTAGTTTAGTTTTA
Found at i:4316763 original size:20 final size:20
Alignment explanation
Indices: 4316730--4316779 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
4316720 TACAAAATCG
* *
4316730 CAACGAGATACTGACTTTCA
1 CAACGCGATTCTGACTTTCA
* *
4316750 CAACTCGATTCTGACTTTCG
1 CAACGCGATTCTGACTTTCA
4316770 CAACGCGATT
1 CAACGCGATT
4316780 TACATAGCGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (20 bp):
CAACGCGATTCTGACTTTCA
Found at i:4317377 original size:19 final size:19
Alignment explanation
Indices: 4317355--4317533 Score: 136
Period size: 19 Copynumber: 10.1 Consensus size: 19
4317345 GAAACCAAAA
*
4317355 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4317374 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
4317388 TCTCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4317407 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4317426 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
4317440 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
4317459 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
4317473 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
4317492 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
4317512 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
4317532 TC
1 TC
4317534 AACCAAAAGA
Statistics
Matches: 127, Mismatches: 16, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
14 29 0.23
16 7 0.06
17 8 0.06
19 51 0.40
20 31 0.24
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4317438 original size:52 final size:52
Alignment explanation
Indices: 4317355--4317471 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
4317345 GAAACCAAAA
* **
4317355 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATT
*
4317407 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATT
4317459 TCGCGTTGCGATT
1 TCGCGTTGCGATT
4317472 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTACGATAGTCATT
Found at i:4317447 original size:33 final size:33
Alignment explanation
Indices: 4317410--4317508 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
4317400 TTTCATTTCG
**
4317410 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
4317443 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
4317476 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
4317509 ATTATCTCGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 48 0.76
34 15 0.24
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:4317448 original size:14 final size:14
Alignment explanation
Indices: 4317429--4317484 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
4317419 TTTCATTTCG
4317429 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4317443 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
4317462 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4317476 CGTTGCGAT
1 CGTTGCGAT
4317485 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4319702 original size:21 final size:21
Alignment explanation
Indices: 4319678--4319744 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
4319668 TCATTCCTCG
4319678 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
4319699 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
4319720 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
4319741 AGAG
1 AGAG
4319745 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:4319702 original size:42 final size:42
Alignment explanation
Indices: 4319626--4319744 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
4319616 GACTCGCCTT
* * * *
4319626 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
4319668 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
4319710 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
4319745 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:4321121 original size:14 final size:14
Alignment explanation
Indices: 4321102--4321137 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4321092 ATTGTTTAAT
4321102 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
4321116 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4321130 TGATTTGT
1 TGATTTGT
4321138 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:4321268 original size:19 final size:19
Alignment explanation
Indices: 4321244--4321310 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
4321234 AAAAAGTACT
4321244 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4321263 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
4321277 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4321296 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
4321311 TCACGTTGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4321334 original size:33 final size:33
Alignment explanation
Indices: 4321297--4321439 Score: 177
Period size: 33 Copynumber: 4.3 Consensus size: 33
4321287 GAAATGAAAA
*
4321297 TCGCAATGCGAAATTCACGTTGCGATTTTCATT
1 TCGCATTGCGAAATTCACGTTGCGATTTTCATT
*
4321330 TCGCATTGCG--ATTCCCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATT--CACGTTGCGATTTTCATT
*
4321363 TCGCATTGCGAAATT-AGCTTTGCGATTTTCATT
1 TCGCATTGCGAAATTCA-CGTTGCGATTTTCATT
* *
4321396 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAAT-TCACGTTGCGATTTTCATT
4321429 TCGCATTGCGA
1 TCGCATTGCGA
4321440 TAGTAATTTC
Statistics
Matches: 95, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
31 3 0.03
32 2 0.02
33 87 0.92
35 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (33 bp):
TCGCATTGCGAAATTCACGTTGCGATTTTCATT
Found at i:4321340 original size:19 final size:19
Alignment explanation
Indices: 4321316--4321440 Score: 91
Period size: 19 Copynumber: 7.4 Consensus size: 19
4321306 GAAATTCACG
4321316 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
4321335 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
4321349 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
4321368 TTGCGA-----AATTAGCT
1 TTGCGATTTTCATTTCGCA
4321382 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4321401 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4321415 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4321434 TTGCGAT
1 TTGCGAT
4321441 AGTAATTTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 30
0.65 0.10 0.25
Matches are distributed among these distances:
14 23 0.29
16 13 0.16
17 13 0.16
19 30 0.38
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4321375 original size:66 final size:66
Alignment explanation
Indices: 4321297--4321439 Score: 243
Period size: 66 Copynumber: 2.2 Consensus size: 66
4321287 GAAATGAAAA
*
4321297 TCGCAATGCGAAATTCA-CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCA
1 TCGCATTGCGAAATT-AGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCA
4321361 TT
65 TT
* *
4321363 TCGCATTGCGAAATTAGCTTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCATTGCGAAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
4321428 T
66 T
4321429 TCGCATTGCGA
1 TCGCATTGCGA
4321440 TAGTAATTTC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
65 1 0.01
66 72 0.99
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
TCGCATTGCGAAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
T
Found at i:4321440 original size:33 final size:33
Alignment explanation
Indices: 4321314--4321440 Score: 195
Period size: 33 Copynumber: 3.8 Consensus size: 33
4321304 GCGAAATTCA
4321314 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
**
4321347 CGTTGCGATTTTCATTTCGCATTGCGAAATTAGCT
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCCT
*
4321382 --TTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
