Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 56 of 150
Found at i:16803280 original size:18 final size:18
Alignment explanation
Indices: 16803254--16803296 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16803244 GACTAGAAAA
* * *
16803254 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
16803272 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
16803290 AGGATAC
1 AGGATAC
16803297 GCACTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:16804746 original size:122 final size:122
Alignment explanation
Indices: 16804529--16804772 Score: 488
Period size: 122 Copynumber: 2.0 Consensus size: 122
16804519 ATCTCGATCC
16804529 GACCTCCGTTAATTTTCTCCGGAATAGAGCCCAAAAGCTCGTAGCACATTGCTCCCCAATCGCCA
1 GACCTCCGTTAATTTTCTCCGGAATAGAGCCCAAAAGCTCGTAGCACATTGCTCCCCAATCGCCA
16804594 GATTGAACATACCCGGTGACTGGTACCCGTCCACCAATAATCCCAATTGCAGATTGA
66 GATTGAACATACCCGGTGACTGGTACCCGTCCACCAATAATCCCAATTGCAGATTGA
16804651 GACCTCCGTTAATTTTCTCCGGAATAGAGCCCAAAAGCTCGTAGCACATTGCTCCCCAATCGCCA
1 GACCTCCGTTAATTTTCTCCGGAATAGAGCCCAAAAGCTCGTAGCACATTGCTCCCCAATCGCCA
16804716 GATTGAACATACCCGGTGACTGGTACCCGTCCACCAATAATCCCAATTGCAGATTGA
66 GATTGAACATACCCGGTGACTGGTACCCGTCCACCAATAATCCCAATTGCAGATTGA
16804773 CATCTTCCAA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (122 bp):
GACCTCCGTTAATTTTCTCCGGAATAGAGCCCAAAAGCTCGTAGCACATTGCTCCCCAATCGCCA
GATTGAACATACCCGGTGACTGGTACCCGTCCACCAATAATCCCAATTGCAGATTGA
Found at i:16805255 original size:11 final size:11
Alignment explanation
Indices: 16805241--16805338 Score: 71
Period size: 11 Copynumber: 9.3 Consensus size: 11
16805231 GAGAAATTTA
16805241 AGAGGAAATTG
1 AGAGGAAATTG
*
16805252 AGAGCAAATTG
1 AGAGGAAATTG
**
16805263 AGATTAAA-T-
1 AGAGGAAATTG
* *
16805272 A-TGG-ATTTG
1 AGAGGAAATTG
16805281 AGA-GAAATTTG
1 AGAGGAAA-TTG
*
16805292 AAAGGAAATTG
1 AGAGGAAATTG
* *
16805303 AGAGCAATTTG
1 AGAGGAAATTG
16805314 AGAGGAAATTG
1 AGAGGAAATTG
*
16805325 AAAGGAAATTG
1 AGAGGAAATTG
16805336 AGA
1 AGA
16805339 AAGGATTAAT
Statistics
Matches: 64, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 2 0.03
11 53 0.83
12 4 0.06
ACGTcount: A:0.46, C:0.02, G:0.29, T:0.23
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:16805316 original size:33 final size:33
Alignment explanation
Indices: 16805276--16805338 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
16805266 TTAAATATGG
16805276 ATTTGAGA-GAAATTTGAAAGGAAATTGAGAGCA
1 ATTTGAGAGGAAA-TTGAAAGGAAATTGAGAGCA
16805309 ATTTGAGAGGAAATTGAAAGGAAATTGAGA
1 ATTTGAGAGGAAATTGAAAGGAAATTGAGA
16805339 AAGGATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.29, T:0.24
Consensus pattern (33 bp):
ATTTGAGAGGAAATTGAAAGGAAATTGAGAGCA
Found at i:16811645 original size:31 final size:30
Alignment explanation
Indices: 16811576--16811648 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
16811566 AGATGATAAT
* *
16811576 GTTAAATGA-TAAAATTGAAAATTTTTATA
1 GTTAAATGATTAAAATTAAAAATTTTTACA
* *
16811605 ATTTAATGATTAAAA-TAAAAATATGTTTACA
1 GTTAAATGATTAAAATTAAAAAT-T-TTTACA
16811636 GTTAAATGATTAA
1 GTTAAATGATTAA
16811649 TTATATAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 13 0.37
30 6 0.17
31 16 0.46
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.40
Consensus pattern (30 bp):
GTTAAATGATTAAAATTAAAAATTTTTACA
Found at i:16828400 original size:24 final size:24
Alignment explanation
Indices: 16828368--16828420 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
16828358 AAATCTAGAA
16828368 TGTCTAGCCCTTTGGGACGAACTG
1 TGTCTAGCCCTTTGGGACGAACTG
16828392 TGTCTAGCCCTTTGGGACGAACTG
1 TGTCTAGCCCTTTGGGACGAACTG
16828416 TGTCT
1 TGTCT
16828421 GTAGATAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.32
Consensus pattern (24 bp):
TGTCTAGCCCTTTGGGACGAACTG
Found at i:16833380 original size:17 final size:17
Alignment explanation
Indices: 16833358--16833391 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16833348 TCACTTAGTG
16833358 GTAATCCTTCATAGTAA
1 GTAATCCTTCATAGTAA
16833375 GTAATCCTTCATAGTAA
1 GTAATCCTTCATAGTAA
16833392 TTGAATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (17 bp):
GTAATCCTTCATAGTAA
Found at i:16833456 original size:14 final size:15
Alignment explanation
Indices: 16833432--16833473 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
16833422 ACTTTGTGTG
*
16833432 AGCTATTTTTTT-AT
1 AGCTTTTTTTTTCAT
*
16833446 GGCTTTTTTTTTCAT
1 AGCTTTTTTTTTCAT
*
16833461 AGCTTCTTTTTTC
1 AGCTTTTTTTTTC
16833474 TTTAGAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.12, C:0.14, G:0.10, T:0.64
Consensus pattern (15 bp):
AGCTTTTTTTTTCAT
Found at i:16839392 original size:45 final size:46
Alignment explanation
Indices: 16839334--16839420 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
16839324 CATATTATTA
* * **
16839334 TTATAATTTTATAT-TTTATAATATACTTACTTATTTTTTATATACT
1 TTATAATTTTATATATGTAT-ATATACATACTTACATTTTATATACT
16839380 TTATAA-TTTATATATGTATATATACATACTTACATTTTATA
1 TTATAATTTTATATATGTATATATACATACTTACATTTTATA
16839421 ATATATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 26 0.72
46 10 0.28
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (46 bp):
TTATAATTTTATATATGTATATATACATACTTACATTTTATATACT
Found at i:16839689 original size:37 final size:35
Alignment explanation
Indices: 16839607--16839689 Score: 85
Period size: 37 Copynumber: 2.3 Consensus size: 35
16839597 CCCCTTTTTT
* * *
16839607 ATATATATAGTTTTTATATTTTATAATTCGCATAT
1 ATATATATATTTTTTATATTTTACAATTCGCATAC
* ** *
16839642 ACATGCATATTTTTCGTATATTTTACAATTCGTATAC
1 ATATATATATTTTT--TATATTTTACAATTCGCATAC
16839679 ATATATATATT
1 ATATATATATT
16839690 AGAGGTGCTC
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
35 10 0.28
37 26 0.72
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.51
Consensus pattern (35 bp):
ATATATATATTTTTTATATTTTACAATTCGCATAC
Found at i:16839928 original size:40 final size:40
Alignment explanation
Indices: 16839873--16840043 Score: 258
Period size: 40 Copynumber: 4.3 Consensus size: 40
16839863 AATAAATATA
16839873 TTTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAA-TTTTTTTAATTTTAAAATATTTTTAAAATACT
*
16839914 TTTTTTTATTTTTTT-ATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
16839953 TTTTTT-A-TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
** * * *
16839991 TTTTAAAAATTTTTTAATGTTGAAATATTTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
16840031 TTTTTTAATTTTT
1 TTTTTTAATTTTT
16840044 AAAATAAATT
Statistics
Matches: 119, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
37 6 0.05
38 29 0.24
39 31 0.26
40 46 0.39
41 7 0.06
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (40 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:16839933 original size:39 final size:39
Alignment explanation
Indices: 16839873--16840043 Score: 254
Period size: 39 Copynumber: 4.3 Consensus size: 39
16839863 AATAAATATA
16839873 TTTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAA--TTTTTTAATTTTAAAATATTTTTAAAATACT
* *
16839914 TTTTTTTATTTTTTTATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTTTAATTTTAAAATATTTTTAAAATACT
16839953 TTTTTT-ATTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTTTAATTTTAAAATATTTTTAAAATACT
** * *
16839991 TTTTAAAAATTTTTTAATGTTGAAATATTTTTAAAATACT
1 TTTT-TTAATTTTTTAATTTTAAAATATTTTTAAAATACT
16840031 TTTTTTAATTTTT
1 TTTTTTAATTTTT
16840044 AAAATAAATT
Statistics
Matches: 119, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
38 35 0.29
39 43 0.36
40 34 0.29
41 7 0.06
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (39 bp):
TTTTTTAATTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:16840055 original size:21 final size:21
Alignment explanation
Indices: 16840017--16840056 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16840007 ATGTTGAAAT
**
16840017 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
16840038 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
16840057 GGTATTTATT
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:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:16840063 original size:22 final size:20
Alignment explanation
Indices: 16840016--16840070 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
16840006 AATGTTGAAA
* *
16840016 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
16840036 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
16840059 TATTTATTAAAA
1 TATTT-TTAAAA
16840071 AATGGGCCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:16840313 original size:13 final size:13
Alignment explanation
Indices: 16840295--16840345 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
16840285 TTTTTATATT
16840295 TTTATTCATTTTC
1 TTTATTCATTTTC
*
16840308 TTTATTCA-TTTA
1 TTTATTCATTTTC
16840320 TTTATTTACATTTTC
1 TTTA-TT-CATTTTC
*
16840335 ATTATT-ATTTT
1 TTTATTCATTTT
16840346 GAGAGAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 12 0.38
13 10 0.31
14 4 0.12
15 6 0.19
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTCATTTTC
Found at i:16840718 original size:74 final size:74
Alignment explanation
Indices: 16840640--16840783 Score: 216
Period size: 74 Copynumber: 1.9 Consensus size: 74
16840630 TCTTTTTAAA
** *
16840640 CTCAAGTTTTAAACGATCTCGGGAATCAAGAAGAGATCATGTCCTAACTTACTGGACATGATCCC
1 CTCAAGTTTTAAACGATCTCAAGAATCAAGAAAAGATCATGTCCTAACTTACTGGACATGATCCC
16840705 TTTTTTTTT
66 TTTTTTTTT
* ** * *
16840714 CTCAAGTTTTAAACGATCTCAAGAATTAAGAAAAGATTGTGTCTTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCAAGAATCAAGAAAAGATCATGTCCTAACTTACTGGACATGATCCC
16840779 TTTTT
66 TTTTT
16840784 CAAATCCGAG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (74 bp):
CTCAAGTTTTAAACGATCTCAAGAATCAAGAAAAGATCATGTCCTAACTTACTGGACATGATCCC
TTTTTTTTT
Found at i:16849770 original size:4 final size:4
Alignment explanation
Indices: 16849761--16849787 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16849751 TACTGTCGCT
16849761 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
16849788 TAACTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:16850446 original size:29 final size:30
Alignment explanation
Indices: 16850404--16850464 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
16850394 TTAACAACCC
**
16850404 AGTGACTTAAATAAAAACTTTTGCATAGTTT
1 AGTGACTT-AATAAAAACTTTTAAATAGTTT
16850435 AGTGACTT-ATAAAAACTTTTAAATAGTTT
1 AGTGACTTAATAAAAACTTTTAAATAGTTT
16850464 A
1 A
16850465 ATAACATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.71
31 8 0.29
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.39
Consensus pattern (30 bp):
AGTGACTTAATAAAAACTTTTAAATAGTTT
Found at i:16850990 original size:3 final size:3
Alignment explanation
Indices: 16850984--16851039 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
16850974 AAGAAGACAG
