Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003744.1 Hibiscus syriacus cultivar Beakdansim tig00008013_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2457414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1522445 original size:14 final size:14
Alignment explanation
Indices: 1522425--1522463 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1522415 ATCTCTCATT
*
1522425 TTTTTTTCTTTTTTC
1 TTTTTTT-TTTCTTC
1522440 TTTTTTTTTTCTTC
1 TTTTTTTTTTCTTC
1522454 TTTCTTTTTT
1 TTT-TTTTTT
1522464 AGCTCTCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTCTTC
Found at i:1532080 original size:14 final size:14
Alignment explanation
Indices: 1532061--1532114 Score: 81
Period size: 14 Copynumber: 3.8 Consensus size: 14
1532051 TATACGAGCT
1532061 GTGGTGACAACATA
1 GTGGTGACAACATA
1532075 GTGGTGACAACATA
1 GTGGTGACAACATA
*
1532089 GTGGTGACAGCATA
1 GTGGTGACAACATA
*
1532103 ATGGTGCACAAC
1 GTGGTG-ACAAC
1532115 CTCAATATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
14 32 0.89
15 4 0.11
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (14 bp):
GTGGTGACAACATA
Found at i:1546330 original size:24 final size:25
Alignment explanation
Indices: 1546302--1546354 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
1546292 AAGGTAATTG
**
1546302 TTTAACTTCATTTATTTAATT-TTT
1 TTTAACTTCATAAATTTAATTATTT
* *
1546326 TTTAATTTCATAAATTTACTTATTT
1 TTTAACTTCATAAATTTAATTATTT
1546351 TTTA
1 TTTA
1546355 TTTGTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTAACTTCATAAATTTAATTATTT
Found at i:1547635 original size:12 final size:12
Alignment explanation
Indices: 1547620--1547644 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1547610 TTTGATTTTA
1547620 TTAATTTTATTT
1 TTAATTTTATTT
1547632 TTAATTTTATTT
1 TTAATTTTATTT
1547644 T
1 T
1547645 AAAATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTAATTTTATTT
Found at i:1554435 original size:79 final size:79
Alignment explanation
Indices: 1554193--1554587 Score: 729
Period size: 79 Copynumber: 5.0 Consensus size: 79
1554183 AACATGAACA
*
1554193 TGGACAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1554258 AAGGTGCAGGAATT
66 AAGGTGCAGGAATT
* **
1554272 TGTAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATT-TTAAAGATCCAAGTTCACATG
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1554336 AAGGTGCAGGAATT
66 AAGGTGCAGGAATT
1554350 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1554415 AAGGTGCAGGAATT
66 AAGGTGCAGGAATT
* *
1554429 TGGAAAACTTATTGCCACTCAGGTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1554494 AAGGTGCAGGAATT
66 AAGGTGCAGGAATT
1554508 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1554573 AAGGTGCAGGAATT
66 AAGGTGCAGGAATT
1554587 T
1 T
1554588 CACAGGTAAT
Statistics
Matches: 304, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
78 75 0.25
79 229 0.75
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (79 bp):
TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
AAGGTGCAGGAATT
Found at i:1557149 original size:31 final size:33
Alignment explanation
Indices: 1557114--1557183 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 33
1557104 ATATTTAAAT
*
1557114 TATCTAATATG-ATTTT-ATTATTTTTACAAAA
1 TATCTAATATGTATTTTAATAATTTTTACAAAA
* * *
1557145 TATCT--TTTGTTTTTTAATAATTTTTATAAAA
1 TATCTAATATGTATTTTAATAATTTTTACAAAA
1557176 TATCTAAT
1 TATCTAAT
1557184 GTAAATTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