4321413 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4321441 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 5 0.06
33 76 0.88
35 5 0.06
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:4323749 original size:12 final size:12
Alignment explanation
Indices: 4323732--4323756 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4323722 TCTTCGGGGA
4323732 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4323744 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4323756 C
1 C
4323757 AGGATTATAT
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:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:4324800 original size:21 final size:20
Alignment explanation
Indices: 4324757--4324808 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
4324747 TTTTCCTAAT
*
4324757 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
4324777 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
4324798 TCGCAACGCGA
1 TCGCAATGCGA
4324809 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:4324882 original size:20 final size:20
Alignment explanation
Indices: 4324793--4324884 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
4324783 TGCGAATTTG
*
4324793 GAAAATCGCAACGCGATACT
1 GAAAATCGCAACGAGATACT
** *
4324813 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
4324833 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
** *
4324854 -AACTTTCGCAACGAGATTCT
1 GAA-AATCGCAACGAGATACT
4324874 GAAAATCGCAA
1 GAAAATCGCAA
4324885 TCATCTTCAA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.04
20 37 0.66
21 17 0.30
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:4325153 original size:20 final size:20
Alignment explanation
Indices: 4325098--4325144 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
4325088 CAACGGGGAA
4325098 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
4325118 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
4325138 ATCGCAA
1 ATCGCAA
4325145 TGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:4325199 original size:14 final size:16
Alignment explanation
Indices: 4325180--4325249 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 16
4325170 AATCGCATTA
4325180 CGATTTTC-TCG-TTG
1 CGATTTTCTTCGATTG
4325194 CGATTTTCATTTCGCATTG
1 CGATTTTC--TTCG-ATTG
4325213 CGATTTTCATTTCGCATTG
1 CGATTTTC--TTCG-ATTG
4325232 CGATTTTC-TCG-TTG
1 CGATTTTCTTCGATTG
4325246 CGAT
1 CGAT
4325250 AGTCAGTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
14 15 0.29
16 3 0.06
17 3 0.06
19 30 0.59
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (16 bp):
CGATTTTCTTCGATTG
Found at i:4325213 original size:19 final size:19
Alignment explanation
Indices: 4325191--4325239 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
4325181 GATTTTCTCG
4325191 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4325210 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4325229 TTGCGATTTTC
1 TTGCGATTTTC
4325240 TCGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4325395 original size:14 final size:14
Alignment explanation
Indices: 4325376--4325412 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4325366 CATCAATTAA
4325376 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
4325390 ACAAATCATCTTTT
1 ACAAATCAACATTT
4325404 ACAAATCAA
1 ACAAATCAA
4325413 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:4327304 original size:20 final size:19
Alignment explanation
Indices: 4327281--4327348 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
4327271 GAAACTTAAA
4327281 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
4327301 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
4327321 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
4327340 ATCGCAACG
1 ATCGCAACG
4327349 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4327356 original size:14 final size:14
Alignment explanation
Indices: 4327337--4327426 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
4327327 ATGCGAAATG
*
4327337 AAAATCGCAACGAC
1 AAAATCGCAACGAA
4327351 AAAATCGCAATGCGAAA
1 AAAATCGCAA--CG-AA
*
4327368 TGAAAATCGCAACGAC
1 --AAAATCGCAACGAA
4327384 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
4327400 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
4327416 AAAATCGCAAC
1 AAAATCGCAAC
4327427 TCGAAACACA
Statistics
Matches: 64, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
14 30 0.47
16 12 0.19
17 3 0.05
18 9 0.14
19 10 0.16
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:4327432 original size:32 final size:33
Alignment explanation
Indices: 4327321--4327425 Score: 194
Period size: 33 Copynumber: 3.2 Consensus size: 33
4327311 GGAAATGGCT
4327321 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
4327354 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
4327387 ATCGCAATGCGAAATG-AAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
4327419 ATCGCAA
1 ATCGCAA
4327426 CTCGAAACAC
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 22 0.31
33 49 0.69
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:4327440 original size:65 final size:66
Alignment explanation
Indices: 4327321--4327443 Score: 189
Period size: 65 Copynumber: 1.9 Consensus size: 66
4327311 GGAAATGGCT
* *
4327321 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAAATCGCAATGCGAAATCAAAATCGCAACGACAA
4327386 A
66 A
4327387 ATCGCAATGCGAAATG-AAATCGCAACGAAAAAATCGCAACT-CGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAAATCGCAA-TGCGAAATCA-AAATCGCA
4327444 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
64 1 0.02
65 35 0.66
66 17 0.32
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAAATCGCAATGCGAAATCAAAATCGCAACGACAA
A
Found at i:4327461 original size:19 final size:19
Alignment explanation
Indices: 4327439--4327535 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
4327429 GAAACACAAA
4327439 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4327458 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
4327474 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4327491 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
4327507 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4327524 TTGCATTGCGAT
1 TCGCATTGCGAT
4327536 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 7 0.11
18 6 0.10
19 24 0.38
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:4327482 original size:14 final size:14
Alignment explanation
Indices: 4327463--4327519 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4327453 TCATTTCGCA
4327463 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
4327477 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
4327494 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
4327510 TTGCGATTTT
1 TTGCGATTTT
4327520 CATTTTGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:4327486 original size:33 final size:33
Alignment explanation
Indices: 4327444--4327535 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
4327434 ACAAATCGCA
4327444 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
4327477 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
4327510 TTGCGATTTTCATTTTGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
4327536 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:4327554 original size:20 final size:20
Alignment explanation
Indices: 4327529--4327574 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
4327519 TCATTTTGCA
4327529 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