16850984 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16851032 ATA ATA AT
1 ATA ATA AT
16851040 GTTCTATAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:16851764 original size:27 final size:28
Alignment explanation
Indices: 16851704--16851778 Score: 118
Period size: 27 Copynumber: 2.7 Consensus size: 28
16851694 AAAAATAAAA
16851704 ATTTACCAAAATAT-TACAACTTTTTTTTT
1 ATTTACCAAAATATATA-AAC-TTTTTTTT
16851733 ATTTACCAAAATATATAAAC-TTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTTT
16851760 ATTTACCAAAATATATAAA
1 ATTTACCAAAATATATAAA
16851779 AAAAACCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
27 26 0.58
29 17 0.38
30 2 0.04
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTTACCAAAATATATAAACTTTTTTTT
Found at i:16851874 original size:27 final size:27
Alignment explanation
Indices: 16851835--16851910 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
16851825 TACTGGTCAC
*
16851835 GCCAATGGAATTGGCGGCACCAATGGT
1 GCCAATGCAATTGGCGGCACCAATGGT
*
16851862 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCAATTGGCGGCACCAATGGT
*
16851889 GCC-ATACTAATTGGCGGCACCA
1 GCCAATGC-AATTGGCGGCACCA
16851911 CTCGTATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.07
27 41 0.93
ACGTcount: A:0.25, C:0.28, G:0.29, T:0.18
Consensus pattern (27 bp):
GCCAATGCAATTGGCGGCACCAATGGT
Found at i:16852073 original size:19 final size:21
Alignment explanation
Indices: 16852035--16852073 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
16852025 ACTAATTGAT
*
16852035 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
16852056 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
16852074 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:16852137 original size:3 final size:3
Alignment explanation
Indices: 16852119--16852153 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
16852109 AAAATAAAAG
*
16852119 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16852154 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:16852158 original size:3 final size:3
Alignment explanation
Indices: 16852152--16852201 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
16852142 ATTATTATTA
16852152 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
16852200 TT
1 TT
16852202 AGTATGAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:16852396 original size:12 final size:12
Alignment explanation
Indices: 16852379--16852409 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16852369 ATAATTTTAG
16852379 TGTGTATTATTT
1 TGTGTATTATTT
16852391 TGTGTATTATTT
1 TGTGTATTATTT
*
16852403 TGAGTAT
1 TGTGTAT
16852410 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:16853006 original size:18 final size:18
Alignment explanation
Indices: 16852963--16853007 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
16852953 TTGACATGAT
*
16852963 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
**
16852981 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
16852999 TGGTGGCGA
1 TGGTGGCGA
16853008 TCATTGGGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.49, T:0.13
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:16857714 original size:19 final size:19
Alignment explanation
Indices: 16857679--16857716 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
16857669 TTTAAACACG
16857679 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
16857698 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
16857717 ACATTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:16857773 original size:12 final size:12
Alignment explanation
Indices: 16857758--16857908 Score: 92
Period size: 12 Copynumber: 13.0 Consensus size: 12
16857748 CTCTTCCTCT
16857758 TCTTCTTCTTTC
1 TCTTCTTCTTTC
*
16857770 TCTTCTCCTTTC
1 TCTTCTTCTTTC
*
16857782 -CCT-TTCTTTC
1 TCTTCTTCTTTC
16857792 -CTTCTTTCTTTC
1 TCTTC-TTCTTTC
*
16857804 T-TTTTTC-TTC
1 TCTTCTTCTTTC
*
16857814 TCTTCTCCTTT-
1 TCTTCTTCTTTC
*
16857825 TCTCCTTCTTTC
1 TCTTCTTCTTTC
*
16857837 T-TTCCTTTTTTC
1 TCTT-CTTCTTTC
*
16857849 TCTTCTCCTTTC
1 TCTTCTTCTTTC
16857861 -CTT-TTCTTTC
1 TCTTCTTCTTTC
16857871 T-TTCCTCTCCTTTC
1 TCTT-CT-T-CTTTC
16857885 T-TTCTTTCTTTC
1 TCTTC-TTCTTTC
16857897 T-TTCTTTCTTTC
1 TCTTC-TTCTTTC
16857909 CCTCCTTTTG
Statistics
Matches: 111, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
10 20 0.18
11 22 0.20
12 55 0.50
13 5 0.05
14 9 0.08
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TCTTCTTCTTTC
Found at i:16857788 original size:22 final size:21
Alignment explanation
Indices: 16857763--16857897 Score: 85
Period size: 22 Copynumber: 6.6 Consensus size: 21
16857753 CCTCTTCTTC
16857763 TTCTTTCTCTTCTCCTTTCCCT
1 TTCTTTCTCTTCTCCTTT-CCT
* *
16857785 TTCTTTC-CTTCTTTCTTTCTT
1 TTCTTTCTCTTC-TCCTTTCCT
* *
16857806 TTTTCTTCTCTTCTCCTTTTCTCC
1 TTCT-TTCTCTTCTCC-TTTC-CT
16857830 TTC-TT-TCTT-TCCTTT--T
1 TTCTTTCTCTTCTCCTTTCCT
*
16857846 TTCTCTTCTCCTT-TCCTTTTCT
1 TTCT-TTCT-CTTCTCCTTTCCT
16857868 TTCTTTC-C-TCTCCTTT-CT
1 TTCTTTCTCTTCTCCTTTCCT
16857886 TTCTTTCT-TTCT
1 TTCTTTCTCTTCT
16857898 TTCTTTCTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 31
0.70 0.06 0.24
Matches are distributed among these distances:
16 3 0.03
18 12 0.13
19 14 0.15
20 12 0.13
21 16 0.18
22 24 0.26
23 8 0.09
24 2 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (21 bp):
TTCTTTCTCTTCTCCTTTCCT
Found at i:16857800 original size:4 final size:4
Alignment explanation
Indices: 16857783--16857908 Score: 98
Period size: 4 Copynumber: 30.2 Consensus size: 4
16857773 TCTCCTTTCC
* * *
16857783 CTTT CTTT CCTT CTTT CTTT CTTT -TTT CTTCT CTTCT CCTTT -TCT CCTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT-T CTT-T -CTTT CTTT CTTT
* *
16857832 CTTT CTTT CCTTT -TTT CTCTT C-TC CTTT CCTTTT CTTT CTTT CCTCTC
1 CTTT CTTT -CTTT CTTT CT-TT CTTT CTTT -C-TTT CTTT CTTT -CT-TT
16857880 CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
16857909 CCTCCTTTTG
Statistics
Matches: 100, Mismatches: 10, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
3 10 0.10
4 63 0.63
5 20 0.20
6 7 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:16857831 original size:37 final size:35
Alignment explanation
Indices: 16857790--16857876 Score: 122
Period size: 35 Copynumber: 2.5 Consensus size: 35
16857780 TCCCTTTCTT
* *
16857790 TCCTTCTTTCTTTCTTTTTTCTTCTCTTCTCCTTTTC
1 TCCTTCTTTCTTTC-CTTTT-TTCTCTTCTCCTTTCC
16857827 TCCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCC
1 TCCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCC
*
16857862 T-TTTCTTTCTTTCCT
1 TCCTTCTTTCTTTCCT
16857877 CTCCTTTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
34 13 0.28
35 16 0.34
36 4 0.09
37 14 0.30
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (35 bp):
TCCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCC
Found at i:16857873 original size:34 final size:33
Alignment explanation
Indices: 16857793--16857909 Score: 112
Period size: 34 Copynumber: 3.4 Consensus size: 33
16857783 CTTTCTTTCC
* *
16857793 TTCTTTCTTTCTTTTTTCTTCTCTTCTCCTTTTCTCC
1 TTCTTTCTTTC-CTTTT-TTCTCTTCTCC-TTTCT-T
16857830 TTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCTT
1 TTCTTTCTTTCCTTTTTTCTCTTCTCCTTT-CTT
* *
16857864 TTCTTTCTTTCCTCTCCTTTCT-TTCTTTCTTTC-T
1 TTCTTTCTTTCCT-T-TTTTCTCTTC-TCCTTTCTT
16857898 TTCTTTCTTTCC
1 TTCTTTCTTTCC
16857910 CTCCTTTTGC
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
34 29 0.40
35 18 0.25
36 14 0.19
37 11 0.15
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (33 bp):
TTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCTT
Found at i:16858090 original size:28 final size:28
Alignment explanation
Indices: 16858050--16858105 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
16858040 TTTTTTTTGG
16858050 TTTTTTTGATATATTTTGGTAAATAAAA
1 TTTTTTTGATATATTTTGGTAAATAAAA
*
16858078 TTTTTTTTATATATTTTGGTAAATAAAA
1 TTTTTTTGATATATTTTGGTAAATAAAA
16858106 AAAAGTTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (28 bp):
TTTTTTTGATATATTTTGGTAAATAAAA
Found at i:16858553 original size:4 final size:4
Alignment explanation
Indices: 16858536--16858626 Score: 66
Period size: 4 Copynumber: 22.2 Consensus size: 4
16858526 TCACCTTTCC
*
16858536 CTTT CTTT CCTT CTTT CTTT CTTT -TTT CTTCT CTTCT CCTTT C-TT C-TT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT-T CTT-T -CTTT CTTT CTTT
*
16858584 CTTT CTTT CATTT -TTT CTCTT C-TC CTTT CCTTTT CTTT CTTT C
1 CTTT CTTT C-TTT CTTT CT-TT CTTT CTTT -C-TTT CTTT CTTT C
16858627 CCTCCTTCTG
Statistics
Matches: 73, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
3 14 0.19
4 38 0.52
5 15 0.21
6 6 0.08
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:16858577 original size:44 final size:41
Alignment explanation
Indices: 16858504--16858627 Score: 125
Period size: 40 Copynumber: 3.0 Consensus size: 41
16858494 TTTCTTCCCT
*
16858504 CTTC-TTCTTCTTTTTT-TTCTCTTCACCTTTCCCTTTCTTTC
1 CTTCTTTCTTCTTTTTTCTTCTCTTCTCCTTT--CTTTCTTTC
16858545 CTTCTTTCTTTCTTTTTTCTTCTCTTCTCCTTTC-TTC-TTC
1 CTTCTTTC-TTCTTTTTTCTTCTCTTCTCCTTTCTTTCTTTC
* *
16858585 TTTCTTTCATT-TTTTCTCTTCTCCTT-TCCTTTTCTTTCTTTC
1 CTTCTTTC-TTCTTTTTTCTTCT-CTTCTCC-TTTCTTTCTTTC
16858627 C
1 C
16858628 CTCCTTCTGC
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
39 13 0.18
40 19 0.27
41 10 0.14
42 7 0.10
43 9 0.13
44 13 0.18
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (41 bp):
CTTCTTTCTTCTTTTTTCTTCTCTTCTCCTTTCTTTCTTTC
Found at i:16858626 original size:34 final size:36
Alignment explanation
Indices: 16858535--16858626 Score: 127
Period size: 34 Copynumber: 2.6 Consensus size: 36
16858525 TTCACCTTTC
*
16858535 CCTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCT
1 CCTTTC-TT-CTTCTTTCTTTCTATTTTCTTCTCTTCT
16858573 CCTTTCTTCTTCTTTCTTTC-ATTTT-TTCTCTTCT
1 CCTTTCTTCTTCTTTCTTTCTATTTTCTTCTCTTCT
16858607 CCTTTCCTT-TTCTTTCTTTC
1 CCTTT-CTTCTTCTTTCTTTC
16858627 CCTCCTTCTG
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
34 25 0.48
35 7 0.13
36 12 0.23
37 2 0.04
38 6 0.12
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (36 bp):
CCTTTCTTCTTCTTTCTTTCTATTTTCTTCTCTTCT
Found at i:16858705 original size:27 final size:27
Alignment explanation
Indices: 16858667--16858742 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
16858657 TAATACCAAC
16858667 TGGTGCCGCCAATGGCATTGGCACCCT
1 TGGTGCCGCCAATGGCATTGGCACCCT
** *
16858694 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCCT
**
16858721 TGGTGCCGCCAATACCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
16858743 TTGATCAGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.14, C:0.30, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCCT
Found at i:16858863 original size:27 final size:28