29 3 0.10
30 4 0.13
31 23 0.74
33 1 0.03
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (33 bp):
TATCTAATATGTATTTTAATAATTTTTACAAAA
Found at i:1557393 original size:30 final size:29
Alignment explanation
Indices: 1557326--1557403 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
1557316 AACATATAGA
*
1557326 TACCATATTGAACATTTTAGAAATATAAG
1 TACCATATTAAACATTTTAGAAATATAAG
*
1557355 TACCATATTAAACATTTTAGAAATCTAAG
1 TACCATATTAAACATTTTAGAAATATAAG
* *
1557384 TCCCCATATTAAACAATTTA
1 T-ACCATATTAAACATTTTA
1557404 TTAAAGTACA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 28 0.64
30 16 0.36
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (29 bp):
TACCATATTAAACATTTTAGAAATATAAG
Found at i:1561256 original size:12 final size:12
Alignment explanation
Indices: 1561239--1561283 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
1561229 GTCGAGTAAT
1561239 GAGCAACGAGTC
1 GAGCAACGAGTC
*
1561251 GAGCAACGAGTAAT
1 GAGCAACGAGT--C
1561265 GAGCAACGAGTC
1 GAGCAACGAGTC
1561277 GAGCAAC
1 GAGCAAC
1561284 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 18 0.62
14 11 0.38
ACGTcount: A:0.38, C:0.22, G:0.31, T:0.09
Consensus pattern (12 bp):
GAGCAACGAGTC
Found at i:1561266 original size:26 final size:26
Alignment explanation
Indices: 1561231--1561283 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1561221 CTAGTCAAGT
1561231 CGAGTAATGAGCAACGAGTCGAGCAA
1 CGAGTAATGAGCAACGAGTCGAGCAA
1561257 CGAGTAATGAGCAACGAGTCGAGCAA
1 CGAGTAATGAGCAACGAGTCGAGCAA
1561283 C
1 C
1561284 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.21, G:0.30, T:0.11
Consensus pattern (26 bp):
CGAGTAATGAGCAACGAGTCGAGCAA
Found at i:1561268 original size:14 final size:14
Alignment explanation
Indices: 1561231--1561275 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
1561221 CTAGTCAAGT
1561231 CGAGTAATGAGCAA
1 CGAGTAATGAGCAA
*
1561245 CGAGT--CGAGCAA
1 CGAGTAATGAGCAA
1561257 CGAGTAATGAGCAA
1 CGAGTAATGAGCAA
1561271 CGAGT
1 CGAGT
1561276 CGAGCAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.18, G:0.31, T:0.13
Consensus pattern (14 bp):
CGAGTAATGAGCAA
Found at i:1561308 original size:31 final size:32
Alignment explanation
Indices: 1561261--1561368 Score: 130
Period size: 32 Copynumber: 3.3 Consensus size: 32
1561251 GAGCAACGAG
*
1561261 TAATGAGCAACGAGTCGAGCAACAAATTTTTT
1 TAATGAGCAACGAGTCGAGCAACAATTTTTTT
1561293 TAATGAGC-ACGAGTCGAGCAA-AATTTTATTGACCT
1 TAATGAGCAACGAGTCGAGCAACAATTTT-TT----T
* *
1561328 TAACGAGCAACGAGTCAAGCAACAATTTTTTT
1 TAATGAGCAACGAGTCGAGCAACAATTTTTTT
1561360 TAATGAGCA
1 TAATGAGCA
1561369 TGAATCGAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
30 5 0.08
31 15 0.23
32 17 0.26
35 8 0.12
36 14 0.22
37 6 0.09
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (32 bp):
TAATGAGCAACGAGTCGAGCAACAATTTTTTT
Found at i:1561319 original size:26 final size:27
Alignment explanation
Indices: 1561235--1561320 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 27
1561225 TCAAGTCGAG
* *
1561235 TAATGAGCAACGAGTCGAGCAACGA--G
1 TAATGAGCAACGAGTCGAGCAA-AATTT
1561261 TAATGAGCAACGAGTCGAGCAACAAATTTTTT
1 TAATGAGCAACGAGTCGAGC-A-AAA---TTT
1561293 TAATGAGC-ACGAGTCGAGCAAAATTT
1 TAATGAGCAACGAGTCGAGCAAAATTT
1561319 TA
1 TA
1561321 TTGACCTTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
26 25 0.49
27 2 0.04
28 1 0.02
29 3 0.06
30 1 0.02
31 11 0.22
32 8 0.16
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (27 bp):