4327549 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
4327569 TTGCGA
1 TTGCGA
4327575 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:4328082 original size:18 final size:18
Alignment explanation
Indices: 4328056--4328100 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4328046 GTCGATCAGA
*
4328056 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
4328074 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
4328092 TGATGGCTC
1 TGATGGCTC
4328101 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:4329445 original size:20 final size:20
Alignment explanation
Indices: 4329420--4329503 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
4329410 AATAGTTTCT
**
4329420 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACAC
4329440 GAAAATGACTATCGCAACAC
1 GAAAATGACTATCGCAACAC
*
4329460 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
** *
4329480 GAATTTGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
4329500 GAAA
1 GAAA
4329504 CTAAAATCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:4329475 original size:40 final size:40
Alignment explanation
Indices: 4329420--4329513 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
4329410 AATAGTTTCT
4329420 GAAAATGAAAATCGCAACACGAAAATGACTATCGCAACAC
1 GAAAATGAAAATCGCAACACGAAAATGACTATCGCAACAC
** * ** *
4329460 GAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACACGAAAATGACTATCGCAACAC
*
4329500 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
4329514 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 6 0.13
40 39 0.87
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (40 bp):
GAAAATGAAAATCGCAACACGAAAATGACTATCGCAACAC
Found at i:4329774 original size:22 final size:22
Alignment explanation
Indices: 4329747--4329790 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4329737 GATGGAGATA
*
4329747 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
4329769 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
4329791 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:4330064 original size:20 final size:20
Alignment explanation
Indices: 4329978--4330092 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
4329968 GCTTATGTAT
* *
4329978 TATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGATAGTCAG
* * *
4329998 AATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGATAGTCAG
* * * *
4330018 TATCTCGTTGCGATTTTGT-AT
1 TATCGCATTGCGA--TAGTCAG
4330039 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
4330059 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
4330079 TATCGCATTGCGAT
1 TATCGCATTGCGAT
4330093 TTTCCCAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 65 0.79
21 12 0.15
22 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAG
Found at i:4330064 original size:61 final size:61
Alignment explanation
Indices: 4329958--4330095 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
4329948 CGCTTTGAAA
* * * *
4329958 ATCGCATTGCGCTTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
* * * * *
4330019 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
4330080 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
4330096 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
Found at i:4330110 original size:21 final size:21
Alignment explanation
Indices: 4330081--4330152 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 21
4330071 ATAGTCAGTA
* *
4330081 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
**
4330102 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTACCAAT
**
4330122 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTACCAAT
*
4330142 TCGCATTGCGA
1 TCGCGTTGCGA
4330153 ATTGGGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 36 0.78
21 10 0.22
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTACCAAT
Found at i:4330111 original size:61 final size:61
Alignment explanation
Indices: 4329978--4330113 Score: 166
Period size: 61 Copynumber: 2.2 Consensus size: 61
4329968 GCTTATGTAT
* * * * ** *
4329978 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAA
* * *
4330039 TATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAA
4330101 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
4330114 TTACTTATTC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 61 0.97
62 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAA
Found at i:4330125 original size:20 final size:20
Alignment explanation
Indices: 4330100--4330152 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
4330090 GATTTTCCCA
4330100 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
4330120 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
*
4330140 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
4330153 ATTGGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:4330223 original size:21 final size:21
Alignment explanation
Indices: 4330183--4330223 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4330173 ACTGTAGACC
** *
4330183 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
4330204 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
4330224 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:4335636 original size:12 final size:12
Alignment explanation
Indices: 4335621--4335650 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
4335611 AGAGCAGGCA
4335621 AGATCATGCATT
1 AGATCATGCATT
4335633 AGATCATGCATT
1 AGATCATGCATT
4335645 ATGATC
1 A-GATC
4335651 CGAAAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (12 bp):
AGATCATGCATT
Found at i:4336906 original size:74 final size:74
Alignment explanation
Indices: 4336782--4337112 Score: 556
Period size: 74 Copynumber: 4.5 Consensus size: 74
4336772 TAACCTATTT
4336782 TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATG
1 TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATG
4336847 CTAGTTGAA
66 CTAGTTGAA
* * *
4336856 TGGGCATTATCATTATCAAAATTGAGCATTATCAAGAAATCACAATTTTGACCATATTTACAATG
1 TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATG
4336921 CTAGTTGAA
66 CTAGTTGAA
* *
4336930 TGAGCATTATCATTATAAAAATTGAGCATTATCAAGAAATGACAATTTTGAGCATCTTTACAATG
1 TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATG
4336995 CTAGTTGAA
66 CTAGTTGAA
* *
4337004 TGAGCATGATCATTATCAACATTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATG
1 TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATG
4337069 CTAGTTGAA
66 CTAGTTGAA
* **
4337078 TGAGCATTATCCAATA-CTTAATTGAGCATTATCAA
1 TGAGCATTAT-CATTATCAAAATTGAGCATTATCAA
4337113 CATTCCCCCA
Statistics
Matches: 239, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
74 235 0.98
75 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (74 bp):
TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATG
CTAGTTGAA
Found at i:4342544 original size:74 final size:74
Alignment explanation
Indices: 4342420--4342751 Score: 513
Period size: 74 Copynumber: 4.5 Consensus size: 74
4342410 TAACCTAATT
* *
4342420 TGAGCATTATCATTATCAAAATTGCGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATG
1 TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGAAAATTTTGAGCATATTTACAATG
4342485 CTAGTTGAA
66 CTAGTTGAA
* * *
4342494 TAAGCATTATCATTATCAAAATTGAGCATTATAAAGAAATGAAAAATTTGAGCATATTTACAATG
1 TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGAAAATTTTGAGCATATTTACAATG
4342559 CTAGTTGAA
66 CTAGTTGAA
* *
4342568 TGAGCATTATCATTATAAAAATTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATG
1 TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGAAAATTTTGAGCATATTTACAATG