Alignment explanation
Indices: 16858803--16858873 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
16858793 TGGTTTTTTG
*
16858803 ATATATTGTGGTAAATAAAAAAAAGTTT
1 ATATATTTTGGTAAATAAAAAAAAGTTT
16858831 ATATATTTTGGTAAAT-AAAAAAAGTTGT
1 ATATATTTTGGTAAATAAAAAAAAGTT-T
16858859 A-ATATTTTGGTAAAT
1 ATATATTTTGGTAAAT
16858874 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAAGTTT
Found at i:16859422 original size:744 final size:737
Alignment explanation
Indices: 16857950--16859320 Score: 1697
Period size: 744 Copynumber: 1.9 Consensus size: 737
16857940 TAATACCAAC
16857950 TGGTGCCGCCAATGGCATTCGCACCATTGGTGCCGCCAATACCATTGGCGTGACCAGTGAATTGT
1 TGGTGCCGCCAATGGCATTCGCACCATTGGTGCCGCCAATACCATTGGCGTGACCAGTGAATTGT
* **
16858015 CACATCAGTCTGATTTTTTTCAGGTTTTTTTTTGGTTTTTTTGATATATTTTGGTAAATAAAATT
66 CACATCAGTCTGATTTTTTTCAGGTTTTTTTTTGGTTTTTTTGATATATTGTGGTAAATAAAAAA
***
16858080 TTTTTTATATATTTTGGTAAATAAAAAAAAGTTGTAATATTTTGGTAAATTTTTATTTTTTATAA
131 AAGTTTATATATTTTGGTAAATAAAAAAAAGTTGTAATATTTTGGTAAATTTTTATTTTTTATAA
16858145 TATTTTTGTAAAAAACCCTGAAAATCAATTAAAAACAAAAAAAATAAAAAAATAAAAATACTGAT
196 TATTTTTGTAAAAAACCCTGAAAATCAATTAAAAACAAAAAAAAT-----AATAAAAATACTGAT
16858210 TATTCCGTTTATTTTATAAAATAATATTAAAAAACAAAAAAAATTTATAAGATTTAGATTAATTA
256 TATTCCGTTTATTTTATAAAATAATATTAAAAAACAAAAAAAATTTATAAGATTTAGATTAATTA
16858275 CAAAAATAGGTTATTTTCTACCATGTTTTCGGGTGCTGCGAATGTGTCAGGTAGCACCACCCTAA
321 CAAAAATAGGTTATTTTCTACCATGTTTTCGGGTGCTGCGAATGTGTCAGGTAGCACCACCCTAA
*
16858340 ATTTACCCAAAACATTTTACACTGATTTTGTGGAAAAAAATATTTTTTAATTGGTGTCGCTTGAC
386 ATTTACCCAAAACATCTTACACTGATTTTGTGGAAAAAAATATTTTTTAATTGGTGTCGCTTGAC
16858405 AAATTAGCGGCACTAGTACGATTTTTTTTAAAAATACATATATTTATGAGTTTATATAGCACGAA
451 AAATTAGCGGCACTAGTACGATTTTTTTTAAAAATACATATATTTATGAGTTTATATAGCACGAA
* * * * ***** * *
16858470 AATATACGGTACAAAATTTTTTCCTTTCTTCCCTCTTCTTCTTCTTTTTTTTCTCTTCACCTTTC
516 AATATACGGTACAAAATTTTTT-CTTTCTTCACTC-TCTACTACATTGACGGCCCTTCACCTTTA
****** ** *************** *** ** ******** * * *****
16858535 CCTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCTCCTTTCTTCTTCTTTCTTTCATTTTTT
579 AAAAGATGGCAGAAAGGAAAAAAAGTTGAATAACTGAAAAAAACTTATTCTTTCGTTCATGGGAG
* * * ** ** * * *
16858600 CTCTTCTCCTTTCCTTTTCTTTCTTTCCCTCCTTCTGCCCCCACCACTGACCCCCCATAATACCA
644 CCCATCACCTTTCCTTGGCAGTCTTGCCCTCCTTCTGCCCCCACCAATGACCCCCCACAATACCA
*
16858665 ACTGGTGCCGCCAATGGCATTGGCACCCT
709 ACTGCTGCCGCCAATGGCATTGGCACCCT
** * * * *
16858694 TGGTGCCGCCAATGGTTTTGGCACCTTTGGTGCCGCCAATACCATTGGCTTGATCAGTGAATTGT
1 TGGTGCCGCCAATGGCATTCGCACCATTGGTGCCGCCAATACCATTGGCGTGACCAGTGAATTGT
*
16858759 CACATCGGTCTGATTTTTTTTGCAGGTTTTTTTTTGG-TTTTTTGATATATTGTGGTAAATAAAA
66 CACATCAGTCTGA-TTTTTTT-CAGGTTTTTTTTTGGTTTTTTTGATATATTGTGGTAAATAAAA
16858823 AAAAGTTTATATATTTTGGTAAAT-AAAAAAAGTTGTAATATTTTGGTAAATTTTTATTTTTTAT
129 AAAAGTTTATATATTTTGGTAAATAAAAAAAAGTTGTAATATTTTGGTAAATTTTTATTTTTTAT
16858887 AATATTTTTGTAAAAAACCCTGAAAATCAATTAAAAAC-AAAAAAAT-A-AAAAATACTGATTAT
194 AATATTTTTGTAAAAAACCCTGAAAATCAATTAAAAACAAAAAAAATAATAAAAATACTGATTAT
16858949 TCCGTTTATTTTATAAAATAATATTAAAAAACAAAAAAAA-TTATAAGATTTAGATTAATTACAA
259 TCCGTTTATTTTATAAAATAATATTAAAAAACAAAAAAAATTTATAAGATTTAGATTAATTACAA
*
16859013 AAATAGGTTATTTTCTACCGTGTTTTCGGGTGCTGCGAATGTGTCAGGTAGCACCACCCTAAATT
324 AAATAGGTTATTTTCTACCATGTTTTCGGGTGCTGCGAATGTGTCAGGTAGCACCACCCTAAATT
*
16859078 TACCCAAAACATCTTACACTGATTTTGTTGAAAAAAATATTTTTTTAATTGGTGTCGCTTGACAA
389 TACCCAAAACATCTTACACTGATTTTGTGGAAAAAAATA-TTTTTTAATTGGTGTCGCTTGACAA
*
16859143 ATTAGCGGCACTAGTATGATTTTTTTTTAAAAAAATACATATATTTATGAGTTTATATAGCACGA
453 ATTAGCGGCACTAGTACGA-TTTTTTTT--AAAAATACATATATTTATGAGTTTATATAGCACGA
*
16859208 AAATATACGGTAC-AAATTTTTT-TTT-TT-ACTAC-CTGAC-ACATTGACGGCACCAATGTGA-
515 AAATATACGGTACAAAATTTTTTCTTTCTTCACT-CTCT-ACTACATTGACGGC-CC--T-TCAC
* * *
16859266 TTTTAAAAAAGATGGCAGAAAGGAAAAAAAGTTGAATAAGTGAAAAAAAGTTATT
574 CTTT-AAAAAGATGGCAGAAAGGAAAAAAAGTTGAATAACTGAAAAAAACTTATT
16859321 GTTTAGGTTA
Statistics
Matches: 545, Mismatches: 69, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
733 6 0.01
734 4 0.01
735 128 0.23
736 105 0.19
737 21 0.04
738 9 0.02
739 48 0.09
743 8 0.01
744 149 0.27
745 52 0.10
746 15 0.03
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (737 bp):
TGGTGCCGCCAATGGCATTCGCACCATTGGTGCCGCCAATACCATTGGCGTGACCAGTGAATTGT
CACATCAGTCTGATTTTTTTCAGGTTTTTTTTTGGTTTTTTTGATATATTGTGGTAAATAAAAAA
AAGTTTATATATTTTGGTAAATAAAAAAAAGTTGTAATATTTTGGTAAATTTTTATTTTTTATAA
TATTTTTGTAAAAAACCCTGAAAATCAATTAAAAACAAAAAAAATAATAAAAATACTGATTATTC
CGTTTATTTTATAAAATAATATTAAAAAACAAAAAAAATTTATAAGATTTAGATTAATTACAAAA
ATAGGTTATTTTCTACCATGTTTTCGGGTGCTGCGAATGTGTCAGGTAGCACCACCCTAAATTTA
CCCAAAACATCTTACACTGATTTTGTGGAAAAAAATATTTTTTAATTGGTGTCGCTTGACAAATT
AGCGGCACTAGTACGATTTTTTTTAAAAATACATATATTTATGAGTTTATATAGCACGAAAATAT
ACGGTACAAAATTTTTTCTTTCTTCACTCTCTACTACATTGACGGCCCTTCACCTTTAAAAAGAT
GGCAGAAAGGAAAAAAAGTTGAATAACTGAAAAAAACTTATTCTTTCGTTCATGGGAGCCCATCA
CCTTTCCTTGGCAGTCTTGCCCTCCTTCTGCCCCCACCAATGACCCCCCACAATACCAACTGCTG
CCGCCAATGGCATTGGCACCCT
Found at i:16861223 original size:20 final size:20
Alignment explanation
Indices: 16861200--16861253 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
16861190 ATATTATATG
16861200 TTTATATTTTAT-TTTCAATA
1 TTTATATTTTATGTTT-AATA
* *
16861220 TTTAGATTTAATGTTTAATA
1 TTTATATTTTATGTTTAATA
16861240 -TTATATTTT-TGTTT
1 TTTATATTTTATGTTT
16861254 GTAAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 5 0.17
19 7 0.24
20 14 0.48
21 3 0.10
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.65
Consensus pattern (20 bp):
TTTATATTTTATGTTTAATA
Found at i:16862121 original size:18 final size:17
Alignment explanation
Indices: 16862089--16862123 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16862079 TGCATAAATT
*
16862089 AAATACAAAGAAATAAA
1 AAATAAAAAGAAATAAA
16862106 AAATAAAAATGAAATAAA
1 AAATAAAAA-GAAATAAA
16862124 TACACATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (17 bp):
AAATAAAAAGAAATAAA
Found at i:16863700 original size:39 final size:39
Alignment explanation
Indices: 16863654--16864173 Score: 745
Period size: 39 Copynumber: 13.3 Consensus size: 39
16863644 CGTATTCATT
* * *
16863654 TTTAAGCATATATCATATTACACATATAATCACCTAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
16863693 TTCAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
16863732 TTTAAGCATATATAACAATATACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* * *
16863771 TTTAAGCATATCTCAAAATATACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
16863810 TTTAAGCATATGTCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
*
16863849 TTTAAGCATATATCACAATATC-CATATAATCACATAATA
1 TTTAAGCATATATCACAATA-CACATATAATCACATAACA
* * *
16863888 TTTAAACATATATCACAATACTCGTATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
16863927 TTTAAGCATATATCACAATATACATATAATCACATAATA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* * ***
16863966 TTTAAACATATATCATAATACTTGTATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
16864005 TTCAAGCATATATCACAATATACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
*
16864044 TTTAAGCATATATCACAATATACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* * *
16864083 TTTAAGCATATATCACAATACTCATATAACCATATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
16864122 TTTAAACATATATCACAATATACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
16864161 TTTAAGCATATAT
1 TTTAAGCATATAT
16864174 TGTAATACTC
Statistics
Matches: 428, Mismatches: 51, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
38 1 0.00
39 426 1.00
40 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACATAACA
Found at i:16878146 original size:41 final size:41
Alignment explanation
Indices: 16878101--16878374 Score: 140
Period size: 41 Copynumber: 6.6 Consensus size: 41
16878091 CTTTGAATGT
* * *
16878101 AAGGGGTTGCTAAGTGCAGATTTCGCGAATCATTGATCAAA
1 AAGGGGTTCCTAAGTGCAGATTCCCCGAATCATTGATCAAA
* * * * *
16878142 AAGGGGTTCCTATGTGCTGATTCCCCGTATCATTGAT-TAT
1 AAGGGGTTCCTAAGTGCAGATTCCCCGAATCATTGATCAAA
* ** * * ***
16878182 AAGGTGGTTTCTAAGTGTTGATTCCACCGTATCCTTGATTGTGA
1 AAGG-GGTTCCTAAGTGCAGATTCC-CCGAATCATTGA-TCAAA
* * * * * *
16878226 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGAT-TAT
1 AAGGGGTTCCTAAGTGCAGATTCCCCGAATCATTGATCAAA
* * * * ***
16878266 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGA
1 AAGG-GGTTCCTAAGTGCAGATTCC-CCGAATCATTGA-TCAAA
* * * * *
16878310 AAGGGGTTCCTATGTGCTGATTCCCCGTATCATTGAT-TAT
1 AAGGGGTTCCTAAGTGCAGATTCCCCGAATCATTGATCAAA
* *
16878350 AAGGTGGTTGCTAAGTGCTGATTCC
1 AAGG-GGTTCCTAAGTGCAGATTCC
16878375 ACCGGGATCC
Statistics
Matches: 193, Mismatches: 31, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
40 15 0.08
41 87 0.45
42 44 0.23
43 37 0.19
44 10 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (41 bp):
AAGGGGTTCCTAAGTGCAGATTCCCCGAATCATTGATCAAA
Found at i:16878239 original size:84 final size:84
Alignment explanation
Indices: 16878141--16878378 Score: 449
Period size: 84 Copynumber: 2.8 Consensus size: 84
16878131 CATTGATCAA
* *
16878141 AAAGGGGTTCCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTTCTAAGTGTTGATTC
1 AAAGGGGTTCCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
16878206 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
*
16878225 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTCCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
16878290 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
16878309 AAAGGGGTTCCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTCCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
16878374 CACCG
66 CACCG
16878379 GGATCCTTTG
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 150 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (84 bp):
AAAGGGGTTCCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
CACCGTATCCTTGATTGTG
Found at i:16878405 original size:44 final size:42
Alignment explanation
Indices: 16878146--16878423 Score: 305
Period size: 42 Copynumber: 6.6 Consensus size: 42
16878136 ATCAAAAAGG
* * * *
16878146 GGTTCCTATGTGCTGATTCC-CCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
* * *
16878187 GGTTTCTAAGTGTTGATTCCACCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG--AGGT
* * *
16878230 GGTTGCTATGTGCTGATTCC-CCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
*
16878271 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG--AGGT
* * * *
16878314 GGTTCCTATGTGCTGATTCC-CCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
* **
16878355 GGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATGAGGT
1 GGTTGCTAAGTGCTGATTCCACC-GTATCC-TTGATTATGAGGT
16878399 GGTTGCTAAGTGCTGATTCCACCGT
1 GGTTGCTAAGTGCTGATTCCACCGT
16878424 GTAACGCTTA
Statistics