4342633 CTAGTTGAA
66 CTAGTTGAA
* * * *
4342642 TGAGCATGATAATTATCAACATTGAGCATTATCAAGAAATGACAATTTTTGAGCATATTTACAAT
1 TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGA-AAATTTTGAGCATATTTACAAT
4342707 GCTAGTTGAA
65 GCTAGTTGAA
* **
4342717 TGAGCATTATCCAATA-CTTAATTGAGCATTATCAA
1 TGAGCATTAT-CATTATCAAAATTGAGCATTATCAA
4342752 CATTTTCCAC
Statistics
Matches: 234, Mismatches: 22, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
74 176 0.75
75 55 0.24
76 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (74 bp):
TGAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGAAAATTTTGAGCATATTTACAATG
CTAGTTGAA
Found at i:4347286 original size:13 final size:14
Alignment explanation
Indices: 4347263--4347292 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4347253 TTTCCCATTC
4347263 AGACGTGCATATGA
1 AGACGTGCATATGA
4347277 AGAC-TGCATATGA
1 AGACGTGCATATGA
4347290 AGA
1 AGA
4347293 ATGTTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:4352604 original size:3 final size:3
Alignment explanation
Indices: 4352596--4352670 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
4352586 TTAATGTATT
* * * * * * *
4352596 TAA TAA TAA TAA TAA TAA TAT TAT TAT TAT TAT TTA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4352644 TAA TAA T-A TTA TAA TTA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA
4352671 ATAAATAATG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
2 2 0.03
3 57 0.93
4 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (3 bp):
TAA
Found at i:4352638 original size:33 final size:33
Alignment explanation
Indices: 4352579--4352679 Score: 114
Period size: 33 Copynumber: 3.0 Consensus size: 33
4352569 ATTATTATTT
4352579 ATAATATT-TAATGTATTTAATAATAATAATAATA
1 ATAATATTATAAT-TATTT-ATAATAATAATAATA
* * *
4352613 ATATTATTATTATTATTTATAATAATTATAATA
1 ATAATATTATAATTATTTATAATAATAATAATA
**
4352646 ATAATATTATAATTATAAATAATAAATAAATAAT
1 ATAATATTATAATTATTTATAAT-AAT-AATAAT
4352680 GGGTAAAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
33 33 0.59
34 15 0.27
35 8 0.14
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
ATAATATTATAATTATTTATAATAATAATAATA
Found at i:4353291 original size:73 final size:74
Alignment explanation
Indices: 4353169--4353333 Score: 314
Period size: 73 Copynumber: 2.2 Consensus size: 74
4353159 CTTGTTAATC
*
4353169 TGAGCCTTCAAAATGCCCCAACATTTGCTGATACAGATGCTAAAAGTAGGCTTAGTCATTACTTC
1 TGAGCCTTCAAAATGCCCCAACATTTACTGATACAGATGCTAAAAGTAGGCTTAGTCATTACTTC
4353234 TTGTTGAGA
66 TTGTTGAGA
4353243 TGAGCCTTCAAAATGCCCC-ACATTTACTGATACAGATGCTAAAAGTAGGCTTAGTCATTACTTC
1 TGAGCCTTCAAAATGCCCCAACATTTACTGATACAGATGCTAAAAGTAGGCTTAGTCATTACTTC
4353307 TTGTTGAGA
66 TTGTTGAGA
4353316 TGAGCCTTCAAAATGCCC
1 TGAGCCTTCAAAATGCCC
4353334 AAATATTCAT
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 71 0.79
74 19 0.21
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (74 bp):
TGAGCCTTCAAAATGCCCCAACATTTACTGATACAGATGCTAAAAGTAGGCTTAGTCATTACTTC
TTGTTGAGA
Found at i:4354759 original size:114 final size:114
Alignment explanation
Indices: 4354559--4354784 Score: 362
Period size: 114 Copynumber: 2.0 Consensus size: 114
4354549 GATCATGCAG
* * * *
4354559 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
4354624 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAAAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
4354673 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
4354738 ACACTTCCAAAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAAAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
4354785 CATGGCACTT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAAAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:4355633 original size:13 final size:13
Alignment explanation
Indices: 4355615--4355641 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4355605 TCCTGTAACC
4355615 AATGTTACCCTAT
1 AATGTTACCCTAT
4355628 AATGTTACCCTAT
1 AATGTTACCCTAT
4355641 A
1 A
4355642 TAAAAGGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
AATGTTACCCTAT
Found at i:4360433 original size:14 final size:14
Alignment explanation
Indices: 4360395--4360448 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
4360385 CATAAAAATA
* *
4360395 CAAATGCAAAGATG
1 CAAATGTAAATATG
4360409 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
4360424 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
4360438 TAAATGTAAAT
1 CAAATGTAAAT
4360449 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:4362139 original size:11 final size:10
Alignment explanation
Indices: 4362111--4362142 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
4362101 AAATAAATAC
4362111 ATAAAATAAT
1 ATAAAATAAT
4362121 ATAAAATAAT
1 ATAAAATAAT
4362131 ATAAAAATAAT
1 AT-AAAATAAT
4362142 A
1 A
4362143 AGTAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAAATAAT
Found at i:4364162 original size:9 final size:9
Alignment explanation
Indices: 4364139--4364223 Score: 57
Period size: 9 Copynumber: 9.6 Consensus size: 9
4364129 GACTGGCTTG
*
4364139 TAATTTTTA
1 TAATATTTA
*
4364148 TTATATTTA
1 TAATATTTA
4364157 TAATATTTA
1 TAATATTTA
*
4364166 -ATGTATTTA
1 TA-ATATTTA
*
4364175 TAATA-ATA
1 TAATATTTA
* *
4364183 TAATAATAA
1 TAATATTTA
* *
4364192 TAATAATAA
1 TAATATTTA
*
4364201 TATTATTTA
1 TAATATTTA
*
4364210 TAATAATTA
1 TAATATTTA
4364219 TAATA
1 TAATA
4364224 ATAATAATTA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
8 8 0.13
9 51 0.85
10 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (9 bp):
TAATATTTA
Found at i:4364182 original size:3 final size:3
Alignment explanation
Indices: 4364174--4364251 Score: 104
Period size: 3 Copynumber: 26.3 Consensus size: 3
4364164 TAATGTATTT
* * * *
4364174 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA TTA TTT ATA ATA ATT ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
4364221 ATA ATA ATA ATT ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4364252 ATAAATTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:4364261 original size:15 final size:13
Alignment explanation
Indices: 4364174--4364262 Score: 89
Period size: 12 Copynumber: 7.0 Consensus size: 13
4364164 TAATGTATTT
4364174 ATAATAATATAATA
1 ATAATAAT-TAATA
4364188 ATAATAA-TAATA
1 ATAATAATTAATA
* *
4364200 AT-ATTATTTATA
1 ATAATAATTAATA
*
4364212 ATAATTA-TAATA
1 ATAATAATTAATA
4364224 ATAATAATT-ATA
1 ATAATAATTAATA
4364236 ATAATAA-TAATA
1 ATAATAATTAATA
4364248 ATAAATAAATTAATA
1 AT-AAT-AATTAATA
4364263 TGGGTAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
11 4 0.06
12 38 0.59
13 8 0.12
14 9 0.14
15 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATAATTAATA
Found at i:4366302 original size:19 final size:19
Alignment explanation
Indices: 4366278--4366315 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4366268 ATACTAAGGT
* *
4366278 GAGTATTGATACCGTAATA
1 GAGTATCGATACCATAATA
4366297 GAGTATCGATACCATAATA
1 GAGTATCGATACCATAATA
4366316 TAGAAGAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (19 bp):
GAGTATCGATACCATAATA
Found at i:4366864 original size:55 final size:55
Alignment explanation
Indices: 4366776--4367221 Score: 693
Period size: 55 Copynumber: 8.1 Consensus size: 55
4366766 TGGCAATATA
* *
4366776 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGAACTTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
* * * * *
4366831 TTTACAAAACTAAGTAATTCATAATAAGTTTATGAATATCCGTATGGGCACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
*
4366886 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
*
4366941 TGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGCA-TTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT-TG
* * *
4366995 TGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTC
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
4367050 TGTGCAAAACTAA-AAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
* * * *
4367104 TGTGCAAAACTAATAAATTCATAATAAATTTATGAATTTTCGTATGGGCACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
*
4367159 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCA-TTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT-TG
4367214 TGTGCAAA
1 TGTGCAAA
4367222 TTTTATGAAT
Statistics
Matches: 358, Mismatches: 28, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
53 2 0.01
54 102 0.28
55 252 0.70
56 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (55 bp):
TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
Found at i:4366969 original size:110 final size:110
Alignment explanation
Indices: 4366776--4367221 Score: 707
Period size: 109 Copynumber: 4.1 Consensus size: 110
4366766 TGGCAATATA
* * * *
4366776 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGAACTTTGTTTACAAAAC
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
* *
4366841 TAAGTAATTCATAATAAGTTTATGAATATCCGTATGGGCACTGTG
66 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTG
* *
4366886 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTGTGTGTAAAAC
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
*
4366951 TAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGCATTGTG
66 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTG
* * *
4366995 TGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTCTGTGCAAAAC
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
*
4367060 TAA-AAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTG
66 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTG
* * * *
4367104 TGTGCAAAACTAATAAATTCATAATAAATTTATGAATTTTCGTATGGGCACTGTGTGTGCAAAAC
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
* *
4367169 TAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCATTGTG
66 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTG
4367214 TGTGCAAA
1 TGTGCAAA
4367222 TTTTATGAAT
Statistics
Matches: 311, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
108 31 0.10
109 141 0.45
110 139 0.45
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (110 bp):
TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTG
Found at i:4367234 original size:36 final size:36
Alignment explanation
Indices: 4367187--4367257 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
4367177 TCATAATAAG
* *
4367187 TTTATGAATTTCTGTATGGGCATTGTGTGTGCAAAT
1 TTTATGAATTTCTGTATGGGCACTGTATGTGCAAAT
4367223 TTTATGAATTTCTGTATGGGCACTGTATGTGCAAA
1 TTTATGAATTTCTGTATGGGCACTGTATGTGCAAA
4367258 ACTAAGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (36 bp):
TTTATGAATTTCTGTATGGGCACTGTATGTGCAAAT
Found at i:4367287 original size:91 final size:91
Alignment explanation
Indices: 4367132--4367307 Score: 327
Period size: 91 Copynumber: 1.9 Consensus size: 91
4367122 TCATAATAAA
*
4367132 TTTATGAATTTTCGTATGGGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATT
1 TTTATGAATTTTCGTATGGGCACTGTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATT
4367197 TCTGTATGGGCATTGTGTGTGCAAAT
66 TCTGTATGGGCATTGTGTGTGCAAAT
4367223 TTTATGAA-TTTCTGTATGGGCACTGTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAAT
1 TTTATGAATTTTC-GTATGGGCACTGTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAAT
4367287 TTCTGTATGGGCATTGTGTGT
65 TTCTGTATGGGCATTGTGTGT
4367308 ACAATCTAAG
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
90 4 0.05
91 79 0.95
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.39
Consensus pattern (91 bp):
TTTATGAATTTTCGTATGGGCACTGTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATT
TCTGTATGGGCATTGTGTGTGCAAAT
Found at i:4367335 original size:54 final size:54
Alignment explanation
Indices: 4367223--4367407 Score: 280
Period size: 54 Copynumber: 3.4 Consensus size: 54
4367213 GTGTGCAAAT
* *
4367223 TTTATGAATTTCTGTATGGGCACTGTATGTGCAAAACTAAGAAATTCATAATAAG
1 TTTATGAATTTCTGTATGGGCACTGTGTGTGC-AAACTAAGAAATTCATAATGAG
* * *
4367278 TTTATGAATTTCTGTATGGGCATTGTGTGTACAATCTAAGAAATTCATAATGAG
1 TTTATGAATTTCTGTATGGGCACTGTGTGTGCAAACTAAGAAATTCATAATGAG
* *
4367332 TTTATGAATTTCTGTATTGGCACTGTGTGTGCAACCTAAGAAATTCATAATGAG
1 TTTATGAATTTCTGTATGGGCACTGTGTGTGCAAACTAAGAAATTCATAATGAG
* *
4367386 TTTATGAATTTCCGTATTGGCA
1 TTTATGAATTTCTGTATGGGCA
4367408 TTAGGTGTGC
Statistics
Matches: 120, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
54 91 0.76
55 29 0.24
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38
Consensus pattern (54 bp):
TTTATGAATTTCTGTATGGGCACTGTGTGTGCAAACTAAGAAATTCATAATGAG
Found at i:4367449 original size:109 final size:109
Alignment explanation
Indices: 4367226--4367458 Score: 283
Period size: 109 Copynumber: 2.1 Consensus size: 109
4367216 TGCAAATTTT
* *
4367226 ATGAATTTCTGTATGGGCACTGTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCT
1 ATGAATTTCTGTATTGGCACTGTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCC
* * *
4367291 GTATGGGCATTGTGTGTACAATCTAAGAAATTCATAATGAGTTT
66 GTATGGGCATTGTGTGTACAATCCAAGAAATTCATAATGAGGTG
* * *
4367335 ATGAATTTCTGTATTGGCACTGTGTGTGC-AACCTAAGAAATTCATAATGAGTTTATGAATTTCC
1 ATGAATTTCTGTATTGGCACTGTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCC
* * * * * *
4367399 GTATTGGCATTAG-GTGTGCATTCCAACGCAATTCTTAATGTGGTG
66 GTATGGGCATT-GTGTGTACAATCCAA-GAAATTCATAATGAGGTG
*
4367444 GTGAATTAT-TGTATT
1 ATGAATT-TCTGTATT
4367459 AGCTAATTAA
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
108 52 0.49
109 53 0.50
110 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.38
Consensus pattern (109 bp):
ATGAATTTCTGTATTGGCACTGTATGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCC
GTATGGGCATTGTGTGTACAATCCAAGAAATTCATAATGAGGTG
Found at i:4367659 original size:80 final size:81
Alignment explanation
Indices: 4367526--4367746 Score: 284
Period size: 80 Copynumber: 2.7 Consensus size: 81
4367516 TTCTAAAATA
* * * *
4367526 AAAGAATAAATGCCTAACTATGCATTTGGTAGAAAAGTGCCAATAATGCAAGTTGGATGAAAGG-
1 AAAGAATAAATGCTTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTGGATGAAAGGT
*
4367590 TAAATACCCTTGGATG
66 TAAATACCCTTAGATG
*
4367606 AAAGAATAAATGCTTAACTGTGCATTTGGCAGAAAGGTGCTAATAATGCAAGTTGGATGAAAGGT
1 AAAGAATAAATGCTTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTGGATGAAAGGT
* *
4367671 TAAATGCCTTTAGATG
66 TAAATACCCTTAGATG
* * * * * *
4367687 AAAGAATAAATG-TCTAACTGTGCTTTTTGGCATAAAGGTGTCATTAAAGTAAGTTGGATG
1 AAAGAATAAATGCT-TAACTGTGC-ATTTGGCAGAAAGGTGCCAATAATGCAAGTTGGATG
4367747 CTTAACGGTG
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
80 60 0.49
81 34 0.28
82 29 0.24
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (81 bp):
AAAGAATAAATGCTTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTGGATGAAAGGT
TAAATACCCTTAGATG
Found at i:4367854 original size:45 final size:46
Alignment explanation
Indices: 4367798--4367884 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 46
4367788 GTTAGATGAA
* *
4367798 TAACAGTGCATTACCGGCTTGAAAGGATGTCATAAAT-AAAATGCG
1 TAACAGTGCATTACCGGCATGAAAGGATGCCATAAATGAAAATGCG
* *
4367843 TAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAA
1 TAACAGTGCATTACCGGCATGAAAGGATGCCATAAATGAAAA
4367885 GAACGAACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 33 0.89
46 4 0.11