Matches: 197, Mismatches: 29, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
40 6 0.03
41 54 0.27
42 58 0.29
43 40 0.20
44 39 0.20
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
Found at i:16883328 original size:43 final size:44
Alignment explanation
Indices: 16883264--16883617 Score: 372
Period size: 43 Copynumber: 8.3 Consensus size: 44
16883254 TTTTAGAAAT
* *
16883264 AAACGCCGCTAAAG-GTCATGACCTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACTCATGACCTTTAGCGGCGCTTTTCCCAC
*
16883307 AAACGCCGCTAAAGACT-ATGACCTTTAGCGGC-CCTTTCCCAC
1 AAACGCCGCTAAAGACTCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
16883349 AATCGCCGCTAAAGA-TGATGACTTTTAGCGGCGC-TTTCCCAC
1 AAACGCCGCTAAAGACTCATGACCTTTAGCGGCGCTTTTCCCAC
*
16883391 AAACGCCGCTAAAGACT-ATGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTAAAGACTCATGACCTTTAGCGGCGCTTTTCCCAC
*
16883434 AAACGCCGCTAAAGAC-CATGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACTCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
16883477 AAACGCCGCTATAGA-TCAAGACCGTTAGCGGCACTTTTCTCAC
1 AAACGCCGCTAAAGACTCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * ***
16883520 AAACGCCACTATAGA-TCAAGGCCTTTAGCGGCGCTTTTTGTAC
1 AAACGCCGCTAAAGACTCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * ** *
16883563 AAATGCCGCTATAGGA--CA-GACCTTTAGTGTCGCTTTTAACAG
1 AAACGCCGCTA-AAGACTCATGACCTTTAGCGGCGCTTTTCCCAC
16883605 AAACGCCGCTAAA
1 AAACGCCGCTAAA
16883618 AACATATATT
Statistics
Matches: 267, Mismatches: 36, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
41 2 0.01
42 101 0.38
43 161 0.60
44 3 0.01
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (44 bp):
AAACGCCGCTAAAGACTCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:16883565 original size:86 final size:86
Alignment explanation
Indices: 16883264--16883557 Score: 414
Period size: 86 Copynumber: 3.4 Consensus size: 86
16883254 TTTTAGAAAT
* *
16883264 AAACGCCGCTAAAGGTCATGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAGACTATGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACTATGAC
*
16883329 CTTTAGCGGC-CCTTTCCCAC
66 CTTTAGCGGCACTTTTCCCAC
* * *
16883349 AATCGCCGCTAAAGATGATGACTTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAGACTATGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACTATGAC
16883413 CTTTAGCGGCACTTTTCCCAC
66 CTTTAGCGGCACTTTTCCCAC
* * * *
16883434 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGA-TCAAGA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACT-ATGA
* *
16883498 CCGTTAGCGGCACTTTTCTCAC
65 CCTTTAGCGGCACTTTTCCCAC
* * * *
16883520 AAACGCCACTATAGATCAAGGCCTTTAGCGGCGCTTTT
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTT
16883558 TGTACAAATG
Statistics
Matches: 186, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
84 40 0.22
85 69 0.37
86 77 0.41
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACTATGAC
CTTTAGCGGCACTTTTCCCAC
Found at i:16883949 original size:43 final size:42
Alignment explanation
Indices: 16883884--16883973 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 42
16883874 CATATGCAAG
* * *
16883884 GTAATAATACATACAATGCATTT-TCTTAATCAAGTAAATCTT
1 GTAATAAAACATACAATACATTTAT-TTAATCAAGGAAATCTT
* *
16883926 AGTAATAAAAGATATAATACATTTATTTAATCAAGGAAATCTT
1 -GTAATAAAACATACAATACATTTATTTAATCAAGGAAATCTT
16883969 GTAAT
1 GTAAT
16883974 GAACTCAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 5 0.12
43 35 0.85
44 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (42 bp):
GTAATAAAACATACAATACATTTATTTAATCAAGGAAATCTT
Found at i:16887508 original size:21 final size:22
Alignment explanation
Indices: 16887469--16887521 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
16887459 ATCTAACTCC
* *
16887469 TAAACCCCTAACCCCTAAACCT
1 TAAATCCCTAACCCCTAAACCA
*
16887491 TAAATCCC-AACCCTTAAACCA
1 TAAATCCCTAACCCCTAAACCA
16887512 T-AATCCCTAA
1 TAAATCCCTAA
16887522 ATTCATACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.22
21 14 0.52
22 7 0.26
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAATCCCTAACCCCTAAACCA
Found at i:16887776 original size:22 final size:21
Alignment explanation
Indices: 16887751--16887849 Score: 65
Period size: 21 Copynumber: 4.6 Consensus size: 21
16887741 CCTCTAATGT
*
16887751 CTAACCCTTAAACCCCTAACCC
1 CTAAACCTTAAACCCC-AACCC
*
16887773 CTAAACCTTAAATCCCAACCC
1 CTAAACCTTAAACCCCAACCC
* * * * *
16887794 TTAAACCATAATCCCTAATCC
1 CTAAACCTTAAACCCCAACCC
* * *
16887815 ATAATCAC-TAAACCCCATACTCT
1 CTAAAC-CTTAAACCCCA-AC-CC
16887838 CTAAACCTTAAA
1 CTAAACCTTAAA
16887850 ATAGTAACTC
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
21 31 0.54
22 17 0.30
23 9 0.16
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (21 bp):
CTAAACCTTAAACCCCAACCC
Found at i:16887798 original size:21 final size:22
Alignment explanation
Indices: 16887751--16887811 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
16887741 CCTCTAATGT
* *
16887751 CTAACCCTTAAACCCCTAACCC
1 CTAAACCTTAAATCCCTAACCC
16887773 CTAAACCTTAAATCCC-AACCC
1 CTAAACCTTAAATCCCTAACCC
* *
16887794 TTAAACCAT-AATCCCTAA
1 CTAAACCTTAAATCCCTAA
16887812 TCCATAATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.18
21 14 0.41
22 14 0.41
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (22 bp):
CTAAACCTTAAATCCCTAACCC
Found at i:16888387 original size:41 final size:40
Alignment explanation
Indices: 16888191--16888500 Score: 200
Period size: 41 Copynumber: 7.8 Consensus size: 40
16888181 TAAAAAGTTT
* * * * *
16888191 TTAGCGGCGCTTATCCAAAAACACCACTAAAACAATGAGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGC-CTGAGCA
* * * *
16888232 TTAGCGACGCTTTCTCAAAAAAGGCCGCTAAAACACTGAGCA
1 TTAGCGGCGCTTT-TCCAAAAACGCCGCTAAAGC-CTGAGCA
* * * * *
16888274 TTAGCAGC-ATTTTCTCAAAAATGCAGCTAAAACACTGAGCA
1 TTAGCGGCGCTTTTC-CAAAAACGCCGCTAAAGC-CTGAGCA
*
16888315 TTAGCGGCGAATTTT-CAAAAACGCCGCTAAAGCCTGGAGCA
1 TTAGCGGCG-CTTTTCCAAAAACGCCGCTAAAGCCT-GAGCA
16888356 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCT-AG--
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCTGAGCA
* * *
16888393 --A-----G-TTCAT-GAAAAATGCCGCTAAAGCCCTGAGCA
1 TTAGCGGCGCTT-TTCCAAAAACGCCGCTAAAG-CCTGAGCA
* *
16888426 TTAGCGGCGCTTTAT-AAAAAACGCCGCTAAAGCCCAGAGCA
1 TTAGCGGCGCTTT-TCCAAAAACGCCGCTAAAG-CCTGAGCA
* ** *
16888467 TTAGCGACGCTTTTTAAAAAATGCCGCTAAAGCC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
16888501 CCGAAAGATA
Statistics
Matches: 221, Mismatches: 27, Indels: 43
0.76 0.09 0.15
Matches are distributed among these distances:
29 17 0.08
30 5 0.02
31 2 0.01
35 2 0.01
39 2 0.01
40 12 0.05
41 147 0.67
42 29 0.13
43 5 0.02
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCTGAGCA
Found at i:16888414 original size:70 final size:70
Alignment explanation
Indices: 16888331--16888464 Score: 209
Period size: 70 Copynumber: 1.9 Consensus size: 70
16888321 GCGAATTTTC
* *
16888331 AAAAACGCCGCTAAAG-CCTGGAGCATTAGCGGCGCTTT-TCCAAAAACGCCGCTAAAGCCTAGA
1 AAAAACGCCGCTAAAGCCCT-GAGCATTAGCGGCGCTTTAT-AAAAAACGCCGCTAAAGCCCAGA
16888394 GTTCATG
64 GTTCATG
*
16888401 AAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCAGAG
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCAGAG
16888465 CATTAGCGAC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
70 55 0.93
71 4 0.07
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (70 bp):
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCAGAGT
TCATG
Found at i:16888487 original size:111 final size:111
Alignment explanation
Indices: 16888290--16888500 Score: 307
Period size: 111 Copynumber: 1.9 Consensus size: 111
16888280 GCATTTTCTC
* **
16888290 AAAAATGCAGCTAAAACACTGAGCATTAGCGGCGAATTTTCAAAAACGCCGCTAAAGCCTGGAGC
1 AAAAATGCAGCTAAAACACTGAGCATTAGCGGCGAATTTTAAAAAACGCCGCTAAAGCCCAGAGC
* *
16888355 ATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCTAGAGTTCATG
66 ATTAGCGACGCTTTTCAAAAAACGCCGCTAAAGCCTAGAGTTCATG
* * * *
16888401 AAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCG-CTTTATAAAAAACGCCGCTAAAGCCCAGAG
1 AAAAATGCAGCTAAAACACTGAGCATTAGCGGCGAATTT-TAAAAAACGCCGCTAAAGCCCAGAG
* *
16888465 CATTAGCGACGCTTTTTAAAAAATGCCGCTAAAGCC
65 CATTAGCGACGCTTTTCAAAAAACGCCGCTAAAGCC
16888501 CCGAAAGATA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
110 3 0.03
111 85 0.97
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (111 bp):
AAAAATGCAGCTAAAACACTGAGCATTAGCGGCGAATTTTAAAAAACGCCGCTAAAGCCCAGAGC
ATTAGCGACGCTTTTCAAAAAACGCCGCTAAAGCCTAGAGTTCATG
Found at i:16892453 original size:26 final size:26
Alignment explanation
Indices: 16892395--16892446 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
16892385 GGAAAAGGGT
* **
16892395 TTCTTTAGTCAAAACATGCAAGGGTA
1 TTCTTTAGTCAAAACACGCAAGACTA
*
16892421 TTCTTTAGTCAAAACACGCTAGACTA
1 TTCTTTAGTCAAAACACGCAAGACTA
16892447 ATTTTTAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (26 bp):
TTCTTTAGTCAAAACACGCAAGACTA
Found at i:16894850 original size:50 final size:50
Alignment explanation
Indices: 16894770--16895005 Score: 373
Period size: 50 Copynumber: 4.7 Consensus size: 50
16894760 ATTTGGGTAA
* *
16894770 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
16894820 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
16894870 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * *
16894920 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
16894970 AGAACATACCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
16895006 TGTGGCTGTT
Statistics
Matches: 173, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 145 0.84
51 28 0.16
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:16906027 original size:20 final size:20
Alignment explanation
Indices: 16905992--16906040 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
16905982 ATCATGGTCT
*
16905992 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
16906011 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
16906031 TTGCTTACTT
1 TTGCTTACTT
16906041 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:16914817 original size:6 final size:6
Alignment explanation
Indices: 16914802--16914841 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
16914792 TTCTTGTTTC
16914802 TTTTTA -TTTTA TTTTTA TTTTTA TTTTTA TTTATTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTT
16914842 CGTATTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:16915306 original size:298 final size:305
Alignment explanation
Indices: 16914758--16915368 Score: 932
Period size: 298 Copynumber: 2.0 Consensus size: 305
16914748 TTTGGGAATG
*
16914758 TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTGTTTCTTTTTATTTTATTTTTATTTT
1 TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTCTTTCTTTTTATTTTATTTTTA-TTT
* * *
16914823 TATTTTTATTTATTATTTTCGTATTCTTTTATTTTTGTGTGTTTGTTTTCTTGTCTATGTAGGTC