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (46 bp):
TAACAGTGCATTACCGGCATGAAAGGATGCCATAAATGAAAATGCG
Found at i:4369980 original size:23 final size:23
Alignment explanation
Indices: 4369954--4369998 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4369944 CACCACAACT
*
4369954 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
4369977 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
4369999 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:4373580 original size:48 final size:48
Alignment explanation
Indices: 4373508--4373604 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
4373498 CTTTAAGTTT
4373508 CGAAGCTTTATGACATTCAGAAGTCCAAACAAATGGTACGTTCTTTCTC
1 CGAAGCTTTATGA-ATTCAGAAGTCCAAACAAATGGTACGTTCTTTCTC
4373557 CGAAGCTTTATTG-ATTCAGAAGTCCAAACAAATGGTACGTTCTTTCTC
1 CGAAGCTTTA-TGAATTCAGAAGTCCAAACAAATGGTACGTTCTTTCTC
4373605 ATTAGCTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
48 35 0.74
49 10 0.21
50 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (48 bp):
CGAAGCTTTATGAATTCAGAAGTCCAAACAAATGGTACGTTCTTTCTC
Found at i:4376910 original size:23 final size:23
Alignment explanation
Indices: 4376884--4376928 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4376874 CACCACAGCT
*
4376884 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
4376907 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
4376929 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:4377095 original size:150 final size:149
Alignment explanation
Indices: 4376896--4377211 Score: 535
Period size: 150 Copynumber: 2.1 Consensus size: 149
4376886 TATAATTGCA
*
4376896 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
* * *
4376960 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCTAGGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTC-ACGACCTCACACATGT
* *
4377025 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
*
4377046 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGAGCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
4377111 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCACGACCTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCACGACCTCACACATGTTC
*
4377176 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
4377195 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
4377212 CCCTCTACCT
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 50 0.32
150 107 0.68
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCACGACCTCACACATGTTC
CAAAGAATATACATATATC
Found at i:4381203 original size:27 final size:27
Alignment explanation
Indices: 4381165--4381216 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
4381155 TAGGAAAATA
4381165 GGTTTTTGAATGATATGTTAAGATATG
1 GGTTTTTGAATGATATGTTAAGATATG
*
4381192 GGTTTTTGAATGATATTTTAAGATA
1 GGTTTTTGAATGATATGTTAAGATA
4381217 CGAGTTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (27 bp):
GGTTTTTGAATGATATGTTAAGATATG
Found at i:4381223 original size:27 final size:27
Alignment explanation
Indices: 4381166--4381223 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
4381156 AGGAAAATAG
* *
4381166 GTTTTTGAATGATATGTTAAGATATGG
1 GTTTTTGAATGATATGTTAAGATACGA
*
4381193 GTTTTTGAATGATATTTTAAGATACGA
1 GTTTTTGAATGATATGTTAAGATACGA
4381220 GTTT
1 GTTT
4381224 ACTAGCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (27 bp):
GTTTTTGAATGATATGTTAAGATACGA
Found at i:4381570 original size:21 final size:21
Alignment explanation
Indices: 4381544--4381597 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
4381534 AGCCGAACAA
4381544 TATCGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
4381565 TATCGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
4381586 TATCGATACTGA
1 TATCGATACTGA
4381598 GGTGAGTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (21 bp):
TATCGATACTGATGCAATTAG
Found at i:4382184 original size:55 final size:55
Alignment explanation
Indices: 4382100--4382904 Score: 1145
Period size: 55 Copynumber: 14.7 Consensus size: 55
4382090 ACACTATATC
4382100 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * *
4382155 TGCAAAACTAAGAAATTCATAATAAGTTTAAGAATTTTCGTATGGGCACTCTGTA
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
*
4382210 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* **
4382265 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGCGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
** *
4382320 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTATGTATGGGCACTTTATG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
4382375 TACAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * *
4382430 TGGAAAACTAAGAAATTCAAAATAAGTTTGTGAATTTTCGTATGGGCACTTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
*
4382485 TGCAAAACTAAGAAATTCATAATAAGTTTACGAATTTCCGTATGGGCA-TTGTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT-TGTG
* *
4382540 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * **
4382595 TGCAAAACTAAGAAATTTATAATAAGTTCATGAATTTCCGTATAAGCA-TTGTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT-TGTG
* * * *
4382650 TGC-AAACAAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGGAACTGTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
** ** * *
4382704 TGCAAAACTAATTAATTCATAATAAGTTTATGAATTTTTGTATGGACACTATGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
4382759 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGTACTGTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * *
4382814 TGC-AATCTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCA-TTGTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT-TGTG
* *
4382868 TGC-AACCTAAGAAATTCATAATGAGTTTATGAATTTC
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTC
4382905 TATATTGACA
Statistics
Matches: 671, Mismatches: 73, Indels: 13
0.89 0.10 0.02
Matches are distributed among these distances:
53 1 0.00
54 124 0.18
55 545 0.81
56 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (55 bp):
TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
Found at i:4382980 original size:109 final size:107
Alignment explanation
Indices: 4382104--4383000 Score: 595
Period size: 110 Copynumber: 8.2 Consensus size: 107
4382094 TATATCTGCA
* ** * * * *
4382104 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAA
1 AAACTAAGAAATTCATAATGAGTTTATGAATTTCTATATGGACACTGTGTGTGC-AATCGAAGAA
* * * * * * *
4382169 ATTCATAATAAGTTTAAGAATTTTCGTATGGGCACTCTGTATGC
65 ATTCATAATGAGGTGATGAATTTT-GTATTGGCACTATGTGTGC
* * * * * *
4382213 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGCAAAACTAAGA
1 -AAACTAAGAAATTCATAATGAGTTTATGAATTTCTATATGGACACTGTGTGTGC-AATCGAAGA
* * * * **
4382278 AATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGCGTGTGC
64 AATTCATAATGAGGTGATGAATTTT-GTATTGGCACTATGTGTGC
* * * * * * * * *
4382323 AAAACTAAGAAATTCATAATAAGTTTATGAATTTATGTATGGGCACTTTATGTACAAAACTAAGA
1 -AAACTAAGAAATTCATAATGAGTTTATGAATTTCTATATGGACACTGTGTGTGC-AATCGAAGA
* * * * * *
4382388 AATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGGA
64 AATTCATAATGAGGTGATGAATTT-TGTATTGGCACTATGTGT-GC
* * * * * * * *
4382434 AAACTAAGAAATTCAAAATAAGTTTGTGAATTT-TCGTATGGGCACTTTGTGTGCAAAACTAAGA
1 AAACTAAGAAATTCATAATGAGTTTATGAATTTCT-ATATGGACACTGTGTGTGC-AATCGAAGA
* * * * * * * *
4382498 AATTCATAATAAGTTTACGAATTTCCGTATGGGCATTGTGTGTGC
64 AATTCATAATGAGGTGATGAATTT-TGTATTGGCACTATGTGTGC
* * * *
4382543 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-TGG-CACTATGTGTGCAAAACTAA
1 -AAACTAAGAAATTCATAATGAGTTTATGAATTT-C-TATATGGACACTGTGTGTGC-AATCGAA
* * * * * ** * *