65 TA--TTTATTTATCATTATCG--TTCTTTTATTTTTGTGTGTTTGTTTTCTTGTCTATGTAGGCC
* ** * **
16914888 ACCCACTCAAGGATTGTACTATACTTTCGAGCTTTAACGGAGAGGAGGACTACTTCAATCTACCT
126 ACCCACTCAAGGATTGTACTACACTTTCGAGCTTTAACAAAGAGGAGCACTACTAAAATCTACCT
* *
16914953 CATGTTGCTTCAAGAAAAATGGGGGAGTTTGAAACTCTTAGCTTTACATTGGGAGCACATTAGGG
191 CATGTTGCTGCAAGAAAAATGGGGGAGTTTGAAACTCTTAGCTTTACATTGGGAGCACACTAGGG
* * * * *
16915018 ACAATTGATTTGTCGTATTTCTATACGTCAAATTAAGTTCTTTTGATACT
256 AAAATTGATCTGTCGTAATTATATACGTCAAAATAAGTTCTTTTGATACT
*
16915068 TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTCTTTCTTTTTCTTTTATTTTTA-TTT
1 TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTCTTTCTTTTTATTTTATTTTTATTTT
*
16915132 A-TTATTT-TCA-TAT-G-T-TTTTATTTTTGTGTGTTTGTTTTCTTTTCTATGTAGGCCACCCA
66 ATTTATTTATCATTATCGTTCTTTTATTTTTGTGTGTTTGTTTTCTTGTCTATGTAGGCCACCCA
16915191 CTCAAGGATTGTACTACACTTTCGAGCTTTAACAAAGAGGAGCACTACTAAAATCTACCTCATGT
131 CTCAAGGATTGTACTACACTTTCGAGCTTTAACAAAGAGGAGCACTACTAAAATCTACCTCATGT
*
16915256 TGCTGCAAGAAAAATGGGGGAGTTCT-AAACTCTTAGCTTTACATTGGGAGCACACTGGGGAAAA
196 TGCTGCAAGAAAAATGGGGGAGTT-TGAAACTCTTAGCTTTACATTGGGAGCACACTAGGGAAAA
16915320 TTGATCTGTCGTAATTATATACGTCAAAATAAGTTCTTTTGATACT
260 TTGATCTGTCGTAATTATATACGTCAAAATAAGTTCTTTTGATACT
16915366 TAA
1 TAA
16915369 AGAGCTTTGT
Statistics
Matches: 280, Mismatches: 20, Indels: 14
0.89 0.06 0.04
Matches are distributed among these distances:
298 204 0.73
299 2 0.01
302 1 0.00
303 2 0.01
304 2 0.01
305 6 0.02
308 4 0.01
310 59 0.21
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (305 bp):
TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTCTTTCTTTTTATTTTATTTTTATTTT
ATTTATTTATCATTATCGTTCTTTTATTTTTGTGTGTTTGTTTTCTTGTCTATGTAGGCCACCCA
CTCAAGGATTGTACTACACTTTCGAGCTTTAACAAAGAGGAGCACTACTAAAATCTACCTCATGT
TGCTGCAAGAAAAATGGGGGAGTTTGAAACTCTTAGCTTTACATTGGGAGCACACTAGGGAAAAT
TGATCTGTCGTAATTATATACGTCAAAATAAGTTCTTTTGATACT
Found at i:16917057 original size:12 final size:12
Alignment explanation
Indices: 16917042--16917067 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16917032 TTAAACCTTT
16917042 CTTTAAGTTTTA
1 CTTTAAGTTTTA
16917054 CTTTAAGTTTTA
1 CTTTAAGTTTTA
16917066 CT
1 CT
16917068 ACATAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.58
Consensus pattern (12 bp):
CTTTAAGTTTTA
Found at i:16925254 original size:57 final size:60
Alignment explanation
Indices: 16925129--16925256 Score: 181
Period size: 61 Copynumber: 2.2 Consensus size: 60
16925119 TAGGTAGATG
* * * *
16925129 ATTATTATTATTAAATATAATTTAACAAAATTAATAATAAATAATTTAATAATATTTTAAC
1 ATTATTATTATTAAATAAAATTTAACAAAATTAATAAT-AATAATTTAATAACATCTTAAA
*
16925190 ATAATTATTATTAAATAAAATTTAACAAAA-TAAT-AT-ATAATTTAATAACATCTTAAA
1 ATTATTATTATTAAATAAAATTTAACAAAATTAATAATAATAATTTAATAACATCTTAAA
16925247 ATTATTATTA
1 ATTATTATTA
16925257 AAATATGAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
57 27 0.44
59 2 0.03
60 4 0.07
61 28 0.46
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (60 bp):
ATTATTATTATTAAATAAAATTTAACAAAATTAATAATAATAATTTAATAACATCTTAAA
Found at i:16925285 original size:57 final size:57
Alignment explanation
Indices: 16925132--16925258 Score: 152
Period size: 57 Copynumber: 2.2 Consensus size: 57
16925122 GTAGATGATT
* * * *
16925132 ATTATTATTAAATATAATTTAACAAAATTAATAATAAATAATTTAATAATATTTTAACATA
1 ATTATTATTAAATAAAATTT-A-AAAA--AATAATATATAATTTAATAACATCTTAACATA
*
16925193 ATTATTATTAAATAAAATTTAACAAAATAATATATAATTTAATAACATCTT-A-A-A
1 ATTATTATTAAATAAAATTTAAAAAAATAATATATAATTTAATAACATCTTAACATA
16925247 ATTATTATTAAA
1 ATTATTATTAAA
16925259 ATATGAATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
54 13 0.21
55 1 0.02
56 1 0.02
57 23 0.38
59 3 0.05
60 1 0.02
61 19 0.31
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (57 bp):
ATTATTATTAAATAAAATTTAAAAAAATAATATATAATTTAATAACATCTTAACATA
Found at i:16925286 original size:24 final size:23
Alignment explanation
Indices: 16925259--16925308 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
16925249 TATTATTAAA
*
16925259 ATATGAAT-TAATAAAAATCATGAT
1 ATAT-AATATAATAAAAATAAT-AT
*
16925283 ATATAATATTATAAAAATAATAT
1 ATATAATATAATAAAAATAATAT
16925306 ATA
1 ATA
16925309 ACCTATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAATATAATAAAAATAATAT
Found at i:16931298 original size:18 final size:19
Alignment explanation
Indices: 16931275--16931311 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
16931265 TTTCTTAAGC
*
16931275 AATAAAAATAATA-ATTAA
1 AATAAAAAGAATATATTAA
16931293 AATAAAAAGAATATATTAA
1 AATAAAAAGAATATATTAA
16931312 GTAAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAAAAAGAATATATTAA
Found at i:16937631 original size:35 final size:35
Alignment explanation
Indices: 16937547--16937697 Score: 142
Period size: 35 Copynumber: 4.3 Consensus size: 35
16937537 AATCCAACCA
* * * * *
16937547 AAACACACTAGATGCTCATAAGATCCAATCCATCC-
1 AAACACACCA-ATGCTCGTAAGAGCTAATCCCTCCG
**
16937582 AAACACACCAATGCTCGTAAGAGCTAATCCCTCTT
1 AAACACACCAATGCTCGTAAGAGCTAATCCCTCCG
* * *
16937617 AAGCACACCAATGCTCATAAGAGCTAATCCTTCCG
1 AAACACACCAATGCTCGTAAGAGCTAATCCCTCCG
* * * ** *
16937652 AAACACATCAGTGCTCGTAAGAGCTAGTCCAACTG
1 AAACACACCAATGCTCGTAAGAGCTAATCCCTCCG
16937687 AAACACACCAA
1 AAACACACCAA
16937698 AACATAGAGT
Statistics
Matches: 94, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
34 19 0.20
35 75 0.80
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (35 bp):
AAACACACCAATGCTCGTAAGAGCTAATCCCTCCG
Found at i:16937694 original size:70 final size:69
Alignment explanation
Indices: 16937537--16937697 Score: 187
Period size: 70 Copynumber: 2.3 Consensus size: 69
16937527 GTACATCGAC
** * *
16937537 AATCCAACCAAAACACACTAGATGCTCATAAGATCCAATCCATCCAAACACACCAATGCTCGTAA
1 AATCCAACTGAAACACACCA-ATGCTCATAAGAGCCAATCCATCCAAACACACCAATGCTCGTAA
16937602 GAGCT
65 GAGCT
** * * * * * *
16937607 AATCCCTCTTAAGCACACCAATGCTCATAAGAGCTAATCCTTCCGAAACACATCAGTGCTCGTAA
1 AATCCAACTGAAACACACCAATGCTCATAAGAGCCAATCCATCC-AAACACACCAATGCTCGTAA
16937672 GAGCT
65 GAGCT
*
16937677 AGTCCAACTGAAACACACCAA
1 AATCCAACTGAAACACACCAA
16937698 AACATAGAGT
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
69 21 0.28
70 53 0.72
ACGTcount: A:0.39, C:0.31, G:0.12, T:0.19
Consensus pattern (69 bp):
AATCCAACTGAAACACACCAATGCTCATAAGAGCCAATCCATCCAAACACACCAATGCTCGTAAG
AGCT
Found at i:16954152 original size:12 final size:12
Alignment explanation
Indices: 16954135--16954164 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16954125 CATTACATGC
16954135 CTGTGTGCTAGG
1 CTGTGTGCTAGG
16954147 CTGTGTGCTAGG
1 CTGTGTGCTAGG
*
16954159 CCGTGT
1 CTGTGT
16954165 AACAGTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.20, G:0.40, T:0.33
Consensus pattern (12 bp):
CTGTGTGCTAGG
Found at i:16955227 original size:31 final size:30
Alignment explanation
Indices: 16955171--16955229 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
16955161 TCAAGTTCCG
*
16955171 ATATACATGTAACATCTATATCATGTATCT
1 ATATACATGTAAAATCTATATCATGTATCT
*
16955201 ATATATCATGTAAAAT-TATTTCCATGTAT
1 ATATA-CATGTAAAATCTATAT-CATGTAT
16955230 TTCATGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (30 bp):
ATATACATGTAAAATCTATATCATGTATCT
Found at i:16963530 original size:22 final size:22
Alignment explanation
Indices: 16963502--16963544 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
16963492 AAAAGGACTA
16963502 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
16963524 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
16963545 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:16974284 original size:3 final size:3
Alignment explanation
Indices: 16974276--16974325 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
16974266 AGGTCGGATA
*
16974276 ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
16974324 AT
1 AT
16974326 AAAGAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:16975179 original size:87 final size:86
Alignment explanation
Indices: 16975075--16975240 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 86
16975065 AGTTTAAATT
* * *
16975075 CGGTGAATTATTCAAGTCCGTCTCAATAGGACTACCCAAATTCTAGGATATGAACTCATTAAGAT
1 CGGTGAATTATTCAAGTCCATCTCAATAGGACCACCCAAATTCTAGGATATGAACTCATTAAGAG
*
16975140 TAAGAAACTCAACCTAACATGC
66 TAAG-AACCCAACCTAACATGC
* *
16975162 CGGTGAATTCA-TCAAGTCCATCTCAATAGGACCACCCAAATTCTGGGATATGAATTCATTAAGA
1 CGGTGAATT-ATTCAAGTCCATCTCAATAGGACCACCCAAATTCTAGGATATGAACTCATTAAGA
16975226 GTAAGAACCCAACCT
65 GTAAGAACCCAACCT
16975241 TATTCGTGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
86 9 0.12
87 62 0.86
88 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (86 bp):
CGGTGAATTATTCAAGTCCATCTCAATAGGACCACCCAAATTCTAGGATATGAACTCATTAAGAG
TAAGAACCCAACCTAACATGC
Found at i:16981902 original size:24 final size:24
Alignment explanation
Indices: 16981870--16981922 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
16981860 ATGTTTTCCG
16981870 TAATGGAGTTTTGTATGCTATCCC
1 TAATGGAGTTTTGTATGCTATCCC
*
16981894 TAATGGAGTTTTGTATGCTATCCG
1 TAATGGAGTTTTGTATGCTATCCC
16981918 TAATG
1 TAATG
16981923 CCCATAAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (24 bp):
TAATGGAGTTTTGTATGCTATCCC
Found at i:16987009 original size:16 final size:17
Alignment explanation
Indices: 16986990--16987023 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
16986980 AAATACTATG
16986990 AAATAAAAAT-AAACAA
1 AAATAAAAATCAAACAA
*
16987006 AAATAAACATCAAACAA
1 AAATAAAAATCAAACAA
16987023 A
1 A
16987024 CGCCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAAAATCAAACAA
Found at i:16992506 original size:20 final size:20
Alignment explanation
Indices: 16992458--16992507 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
16992448 TATGGAATGA
* *
16992458 TTATGCAAAAACATGAATCT
1 TTATGCAACAACATGAACCT
* *
16992478 ATATGCAACGACATGAACCT
1 TTATGCAACAACATGAACCT
16992498 TTATGCAACA
1 TTATGCAACA
16992508 CTATTTAGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (20 bp):
TTATGCAACAACATGAACCT
Found at i:17010308 original size:3 final size:3
Alignment explanation
Indices: 17010300--17010336 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
17010290 AAGAGACCAA
*
17010300 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17010337 CCTTTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:17029968 original size:71 final size:71
Alignment explanation
Indices: 17029852--17029994 Score: 234
Period size: 71 Copynumber: 2.0 Consensus size: 71
17029842 TTTTACAGCT
*
17029852 TCGCTAATTTTTCAGTTAGAAAATTTTAAATAATATACATTTTATATTTATATTATGCTATTTTG
1 TCGCTAATTTTCCAGTTAGAAAATTTTAAATAATATACATTTTATATTTATATTATGCTATTTTG
17029917 ATTTCA
66 ATTTCA
** *
17029923 TCGCTAATTATTCCA-TTAGAATTTTTTAAATTATATACATTTTATATTTATATTATGCTATTTT
1 TCGCTAATT-TTCCAGTTAGAAAATTTTAAATAATATACATTTTATATTTATATTATGCTATTTT
17029987 GATTTCA
65 GATTTCA
17029994 T
1 T
17029995 ATTACAATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 63 0.94
72 4 0.06
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.52
Consensus pattern (71 bp):
TCGCTAATTTTCCAGTTAGAAAATTTTAAATAATATACATTTTATATTTATATTATGCTATTTTG
ATTTCA
Found at i:17030547 original size:20 final size:20
Alignment explanation
Indices: 17030497--17030548 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
17030487 AGTAGCCACG
* *
17030497 TGACTAAAAACATGTTGTAA
1 TGACTAAAAACATGCTATAA
17030517 TGAACCTAAAAACATGCTATAA
1 TG-A-CTAAAAACATGCTATAA
17030539 TGACTAAAAA
1 TGACTAAAAA
17030549 TATGAAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.32
21 2 0.07
22 17 0.61
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (20 bp):
TGACTAAAAACATGCTATAA
Found at i:17030845 original size:14 final size:14
Alignment explanation
Indices: 17030826--17030853 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17030816 AAAAACTTAA
17030826 CTTGATTGAGCTTG
1 CTTGATTGAGCTTG
17030840 CTTGATTGAGCTTG
1 CTTGATTGAGCTTG
17030854 TTTACTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (14 bp):
CTTGATTGAGCTTG
Found at i:17031547 original size:11 final size:12
Alignment explanation
Indices: 17031524--17031553 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
17031514 AAGTAAATAG
17031524 ATATTATATAAA
1 ATATTATATAAA
17031536 ATATTA-ATAAA
1 ATATTATATAAA
17031547 ATATTAT
1 ATATTAT
17031554 TTTTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATTATATAAA
Found at i:17032796 original size:20 final size:20
Alignment explanation
Indices: 17032771--17032808 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17032761 TTATAAATCA
17032771 TAAAAATAGAAATCCAAAAT
1 TAAAAATAGAAATCCAAAAT
*
17032791 TAAAAATATAAATCCAAA
1 TAAAAATAGAAATCCAAA
17032809 GAGGCCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.21
Consensus pattern (20 bp):
TAAAAATAGAAATCCAAAAT
Found at i:17050775 original size:8 final size:8
Alignment explanation
Indices: 17050762--17050790 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
17050752 GTATAGTAAA
17050762 AAAAATAT
1 AAAAATAT
17050770 AAAAATAT
1 AAAAATAT
17050778 AAAAATAT
1 AAAAATAT
17050786 AAAAA
1 AAAAA
17050791 GAATGGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:17051174 original size:9 final size:9
Alignment explanation
Indices: 17051160--17051189 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
17051150 TGTTTAAAAC
17051160 AATAAAGAA
1 AATAAAGAA
17051169 AATAAAGAA
1 AATAAAGAA
17051178 AATAAAGGAA
1 AATAAA-GAA
17051188 AA
1 AA
17051190 AATATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.75
10 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
AATAAAGAA
Found at i:17057760 original size:22 final size:24
Alignment explanation
Indices: 17057735--17057779 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
17057725 AAAGCAGGAA
*
17057735 GCTTGAATCAACA-AT-CTTATTT
1 GCTTCAATCAACACATACTTATTT
*
17057757 GCTTCCATCAACACATACTTATT
1 GCTTCAATCAACACATACTTATT
17057780 AACTTATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (24 bp):
GCTTCAATCAACACATACTTATTT
Found at i:17060254 original size:16 final size:18
Alignment explanation
Indices: 17060228--17060261 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17060218 TTAAAATCGG
17060228 GTTGAGAAAATT-ATTTA
1 GTTGAGAAAATTAATTTA
17060245 GTTG-GAAAATTAATTTA
1 GTTGAGAAAATTAATTTA
17060262 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (18 bp):
GTTGAGAAAATTAATTTA
Found at i:17070411 original size:25 final size:24
Alignment explanation
Indices: 17070372--17070463 Score: 103
Period size: 25 Copynumber: 3.7 Consensus size: 24
17070362 TCATGTATAT
* *
17070372 GTATGCTCATACGAGCTATGAATTG
1 GTATGCTCACACGAGCTAT-AATCG
* *
17070397 GTATGCTCACTCGAGCTGTAGATCG
1 GTATGCTCACACGAGCTATA-ATCG
* *
17070422 GTATGCTCTCACGAGCTATAAATCA
1 GTATGCTCACACGAGCTAT-AATCG
17070447 GTATGCTCACACGAGCT
1 GTATGCTCACACGAGCT
17070464 GTGGGTCGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 1 0.02
25 54 0.96
26 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (24 bp):
GTATGCTCACACGAGCTATAATCG
Found at i:17073211 original size:15 final size:16
Alignment explanation
Indices: 17073191--17073220 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17073181 TAATAACTAA
17073191 TATATAAT-TATATTT
1 TATATAATATATATTT
17073206 TATATAATATATATT
1 TATATAATATATATT
17073221 AATTGTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:17080160 original size:23 final size:23
Alignment explanation
Indices: 17080113--17080181 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
17080103 TCTAATGTTC
17080113 TTTTCAC-TTTCTTTTTCTGATT-T
1 TTTTCACTTTTCTTTTTCT--TTCT
17080136 TTTTCACTTTTCTTTTT-TTTCT
1 TTTTCACTTTTCTTTTTCTTTCT
17080158 TTTTCATTCTTTTCTTTTTCTTTC
1 TTTTCA--CTTTTCTTTTTCTTTC
17080182 ATTTGAGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.05
22 7 0.17
23 8 0.20
24 20 0.49
25 4 0.10
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTTCACTTTTCTTTTTCTTTCT
Found at i:17080167 original size:19 final size:19
Alignment explanation
Indices: 17080145--17080184 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
17080135 TTTTTCACTT
*
17080145 TTCTTTT-TTTTCTTTTTCA
1 TTCTTTTCTTTT-TCTTTCA
17080164 TTCTTTTCTTTTTCTTTCA
1 TTCTTTTCTTTTTCTTTCA
17080183 TT
1 TT
17080185 TGAGTGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (19 bp):
TTCTTTTCTTTTTCTTTCA
Found at i:17096701 original size:25 final size:25
Alignment explanation
Indices: 17096637--17096703 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
17096627 TTACGGATAC
* * * *
17096637 TCAGCTCGTATGAGCGTACCGTTAT
1 TCAGCTCGAAAGAGCTTACCATTAT
*
17096662 TCAGCTCAAAAGAGCTTACCATTAT
1 TCAGCTCGAAAGAGCTTACCATTAT
* *
17096687 TCAGCTCGGAGGAGCTT
1 TCAGCTCGAAAGAGCTT
17096704 GCAGTTTACA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (25 bp):
TCAGCTCGAAAGAGCTTACCATTAT
Found at i:17103823 original size:8 final size:8
Alignment explanation
Indices: 17103809--17103839 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
17103799 AATTAGGGAT
17103809 TAAATTGA
1 TAAATTGA
*
17103817 AAAATTGA
1 TAAATTGA
17103825 TAAATTGA
1 TAAATTGA
17103833 TAAATTG
1 TAAATTG
17103840 TGTGGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (8 bp):
TAAATTGA
Found at i:17104367 original size:25 final size:25
Alignment explanation
Indices: 17104309--17104400 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
17104299 GTTATTAGGG
* * * *
17104309 TTACCGAT-TTCAGCTCTTATAAGC
1 TTACCGATACTCAGCTCATATGAGA
* *
17104333 TTACCGATACTCATCTCGTATGAGA
1 TTACCGATACTCAGCTCATATGAGA
*
17104358 TTACCGATACTCAGCTCATATGAGC
1 TTACCGATACTCAGCTCATATGAGA
*
17104383 TTACC-ATTATTCAGCTCA
1 TTACCGA-TACTCAGCTCA
17104401 GAGGAGCTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.16
25 48 0.84
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (25 bp):
TTACCGATACTCAGCTCATATGAGA
Found at i:17104407 original size:25 final size:25
Alignment explanation
Indices: 17104368--17104435 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
17104358 TTACCGATAC
* *
17104368 TCAGCTCATATGAGCTTACCATTAT
1 TCAGCTCAGAGGAGCTTACCATTAT
17104393 TCAGCTCAGAGGAGCTTACCATTAT
1 TCAGCTCAGAGGAGCTTACCATTAT
* * *
17104418 GCATCTCGGAGGAGCTTA
1 TCAGCTCAGAGGAGCTTA
17104436 TCGTTTACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (25 bp):
TCAGCTCAGAGGAGCTTACCATTAT
Found at i:17109141 original size:50 final size:50
Alignment explanation
Indices: 17109049--17109183 Score: 171
Period size: 50 Copynumber: 2.7 Consensus size: 50
17109039 TCCTGTACTA
* * * * ***
17109049 CCAATGTCATATCCCTGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACTCATATCGGTG
* * * *
17109099 CCCATGCTATGTCCCAGACATGGTCTTACAGGGGACCACTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACTCATATCGGTG
17109149 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
17109184 TCTCATCCCC
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACTCATATCGGTG
Found at i:17113280 original size:13 final size:13
Alignment explanation
Indices: 17113264--17113289 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17113254 GAAATAATTT
17113264 TTTGAAAATTTAG
1 TTTGAAAATTTAG
17113277 TTTGAAAATTTAG
1 TTTGAAAATTTAG
17113290 ACGTTTGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTGAAAATTTAG
Found at i:17114357 original size:45 final size:45
Alignment explanation
Indices: 17114284--17114465 Score: 215
Period size: 45 Copynumber: 4.1 Consensus size: 45
17114274 TACTACGTGT
*
17114284 ACCGAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* ** * * *
17114329 ATCGGGTACCATTGATTATAAAGGTGGTTGCTATGTGCTCACTCC
1 ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* ** * *
17114374 ACCGAAAATCATTGAAAATAAAGGTGGTTGCTATATACTGATTCC
1 ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* * *
17114419 ACCGAATATAATTGATTATAAGGGTGG-TGCTATGTGATGA-TCC
1 ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
17114462 ACCG
1 ACCG
17114466 TGTAACGGTT
Statistics
Matches: 113, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
43 7 0.06
44 10 0.09
45 96 0.85
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (45 bp):
ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
Found at i:17118003 original size:88 final size:88
Alignment explanation
Indices: 17117854--17118029 Score: 343
Period size: 88 Copynumber: 2.0 Consensus size: 88
17117844 CGATCGTCGG
17117854 GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACAGTTATTATTT
1 GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACAGTTATTATTT
17117919 ACTTAAAACATTTTTCTTATTAA
66 ACTTAAAACATTTTTCTTATTAA
*
17117942 GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACATTTATTATTT
1 GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACAGTTATTATTT
17118007 ACTTAAAACATTTTTCTTATTAA
66 ACTTAAAACATTTTTCTTATTAA
17118030 TTTATTTAAA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (88 bp):
GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACAGTTATTATTT
ACTTAAAACATTTTTCTTATTAA
Found at i:17120507 original size:26 final size:26
Alignment explanation
Indices: 17120471--17120570 Score: 101
Period size: 27 Copynumber: 3.8 Consensus size: 26
17120461 TGGTGTGACA
* *
17120471 TTTACTGTCCCAGCGGACTACCCTTG
1 TTTAATGTCCCATCGGACTACCCTTG
* * *
17120497 TTTAACGTCCCATCAGACTATCCCTAG
1 TTTAATGTCCCATCGGACTA-CCCTTG
* *
17120524 TTTAATGTCTCATCGGACTATCCTGTG
1 TTTAATGTCCCATCGGACTACCCT-TG
* *
17120551 TTTAATGTCCTATTGGACTA
1 TTTAATGTCCCATCGGACTA
17120571 ACTATGATGC
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
26 19 0.32
27 40 0.68
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (26 bp):