4382606 GAAATTTATAATAAGTTCATGAATTTCCGTATAAGCATTGTGTGTGC
62 GAAATTCATAATGAGGTGATGAATTT-TGTATTGGCACTATGTGTGC
* * * * *
4382653 AAACAAAGAAATTCATAATAAGTTTATGAATTTC-AGTATGGGA-ACTGTGTGTGCAAAACTAAT
1 AAACTAAGAAATTCATAATGAGTTTATGAATTTCTA-TAT-GGACACTGTGTGTGC-AATCGAAG
* * * *
4382716 TAATTCATAATAAGTTTATGAATTTTTGTA-TGGACACTATGTGTGC
63 AAATTCATAATGAGGTGATGAA-TTTTGTATTGG-CACTATGTGTGC
* * ** *
4382762 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGTACTGTGTGTGCAATCTAAGAA
1 -AAACTAAGAAATTCATAATGAGTTTATGAATTTCTATATGGACACTGTGTGTGCAATCGAAGAA
* * * *
4382827 ATTCATAATGAGTTTATGAATTTTCGTATTGGCATTGTGTGTGC
65 ATTCATAATGAGGTGATGAATTTT-GTATTGGCACTATGTGTGC
* * * * * *
4382871 AACCTAAGAAATTCATAATGAGTTTATGAATTTCTATATTGACATTAG-GTGTGCATTCCGACGT
1 AAACTAAGAAATTCATAATGAGTTTATGAATTTCTATATGGACACT-GTGTGTGCAAT-CGAAGA
* * * *
4382935 AATTCTTAATGAGGTGGTGAATTATTGTATTGGCACTACGGGTGC
64 AATTCATAATGAGGTGATGAATT-TTGTATTGGCACTATGTGTGC
*
4382980 AAACTAA-AGAATTTATAATGA
1 AAACTAAGA-AATTCATAATGA
4383001 AATTAAATAT
Statistics
Matches: 697, Mismatches: 68, Indels: 45
0.86 0.08 0.06
Matches are distributed among these distances:
106 1 0.00
107 1 0.00
108 55 0.08
109 182 0.26
110 451 0.65
111 5 0.01
112 1 0.00
113 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (107 bp):
AAACTAAGAAATTCATAATGAGTTTATGAATTTCTATATGGACACTGTGTGTGCAATCGAAGAAA
TTCATAATGAGGTGATGAATTTTGTATTGGCACTATGTGTGC
Found at i:4383222 original size:49 final size:49
Alignment explanation
Indices: 4383154--4383262 Score: 139
Period size: 49 Copynumber: 2.2 Consensus size: 49
4383144 AATAAATGTC
* * * * **
4383154 TAACTGTGC-TTTTTGGCAGAAAGATGCCATTAATGTAAGTTAGATGCT
1 TAACGGTGCATTTTTAGCAGAAAGATGCCACTAATATAAGTTAGATGAA
* *
4383202 TAACGGTTCATTTTTAGCAGAAAGGTGCCACTAATATAAGTTAGATGAA
1 TAACGGTGCATTTTTAGCAGAAAGATGCCACTAATATAAGTTAGATGAA
4383251 TAACGGTGCATT
1 TAACGGTGCATT
4383263 ACCGACATGA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
48 7 0.14
49 44 0.86
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (49 bp):
TAACGGTGCATTTTTAGCAGAAAGATGCCACTAATATAAGTTAGATGAA
Found at i:4383301 original size:45 final size:46
Alignment explanation
Indices: 4383250--4383337 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
4383240 AGTTAGATGA
*
4383250 ATAACGGTGCATTACCGACATGAAAGGATGTCATAAAT-AAAATGT
1 ATAACGGTGCATTACCGACATGAAAGGATGCCATAAATGAAAATGT
* *
4383295 ATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAA
1 ATAACGGTGCATTACCGACATGAAAGGATGCCATAAATGAAAA
4383338 GAACGAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 35 0.90
46 4 0.10
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (46 bp):
ATAACGGTGCATTACCGACATGAAAGGATGCCATAAATGAAAATGT
Found at i:4384914 original size:23 final size:23
Alignment explanation
Indices: 4384888--4384965 Score: 95
Period size: 23 Copynumber: 3.3 Consensus size: 23
4384878 CACCACAGCT
4384888 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
4384911 CATATAATTGCACC-AGAGTGCCG
1 CATATAATTGCACCGA-AGTGCCA
* *
4384934 CGTATAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
4384957 TATAATAAT
1 CAT-ATAAT
4384966 GTCCATAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
22 1 0.02
23 40 0.87
24 5 0.11
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:4385138 original size:100 final size:102
Alignment explanation
Indices: 4384972--4385184 Score: 342
Period size: 100 Copynumber: 2.1 Consensus size: 102
4384962 TAATGTCCAT
* * *
4384972 AAGGACCATATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
**
4385037 GACTTCACACATGTTTTAAAGAATAC-ATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACAATATGTCCCG
*
4385073 AAGGACCACATATCATT-CTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
4385137 GACTTCACACATGTTCCAAATAATACAATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACAATATGTCCCG
4385174 AAGGA-CACATA
1 AAGGACCACATA
4385185 GACCCTCGAC
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
100 73 0.70
101 31 0.30
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACAATATGTCCCG
Found at i:4393637 original size:13 final size:13
Alignment explanation
Indices: 4393619--4393643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4393609 ACAAAGATTG
4393619 AGATTTGGAAAAT
1 AGATTTGGAAAAT
4393632 AGATTTGGAAAA
1 AGATTTGGAAAA
4393644 AATCAATCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (13 bp):
AGATTTGGAAAAT
Found at i:4394222 original size:3 final size:3
Alignment explanation
Indices: 4394214--4394291 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
4394204 TACATTGTTC
4394214 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4394262 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4394292 GTGAAACCAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4398862 original size:17 final size:18
Alignment explanation
Indices: 4398834--4398888 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 18
4398824 TTTAACTAAA
*
4398834 TTATTGATAATTTAGATT
1 TTATTGATAATTAAGATT
*
4398852 TTATT-ATAATTAAGATA
1 TTATTGATAATTAAGATT
*
4398869 TT-TTGGTAATT--GATT
1 TTATTGATAATTAAGATT
4398884 TTATT
1 TTATT
4398889 TAATAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 5 0.16
16 4 0.13
17 17 0.55
18 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
TTATTGATAATTAAGATT
Found at i:4399044 original size:17 final size:18
Alignment explanation
Indices: 4399022--4399060 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
4399012 TTGGAAGAGT
4399022 GTTTTGGGA-TATATCGG
1 GTTTTGGGACTATATCGG
*
4399039 GTTTTGGTATCTATATCGG
1 GTTTTGGGA-CTATATCGG
4399058 GTT
1 GTT
4399061 ACTCTTCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (18 bp):
GTTTTGGGACTATATCGG
Found at i:4401084 original size:19 final size:19
Alignment explanation
Indices: 4401060--4401109 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
4401050 TACGTTTTCA
*
4401060 ATGAATGGTACTATACGGT
1 ATGAATAGTACTATACGGT
* **
4401079 ATGAATAGTATTATATTGT
1 ATGAATAGTACTATACGGT
*
4401098 ATGAATAATACT
1 ATGAATAGTACT
4401110 GTAAGCAGTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (19 bp):
ATGAATAGTACTATACGGT
Found at i:4401930 original size:32 final size:32
Alignment explanation
Indices: 4401888--4401972 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
4401878 CTGTCCCTAA
*
4401888 GTCCCGAAAGACATAGGTAATATTATCCATAT
1 GTCCCAAAAGACATAGGTAATATTATCCATAT
*
4401920 GTCCCAAAAGACATAGGTAATATTGTCCATAT
1 GTCCCAAAAGACATAGGTAATATTATCCATAT
4401952 GTCCCAAAAGACATAGGTAAT
1 GTCCCAAAAGACATAGGTAAT
4401973 TGTAACATCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (32 bp):
GTCCCAAAAGACATAGGTAATATTATCCATAT
Found at i:4402845 original size:64 final size:63
Alignment explanation
Indices: 4402756--4402896 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 63
4402746 TTGTTTAAGG
* * * * * *
4402756 TGCATCGATGCACATGAAGTGCATCGCTGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGAAGTACATCGATACATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * *
4402820 TGCATCGATGCATAAGGAGTACATCGATACATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGAAGTACATCGATACAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
4402884 TGCATCGATGCAT
1 TGCATCGATGCAT
4402897 GGTGTAGTGC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 58 0.89
65 6 0.09
66 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGAAGTACATCGATACATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:4403602 original size:103 final size:103
Alignment explanation
Indices: 4403377--4403594 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