TTTAATGTCCCATCGGACTACCCTTG
Found at i:17122279 original size:35 final size:35
Alignment explanation
Indices: 17122233--17122303 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
17122223 TTAGGGATCA
*
17122233 CTTTGCATTTATTTTATTTAATTTAATTTAGCAAT
1 CTTTACATTTATTTTATTTAATTTAATTTAGCAAT
* *
17122268 CTTTACATTTATTTTATTTTATTTTATTTAGCAAT
1 CTTTACATTTATTTTATTTAATTTAATTTAGCAAT
17122303 C
1 C
17122304 AGTCACTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.59
Consensus pattern (35 bp):
CTTTACATTTATTTTATTTAATTTAATTTAGCAAT
Found at i:17122640 original size:45 final size:43
Alignment explanation
Indices: 17122530--17122661 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 43
17122520 GCTATCAAAG
* * *
17122530 GATGTCATAGCATCTTTCAGCGATAGTCTTAGTCATGTTTCTATCAT
1 GATGTCATA-CATCTTTCAGCTATGGTCTTACTCA--TTT-TATCAT
*
17122577 GATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTTTATCAT
1 GATGTCAT-ACATCTTTCAGCTATGGTCTTACTCAT-TTTATCAT
* *
17122622 GATGTCATGACATTTTTCAACTATGGTCTTACTCATTTTA
1 GATGTCAT-ACATCTTTCAGCTATGGTCTTACTCATTTTA
17122662 AGCGATAGCC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
44 4 0.05
45 39 0.52
46 2 0.03
47 29 0.39
48 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (43 bp):
GATGTCATACATCTTTCAGCTATGGTCTTACTCATTTTATCAT
Found at i:17126075 original size:18 final size:17
Alignment explanation
Indices: 17126050--17126097 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
17126040 CTTTTCTTTC
17126050 ATAA-ATTATTTTTAATA
1 ATAATATTATTTTTAA-A
17126067 ATAATATTA-TTTTAAA
1 ATAATATTATTTTTAAA
17126083 A-AATATTAATTTTTA
1 ATAATATT-ATTTTTA
17126098 GAGTGGTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.21
16 3 0.11
17 15 0.54
18 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATATTATTTTTAAA
Found at i:17131400 original size:19 final size:19
Alignment explanation
Indices: 17131376--17131414 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
17131366 TATCATCTCC
*
17131376 ATAATGACTGTATAGGCAA
1 ATAATGACTATATAGGCAA
17131395 ATAATGACTATATAGGCAA
1 ATAATGACTATATAGGCAA
17131414 A
1 A
17131415 ATATGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (19 bp):
ATAATGACTATATAGGCAA
Found at i:17135318 original size:3 final size:3
Alignment explanation
Indices: 17135312--17135397 Score: 59
Period size: 3 Copynumber: 27.7 Consensus size: 3
17135302 TATTCAGTAA
* *
17135312 TAT TAT TAT TAAT CTAT TAT TAT TAAT CTAT TAT TAT TAT CAT CAT TAT
1 TAT TAT TAT T-AT -TAT TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT
* * * *
17135361 TAC TACT GA- TAT TAT TAT TAA TAT TGT TAT TA- TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17135398 ATTTATATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
2 3 0.05
3 52 0.79
4 9 0.14
5 2 0.03
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:17135334 original size:17 final size:14
Alignment explanation
Indices: 17135312--17135382 Score: 81
Period size: 14 Copynumber: 4.9 Consensus size: 14
17135302 TATTCAGTAA
17135312 TATTATTATTAATC
1 TATTATTATTAATC
17135326 TATTATTATTAATC
1 TATTATTATTAATC
17135340 TATTATTATT-ATC
1 TATTATTATTAATC
* * *
17135353 ATCATTATTACTACTGA
1 -T-ATTATTATTAAT-C
17135370 TATTATTATTAAT
1 TATTATTATTAAT
17135383 ATTGTTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
13 3 0.06
14 25 0.52
15 18 0.38
16 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.55
Consensus pattern (14 bp):
TATTATTATTAATC
Found at i:17144047 original size:18 final size:19
Alignment explanation
Indices: 17144024--17144072 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
17144014 AAGTTTTATT
*
17144024 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
17144042 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
17144061 TTTAATTTTTAT
1 TTT-ATTTTTAT
17144073 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:17144052 original size:22 final size:22
Alignment explanation
Indices: 17144015--17144072 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
17144005 CAAGTTGTAA
* *
17144015 AGTTTTATTTTTATTTTTATTT
1 AGTTTAATTTTTATTTTTACTT
*
17144037 A-TTTATTTATTTATTTTTACTT
1 AGTTTAATT-TTTATTTTTACTT
17144059 AGTTTAATTTTTAT
1 AGTTTAATTTTTAT
17144073 GTAAATATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 19 0.63
23 6 0.20
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (22 bp):
AGTTTAATTTTTATTTTTACTT
Found at i:17147317 original size:970 final size:970
Alignment explanation
Indices: 17145437--17147383 Score: 3493
Period size: 970 Copynumber: 2.0 Consensus size: 970
17145427 ATCCCAAGGA
** * *
17145437 GACAAAGGAATTGCAAAGGTAAGTTGAGGAATTACTAGACAAAGGGTACATTCGTGAGAGCCTAA
1 GACAAAGGAATTGCAAAGACAAGTTGAGGAATTACTAGACAAAAGGTACATTCGTGAAAGCCTAA
*
17145502 GCCCTTGTGCCATTCCTGTCTTATTGGTACCAAAGAAAGATGGTACGTTTTGTATGTGTGTTGAT
66 GCCCTTGTGCCATTCCTGTCTTATTGGTACCAAAGAAAGATGGTACGTTTAGTATGTGTGTTGAT
17145567 TGTCACCCAATCAACAAGATAACAGTAAAATATCGACATCCAATTCCTAGACTTGATGATATGCT
131 TGTCACCCAATCAACAAGATAACAGTAAAATATCGACATCCAATTCCTAGACTTGATGATATGCT
17145632 TGATGAATTACATGGTTCAAAAATATTTACAAAAATTGATTTAAAAAGCGGTTATCATCAAATTC
196 TGATGAATTACATGGTTCAAAAATATTTACAAAAATTGATTTAAAAAGCGGTTATCATCAAATTC
*
17145697 GAATGAGGGAAGGGGATGAATGGAAAACAGCCTTTAAAACAAAATTTGGATTGTATGGATGGTTA
261 GAATGAGGGAAGGGGATGAATGGAAAACAGCCTTTAAAACAAAATTGGGATTGTATGGATGGTTA
17145762 GTTATGCCTTTCAGCCTTACTAATGCACCTAGTACATTTATGAGATTGATGAATCATGTTTTAAG
326 GTTATGCCTTTCAGCCTTACTAATGCACCTAGTACATTTATGAGATTGATGAATCATGTTTTAAG
17145827 GCTATACTTGGGTAAATTTGTAGTAGTTTACTTTGATGATATCTTAATTTATTCCAAGACTTTAG
391 GCTATACTTGGGTAAATTTGTAGTAGTTTACTTTGATGATATCTTAATTTATTCCAAGACTTTAG
17145892 ATGATCATGTTTTCCATGTTCGAACCGTTTTGGATATTCTGCGAGCTGAAAAATTATTTGCCAAC
456 ATGATCATGTTTTCCATGTTCGAACCGTTTTGGATATTCTGCGAGCTGAAAAATTATTTGCCAAC
17145957 CTTGATAAATGCACATTCTGTTGTGATAAACTAATATTCTTAGGTTTCATAGTTAGTGCTCAAGG
521 CTTGATAAATGCACATTCTGTTGTGATAAACTAATATTCTTAGGTTTCATAGTTAGTGCTCAAGG
17146022 TATTCATGTCGACGAGGACAAAGTCAAGGCAATTAAGGAGTGGCCGACTCCTAAATCGGTAACCG
586 TATTCATGTCGACGAGGACAAAGTCAAGGCAATTAAGGAGTGGCCGACTCCTAAATCGGTAACCG
*
17146087 AGGTGAGATCTTTCCATGGTTTAGCTAGTTTTTATAGACGATTTGTGAAAGATTTCTCTACTATT
651 AGGTGAGATCTTTCCATGGTTTAGCTAGTTTTTATAGACGATTTGTAAAAGATTTCTCTACTATT
17146152 GTTGCCCCATTAACAGAGGTTATAAAAAAATCAGTGGGTTTCAAATGGGGTGAAACCCAAGCAAA
716 GTTGCCCCATTAACAGAGGTTATAAAAAAATCAGTGGGTTTCAAATGGGGTGAAACCCAAGCAAA
* * *
17146217 AACTTTTCAAACTCTAAAAGATAAGTTATGTTCTGCTCCTCTTCTCAAATTACCTGATTTTTCTA
781 AACCTTTCAAACTCTAAAAGATAAGTTATGTTCTGCTCATCTTCTCAAATTACCTGATTTTGCTA
* *
17146282 ATACTTTTGAACTTGAGTGTAATGCTTCAGGAATTGGAATTGGCGCCGTTTTAATGCAAGATAAG
846 AAACTTTTGAACTTGAGTGTAATGCTTCAGGAATTGGAATCGGCGCCGTTTTAATGCAAGATAAG
* * *
17146347 CAACCTATTGCTTACTTGAGTGAGAAATTGAACGGTTCACAGTTAAATTACTCGACTTAT
911 CAACCTATTGCTTACTTGAGTGAGAAATTGAACGGTGCACAGTTAAACTACTCAACTTAT
* * *
17146407 GACAAAGGAATTGCAAAGACAAGTTGAGGAGTTACTAGATAAAAGGTACATTGGTGAAAGCCTAA
1 GACAAAGGAATTGCAAAGACAAGTTGAGGAATTACTAGACAAAAGGTACATTCGTGAAAGCCTAA
***
17146472 GCCCTTGTGTTGTTCCTGTCTTATTGGTACCAAAGAAAGATGGTACGTTTAGTATGTGTGTTGAT
66 GCCCTTGTGCCATTCCTGTCTTATTGGTACCAAAGAAAGATGGTACGTTTAGTATGTGTGTTGAT
*
17146537 TGTCACCCAATCAACAAGATAACGGTAAAATATCGACATCCAATTCCTAGACTTGATGATATGCT
131 TGTCACCCAATCAACAAGATAACAGTAAAATATCGACATCCAATTCCTAGACTTGATGATATGCT
17146602 TGATGAATTACATGGTTCAAAAATATTTACAAAAATTGATTTAAAAAGCGGTTATCATCAAATTC
196 TGATGAATTACATGGTTCAAAAATATTTACAAAAATTGATTTAAAAAGCGGTTATCATCAAATTC
17146667 GAATGAGGGAAGGGGATGAATGGAAAACAGCCTTTAAAACAAAATTGGGATTGTATGGATGGTTA
261 GAATGAGGGAAGGGGATGAATGGAAAACAGCCTTTAAAACAAAATTGGGATTGTATGGATGGTTA
*
17146732 GTTATGCCTTTCGGCCTTACTAATGCACCTAGTACATTTATGAGATTGATGAATCATGTTTTAAG
326 GTTATGCCTTTCAGCCTTACTAATGCACCTAGTACATTTATGAGATTGATGAATCATGTTTTAAG
17146797 GCTATACTTGGGTAAATTTGTAGTAGTTTACTTTGATGATATCTTAATTTATTCCAAGACTTTAG
391 GCTATACTTGGGTAAATTTGTAGTAGTTTACTTTGATGATATCTTAATTTATTCCAAGACTTTAG
*
17146862 ATGATCATGTTTTCCATGTTCGAACCGTTTTGGATATTCTGTGAGCTGAAAAATTATTTGCCAAC
456 ATGATCATGTTTTCCATGTTCGAACCGTTTTGGATATTCTGCGAGCTGAAAAATTATTTGCCAAC
*
17146927 CTTGATAAATGCACATTCTGTTGTGATAAACTAATATTCTTAGGTTTCATAGTTAGTGCTTAAGG
521 CTTGATAAATGCACATTCTGTTGTGATAAACTAATATTCTTAGGTTTCATAGTTAGTGCTCAAGG
*
17146992 TATTCATGTCGACGAGGACAAAGTCAAGGCAATTAAGGAGTGGCCGACTCCTAAATCGGTAACTG
586 TATTCATGTCGACGAGGACAAAGTCAAGGCAATTAAGGAGTGGCCGACTCCTAAATCGGTAACCG
*
17147057 AGGTGAGATCTTTCCATGGTTTAGCTAGTTTTTATAGACGATTTGTAAAAGATTTCTCTATTATT
651 AGGTGAGATCTTTCCATGGTTTAGCTAGTTTTTATAGACGATTTGTAAAAGATTTCTCTACTATT
* * *
17147122 GTTGCCCCATTGATAGAGGTTATAAAGAAATCAGTGGGTTTCAAATGGGGTGAAACCCAAG-AAA
716 GTTGCCCCATTAACAGAGGTTATAAAAAAATCAGTGGGTTTCAAATGGGGTGAAACCCAAGCAAA
* ** *
17147186 AGGCCTTTCAAACTCTAAAATCTAAGTTATGTTCTGCTCAT-TTGCTTAAATTACCTGATTTTGC
781 A-ACCTTTCAAACTCTAAAAGATAAGTTATGTTCTGCTCATCTT-CTCAAATTACCTGATTTTGC
* *
17147250 TAAAACTTTTGAACTTGAGTGTGATGCTTCAGGAATTGGAATCGGCGCCGTTTTAATGTAAGATA
844 TAAAACTTTTGAACTTGAGTGTAATGCTTCAGGAATTGGAATCGGCGCCGTTTTAATGCAAGATA
* * * * *
17147315 AGCAGCCTATTGCTTATTTTAGTGAGAAATTGAATGGTGCACAGTTAAACTATTCAACTTAT
909 AGCAACCTATTGCTTACTTGAGTGAGAAATTGAACGGTGCACAGTTAAACTACTCAACTTAT
17147377 GACAAAG
1 GACAAAG
17147384 AACTCTTGGC
Statistics
Matches: 934, Mismatches: 41, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
969 6 0.01
970 928 0.99
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (970 bp):
GACAAAGGAATTGCAAAGACAAGTTGAGGAATTACTAGACAAAAGGTACATTCGTGAAAGCCTAA
GCCCTTGTGCCATTCCTGTCTTATTGGTACCAAAGAAAGATGGTACGTTTAGTATGTGTGTTGAT
TGTCACCCAATCAACAAGATAACAGTAAAATATCGACATCCAATTCCTAGACTTGATGATATGCT
TGATGAATTACATGGTTCAAAAATATTTACAAAAATTGATTTAAAAAGCGGTTATCATCAAATTC
GAATGAGGGAAGGGGATGAATGGAAAACAGCCTTTAAAACAAAATTGGGATTGTATGGATGGTTA
GTTATGCCTTTCAGCCTTACTAATGCACCTAGTACATTTATGAGATTGATGAATCATGTTTTAAG
GCTATACTTGGGTAAATTTGTAGTAGTTTACTTTGATGATATCTTAATTTATTCCAAGACTTTAG
ATGATCATGTTTTCCATGTTCGAACCGTTTTGGATATTCTGCGAGCTGAAAAATTATTTGCCAAC
CTTGATAAATGCACATTCTGTTGTGATAAACTAATATTCTTAGGTTTCATAGTTAGTGCTCAAGG
TATTCATGTCGACGAGGACAAAGTCAAGGCAATTAAGGAGTGGCCGACTCCTAAATCGGTAACCG
AGGTGAGATCTTTCCATGGTTTAGCTAGTTTTTATAGACGATTTGTAAAAGATTTCTCTACTATT
GTTGCCCCATTAACAGAGGTTATAAAAAAATCAGTGGGTTTCAAATGGGGTGAAACCCAAGCAAA
AACCTTTCAAACTCTAAAAGATAAGTTATGTTCTGCTCATCTTCTCAAATTACCTGATTTTGCTA
AAACTTTTGAACTTGAGTGTAATGCTTCAGGAATTGGAATCGGCGCCGTTTTAATGCAAGATAAG
CAACCTATTGCTTACTTGAGTGAGAAATTGAACGGTGCACAGTTAAACTACTCAACTTAT
Found at i:17148621 original size:7 final size:6
Alignment explanation
Indices: 17148583--17148643 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
17148573 AGTCAGATTC
* * * *
17148583 AAACAA AAA-AA AATCAA AATCAA AAACAA AAACAA AAA-AA GAAGAA
1 AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA
*
17148629 AAAGAA AAATCAA AA