4403367 GTAGAGGGTC
4403377 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
4403442 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
* *
4403480 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
4403545 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
4403583 TATGTGGTCCTT
1 TATGTGGTCCTT
4403595 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:4403645 original size:23 final size:22
Alignment explanation
Indices: 4403611--4403673 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 22
4403601 ATTATTATAT
4403611 GGCACTACGGTGCAATTCTACGC
1 GGCACTA-GGTGCAATTCTACGC
*
4403634 GGCACTCAGGTGCAATTCTACGT
1 GGCACT-AGGTGCAATTCTACGC
4403657 GGCACTTAGGTGCAATT
1 GGCAC-TAGGTGCAATT
4403674 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 35 0.95
24 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (22 bp):
GGCACTAGGTGCAATTCTACGC
Found at i:4409856 original size:64 final size:63
Alignment explanation
Indices: 4409774--4409931 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 63
4409764 TTTAAGGTGT
* * * *
4409774 ATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTATGC
1 ATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTATGC
* * * *
4409838 ATCGATGCATAAGGAGTGCATCGATACATCCCCATTAAATACAAACATCGAATAGGATTTATGC
1 ATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTATGC
*
4409902 ATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 ATCGATGCATAAG-G-AGTGCATCGATGCAT
4409932 ACCTCCATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 58 0.73
65 20 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
ATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTATGC
Found at i:4410615 original size:102 final size:103
Alignment explanation
Indices: 4410391--4410607 Score: 364
Period size: 102 Copynumber: 2.1 Consensus size: 103
4410381 GTAGAGGGTC
4410391 TATGTGGTCCTTCGGGACATATATGTATTCTTAGGAACATGTGTGAGGTATGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTAGGAACATGTGTGAGGTATGGTGAGACACATAC
*
4410456 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATAA
* * * *
4410494 TATGTGGTTCTTCGGGACATATATGTATT-TTTGGAACATGTGTGAGGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTAGGAACATGTGTGAGGTATGGTGAGACACATAC
*
4410558 TTGATCCTTGGCATATGTATATGATTTTTAAGGAATAA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATAA
*
4410596 TATGTTGTCCTT
1 TATGTGGTCCTT
4410608 ATGGACATTA
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 78 0.74
103 28 0.26
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTAGGAACATGTGTGAGGTATGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATAA
Found at i:4410662 original size:23 final size:23
Alignment explanation
Indices: 4410632--4410686 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
4410622 ATGGAACTAC
4410632 GGTGCAATTCTACGCGGCACTCA
1 GGTGCAATTCTACGCGGCACTCA
* * *
4410655 GGTGCAATTCTATGTGGCACTTA
1 GGTGCAATTCTACGCGGCACTCA
4410678 GGTGCAATT
1 GGTGCAATT
4410687 ATATAGCTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCA
Found at i:4414244 original size:11 final size:11
Alignment explanation
Indices: 4414228--4414269 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
4414218 ATCCTCTTCA
4414228 AATAAGTAAGT
1 AATAAGTAAGT
4414239 AATAAGT-AGT
1 AATAAGTAAGT
4414249 ATATAAGTAAGT
1 A-ATAAGTAAGT
4414261 AATAAGTAA
1 AATAAGTAA
4414270 TATAGGGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.14
11 21 0.72
12 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.29
Consensus pattern (11 bp):
AATAAGTAAGT
Found at i:4414254 original size:22 final size:22
Alignment explanation
Indices: 4414229--4414273 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4414219 TCCTCTTCAA
*
4414229 ATAAGTAAGTAATAAGTAGTAT
1 ATAAGTAAGTAATAAGTAATAT
4414251 ATAAGTAAGTAATAAGTAATAT
1 ATAAGTAAGTAATAAGTAATAT
4414273 A
1 A
4414274 GGGAAGAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (22 bp):
ATAAGTAAGTAATAAGTAATAT
Found at i:4426547 original size:9 final size:9
Alignment explanation
Indices: 4426521--4426574 Score: 58
Period size: 9 Copynumber: 5.8 Consensus size: 9
4426511 CCTTCGTCCT
4426521 AAAAAAATA
1 AAAAAAATA
4426530 ATATTAAAAATA
1 A-A--AAAAATA
4426542 AAAAAAAT-
1 AAAAAAATA
4426550 AAAAAAATA
1 AAAAAAATA
4426559 AAAAAAA-A
1 AAAAAAATA
4426567 CAAAAAAA
1 -AAAAAAA
4426575 CACTCATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 9 0.22
9 21 0.52
10 1 0.03
11 1 0.03
12 8 0.20
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAAATA
Found at i:4426553 original size:8 final size:8
Alignment explanation
Indices: 4426535--4426564 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
4426525 AAATAATATT
4426535 AAAAATAAA
1 AAAAAT-AA
4426544 AAAAATAA
1 AAAAATAA
4426552 AAAAATAA
1 AAAAATAA
4426560 AAAAA
1 AAAAA
4426565 AACAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:4426566 original size:18 final size:18
Alignment explanation
Indices: 4426520--4426574 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
4426510 CCCTTCGTCC
*
4426520 TAAAAAAATAATATTAAAAA
1 TAAAAAAA-AATA-AAAAAA
4426540 T-AAAAAAAATAAAAAAA
1 TAAAAAAAAATAAAAAAA
*
4426557 TAAAAAAAAACAAAAAAA
1 TAAAAAAAAATAAAAAAA
4426575 CACTCATGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 6 0.19
18 19 0.59
19 6 0.19
20 1 0.03
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.15
Consensus pattern (18 bp):
TAAAAAAAAATAAAAAAA
Found at i:4430791 original size:53 final size:53
Alignment explanation
Indices: 4430707--4430809 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 53
4430697 AATCATCAAC
* *
4430707 GGGCATGATTTAAATTCCACTAATTCTTCCATTACTACAACTAGAATTTTAGG
1 GGGCATGATTTAAATTCCACTAATTCCTCCATTACTACAACTACAATTTTAGG
* *
4430760 GGGCATGATTTGAATTCCATTAATTCCTCCATTACTACAACTACAATTTT
1 GGGCATGATTTAAATTCCACTAATTCCTCCATTACTACAACTACAATTTT
4430810 GGGAGGACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (53 bp):
GGGCATGATTTAAATTCCACTAATTCCTCCATTACTACAACTACAATTTTAGG
Found at i:4431012 original size:16 final size:16
Alignment explanation
Indices: 4430991--4431021 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4430981 AAGGTCAATG
*
4430991 TTTAGTATTTGAACAT
1 TTTAGTATTCGAACAT
4431007 TTTAGTATTCGAACA
1 TTTAGTATTCGAACA
4431022 GAACATAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (16 bp):
TTTAGTATTCGAACAT
Found at i:4434254 original size:9 final size:8
Alignment explanation
Indices: 4434214--4434283 Score: 62
Period size: 8 Copynumber: 9.2 Consensus size: 8
4434204 AAAATAGTAT
4434214 TAATAA-A
1 TAATAATA
4434221 TAA-AA-A
1 TAATAATA
4434227 TAATAATA
1 TAATAATA
*
4434235 T-ATAACA
1 TAATAATA
4434242 TAATAATCA
1 TAATAAT-A
4434251 TAAT-ATA
1 TAATAATA
4434258 T-ATAATA
1 TAATAATA
*
4434265 TTATAATA
1 TAATAATA
4434273 TAATATATA
1 TAATA-ATA
4434282 TA
1 TA
4434284 GTATATACTG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
6 8 0.15
7 17 0.32
8 18 0.34
9 10 0.19
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (8 bp):
TAATAATA
Found at i:4434276 original size:31 final size:30
Alignment explanation
Indices: 4434229--4434290 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
4434219 AATAAAAATA
4434229 ATAATATATAACATAATA-ATCATAATATAT
1 ATAATATATAACATAATATAT-ATAATATAT
* *
4434259 ATAATATTATAATATAATATATATAGTATAT
1 ATAATA-TATAACATAATATATATAATATAT
4434290 A
1 A
4434291 CTGTATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 6 0.21
31 20 0.71
32 2 0.07
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (30 bp):
ATAATATATAACATAATATATATAATATAT
Done.