1 AAACAA AAA-CAA AA
17148644 TCAAGGTCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
5 8 0.17
6 35 0.74
7 4 0.09
ACGTcount: A:0.80, C:0.10, G:0.05, T:0.05
Consensus pattern (6 bp):
AAACAA
Found at i:17150247 original size:30 final size:30
Alignment explanation
Indices: 17150213--17150269 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
17150203 AGGTTGGAAA
17150213 TTTGAGAAAGAAGAGTCTAAATTTGGATTT
1 TTTGAGAAAGAAGAGTCTAAATTTGGATTT
17150243 TTTGAGAAAGAAGAGTCTAAATTTGGA
1 TTTGAGAAAGAAGAGTCTAAATTTGGA
17150270 CTTTCTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.33
Consensus pattern (30 bp):
TTTGAGAAAGAAGAGTCTAAATTTGGATTT
Found at i:17151108 original size:131 final size:131
Alignment explanation
Indices: 17150874--17151634 Score: 1188
Period size: 131 Copynumber: 5.8 Consensus size: 131
17150864 TCGGTGAAAT
*
17150874 CACAAGTCCTATGTCCCTGGTCAA-CAGTGGAGTAGGTTGGAAGTTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATGTCCCTGGT-AAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAA
* *
17150938 GTAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGTAGATTTAA
65 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAA
17151003 GC
130 GC
*
17151005 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATATTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
17151070 CAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
17151135 C
131 C
* *
17151136 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTGAG
1 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
17151201 CAGTAGCGGAGCAAATCGAAGACGGCGAATCCTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
17151266 C
131 C
* *
17151267 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTGAG
1 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* *
17151332 CAGTAGCGGAGCAGATTGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATGTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
17151397 C
131 C
* * * *
17151398 CACAAGTCCTATCTCCCTGGTCAGCAGTGAAGTAGGTTGGAAATTACAGATCTTGTCTACCTAAG
1 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
*
17151463 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCTCTAGGAGTAGGGAAGCAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
17151528 C
131 C
* * *
17151529 CACAAGTCCTATCTCCCTGGTCAA-CAGTGGAGTAGGTTTGAAATTACAGATCTCGTCTCCCTAA
1 CACAAGTCCTATGTCCCTGGT-AAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAA
* * * * *
17151593 GCAATAGTGGAGCTA-ATCGAAAATGGTGAATCTTATC-TCCCT
65 GCAGTAGCGGAGC-AGATCGAAGACGGCGAATCTTATCTTCCCT
17151635 GAGATTACAG
Statistics
Matches: 588, Mismatches: 39, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
130 6 0.01
131 580 0.99
132 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (131 bp):
CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
C
Found at i:17151867 original size:44 final size:42
Alignment explanation
Indices: 17151620--17151867 Score: 155
Period size: 44 Copynumber: 5.9 Consensus size: 42
17151610 CGAAAATGGT
* *
17151620 GAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCA
1 GAATCTTATCTCCCTGAGATTACAGTGGAACAGATTGAA-CCA
* * * * * **
17151663 GTAATCCTATTTCCCTGAAATTACAGTGGAACGGATTAAAATAAA
1 G-AATCTTATCTCCCTGAGATTACAGTGGAACAGATT-GAA-CCA
* * * ** * * * *
17151708 GGATCTTATCTCTCTGAAGA-TACAGTAGAGTACATCGTATCA
1 GAATCTTATCTCCCTG-AGATTACAGTGGAACAGATTGAACCA
* * **
17151750 G-GTCTTATCTCCCTGAGATTACAGTGGAATAGACCG-A--A
1 GAATCTTATCTCCCTGAGATTACAGTGGAACAGATTGAACCA
* ** *
17151788 GAATCTTATCTCCCTGAGGTTACAGCAGAGCAGATTGAAGCCA
1 GAATCTTATCTCCCTGAGATTACAGTGGAACAGATTGAA-CCA
*
17151831 GAAATCTTATCTCCCTGAGATTACAGTGGAATAGATT
1 G-AATCTTATCTCCCTGAGATTACAGTGGAACAGATT
17151868 AAAACCACAT
Statistics
Matches: 151, Mismatches: 44, Indels: 19
0.71 0.21 0.09
Matches are distributed among these distances:
38 2 0.01
39 27 0.18
40 5 0.03
41 25 0.17
42 2 0.01
43 4 0.03
44 80 0.53
45 6 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (42 bp):
GAATCTTATCTCCCTGAGATTACAGTGGAACAGATTGAACCA
Found at i:17151936 original size:50 final size:50
Alignment explanation
Indices: 17151882--17152045 Score: 163
Period size: 50 Copynumber: 3.3 Consensus size: 50
17151872 CCACATTGGT
* *
17151882 GAATCTCGCTTCCCCAATATTGCAGTTAAAAAGATTAAAGCTACAACAGC
1 GAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * * * * * *
17151932 GAATCTTAC-TCCCCAAGCGA-TGCAGTGAAGCAA-ATTAAAGCCACATCGGT
1 GAATCTTGCTTCCCCAA-C-ATTGCAGTTAA-AAAGATTAAAGCTACAACAGC
* * *
17151982 GAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAATAGC
1 GAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
*
17152032 GAATCTTACTTCCC
1 GAATCTTGCTTCCC
17152046 AAGCGGTGTA
Statistics
Matches: 88, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
49 10 0.11
50 69 0.78
51 9 0.10
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (50 bp):
GAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
Found at i:17152067 original size:50 final size:50
Alignment explanation
Indices: 17151913--17152075 Score: 136
Period size: 50 Copynumber: 3.3 Consensus size: 50
17151903 GCAGTTAAAA
* * * * *
17151913 AGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGATGCAGTGAAGC
1 AGATTAAAGCTACAATAGCGAATCTTACTTCCCAAGCGATGTAATGAAAC
* * * * * * * *
17151963 AAATTAAAGCCAC-ATCGGTGAATCTTGCTTCCC-CGAC-AT-TACAGTTAAAA
1 AGATTAAAGCTACAAT-AGCGAATCTTACTTCCCAAG-CGATGTA-A-TGAAAC
*
17152013 AGATTAAAGCTACAATAGCGAATCTTACTTCCCAAGCGGTGTAATGAAAC
1 AGATTAAAGCTACAATAGCGAATCTTACTTCCCAAGCGATGTAATGAAAC
17152063 AGATTAAAGCTAC
1 AGATTAAAGCTAC
17152076 GACGACAAAT
Statistics
Matches: 83, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
48 1 0.01
49 4 0.05
50 71 0.86
51 5 0.06
52 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCTACAATAGCGAATCTTACTTCCCAAGCGATGTAATGAAAC
Found at i:17152069 original size:100 final size:100
Alignment explanation
Indices: 17151863--17152072 Score: 303
Period size: 100 Copynumber: 2.1 Consensus size: 100
17151853 ACAGTGGAAT
* * * *
17151863 AGATTAAAACCACATTGGTGAATCTCGCTTCCCCAATATTGCAGTTAAAAAGATTAAAGCTACAA
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCAACATTACAGTTAAAAAGATTAAAGCTACAA
* *
17151928 CAGCGAATCTTACTCCCCAAGCGATGCAGTGAAGC
66 CAGCGAATCTTACTCCCCAAGCGATGCAATGAAAC
* * *
17151963 AAATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAA
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCAACATTACAGTTAAAAAGATTAAAGCTACAA
* * * *
17152028 TAGCGAATCTTACTTCCCAAGCGGTGTAATGAAAC
66 CAGCGAATCTTACTCCCCAAGCGATGCAATGAAAC
17152063 AGATTAAAGC
1 AGATTAAAGC
17152073 TACGACGACA
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (100 bp):
AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCAACATTACAGTTAAAAAGATTAAAGCTACAA
CAGCGAATCTTACTCCCCAAGCGATGCAATGAAAC
Found at i:17152087 original size:100 final size:100
Alignment explanation
Indices: 17151883--17152107 Score: 281
Period size: 100 Copynumber: 2.2 Consensus size: 100
17151873 CACATTGGTG
* * *
17151883 AATCTCGCTTCCCCAATATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAA
1 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAA
* * ***
17151948 GCGATGCAGTGAAGCAAATTAAAGCCACATCGGTG
66 GCGATGCAATGAAACAAATTAAAGCCACATCGACA
* * *
17151983 AATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAATAGCGAATCTTACTTCCCAA
1 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAA
* * * *
17152048 GCGGTGTAATGAAACAGATTAAAGCTACGA-CGACA
66 GCGATGCAATGAAACAAATTAAAGCCAC-ATCGACA
* *
17152083 AATCTTGTTTCCCAGACATTGCAGT
1 AATCTTGCTTCCCCGACATTGCAGT
17152108 CAGACAGAAG
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
100 105 0.99
101 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (100 bp):
AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAA
GCGATGCAATGAAACAAATTAAAGCCACATCGACA
Found at i:17153749 original size:3 final size:3
Alignment explanation
Indices: 17153743--17153828 Score: 52
Period size: 3 Copynumber: 28.7 Consensus size: 3
17153733 TATTCAATAA
* * **
17153743 TAT TAT TAT TAAT CTAT TAT TAT TAA T-T TAT TAT TAT TAT CAT CGT
1 TAT TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
17153789 TAT TAC TACT GA- TAT TAT TAT TAA TAT TGT TAT TA- TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17153829 ATTTATATAT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
2 4 0.06
3 53 0.84
4 5 0.08
5 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:17153762 original size:14 final size:14
Alignment explanation
Indices: 17153743--17153781 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
17153733 TATTCAATAA
17153743 TATTATTATTAATC
1 TATTATTATTAATC
*
17153757 TATTATTATTAATT
1 TATTATTATTAATC
17153771 TATTATTATTA
1 TATTATTATTA
17153782 TCATCGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTATTAATC
Found at i:17153765 original size:17 final size:17
Alignment explanation
Indices: 17153743--17153782 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17153733 TATTCAATAA
17153743 TATTATT-ATTAATCTAT
1 TATTATTAATTAAT-TAT
*
17153760 TATTATTAATTTATTAT
1 TATTATTAATTAATTAT
17153777 TATTAT
1 TATTAT
17153783 CATCGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTAATTAATTAT
Found at i:17153773 original size:11 final size:12
Alignment explanation
Indices: 17153740--17153828 Score: 54
Period size: 14 Copynumber: 6.7 Consensus size: 12
17153730 TACTATTCAA
17153740 TAATATTATTAT
1 TAATATTATTAT
17153752 TAATCTATTATTAT
1 TAA--TATTATTAT
17153766 TAATTTATTATTAT
1 TAA--TATTATTAT
*
17153780 TATCATCGTTATTACT
1 TA--AT-ATTATTA-T
*
17153796 ACTGATATTATTAT
1 --TAATATTATTAT
*
17153810 TAATATTGTTAT
1 TAATATTATTAT
17153822 T-ATATTA
1 TAATATTA
17153829 ATTTATATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
11 5 0.08
12 14 0.23
14 26 0.42
15 12 0.19
16 4 0.06
18 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:17153843 original size:30 final size:31
Alignment explanation
Indices: 17153757--17153844 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
17153747 ATTATTAATC
* *
17153757 TATTATTATTAATTTATTATTATTATCATCGT
1 TATTACTATTAATTTATTATT-TAATCATCGT
* * *
17153789 TATTACTACTGATATTATTA-TTAAT-ATTGT
1 TATTACTATTAAT-TTATTATTTAATCATCGT
17153819 TATTA-TATTAATTTATATATTTAATC
1 TATTACTATTAATTTAT-TATTTAATC
17153845 GCCATTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.09
29 7 0.16
30 14 0.31
31 3 0.07
32 11 0.24
33 6 0.13
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTACTATTAATTTATTATTTAATCATCGT
Found at i:17155528 original size:4 final size:4
Alignment explanation
Indices: 17155515--17155545 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
17155505 GGTTTTTTCA
17155515 AATT -ATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT
17155546 GAAGTTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
AATT
Done.