TAATGAGCAACGAGTCGAGCAAAATTT
Found at i:1561343 original size:36 final size:32
Alignment explanation
Indices: 1561265--1561368 Score: 113
Period size: 31 Copynumber: 3.2 Consensus size: 32
1561255 AACGAGTAAT
* *
1561265 GAGCAACGAGTCGAGCAACAAATTTTTTTAAT
1 GAGCAACGAGTCGAGCAACAATTTTTTTTAAC
1561297 GAGC-ACGAGTCGAGCAA-AATTTTATTGACCTTAAC
1 GAGCAACGAGTCGAGCAACAATTTT-TT----TTAAC
* *
1561332 GAGCAACGAGTCAAGCAACAATTTTTTTTAAT
1 GAGCAACGAGTCGAGCAACAATTTTTTTTAAC
1561364 GAGCA
1 GAGCA
1561369 TGAATCGAGC
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
30 5 0.08
31 15 0.25
32 13 0.21
35 8 0.13
36 14 0.23
37 6 0.10
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (32 bp):
GAGCAACGAGTCGAGCAACAATTTTTTTTAAC
Found at i:1566079 original size:11 final size:12
Alignment explanation
Indices: 1566057--1566088 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1566047 AAGGGGTAGC
1566057 AGCAAGAGAAAG
1 AGCAAGAGAAAG
1566069 AGCAA-AGAAAG
1 AGCAAGAGAAAG
1566080 AG-AAGAGAA
1 AGCAAGAGAA
1566089 CGCAGTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 12 0.63
12 5 0.26
ACGTcount: A:0.62, C:0.06, G:0.31, T:0.00
Consensus pattern (12 bp):
AGCAAGAGAAAG
Found at i:1566211 original size:2 final size:2
Alignment explanation
Indices: 1566206--1566237 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1566196 AGGAGAGATC
1566206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1566238 TAGTTGTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1567528 original size:21 final size:21
Alignment explanation
Indices: 1567502--1567556 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1567492 CGAAGGGTGG
1567502 GTATCGATACTGATTCAAACA
1 GTATCGATACTGATTCAAACA
*
1567523 GTATCGATACCGATTCAAACA
1 GTATCGATACTGATTCAAACA
1567544 GTATCGATACTGA
1 GTATCGATACTGA
1567557 AGGCTCAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (21 bp):
GTATCGATACTGATTCAAACA
Found at i:1569590 original size:3 final size:3
Alignment explanation
Indices: 1569582--1569606 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1569572 TTGTTTGCAT
1569582 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1569607 CATAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1572421 original size:12 final size:12
Alignment explanation
Indices: 1572404--1572429 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1572394 CTGGGTTTAT
1572404 TTTTTCATTTGA
1 TTTTTCATTTGA
1572416 TTTTTCATTTGA
1 TTTTTCATTTGA
1572428 TT
1 TT
1572430 ATCAATATAT
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:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTTTCATTTGA
Found at i:1575217 original size:2 final size:2
Alignment explanation
Indices: 1575210--1575248 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1575200 TCAATCTACA
1575210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1575249 ATTTACGACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1575338 original size:13 final size:13
Alignment explanation
Indices: 1575320--1575349 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1575310 AATGACACGC
1575320 AATGTAAGTCATA
1 AATGTAAGTCATA
1575333 AATGTAAGTCATA
1 AATGTAAGTCATA
1575346 AATG
1 AATG
1575350 CGTGTCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:1575369 original size:13 final size:13
Alignment explanation
Indices: 1575320--1575371 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
1575310 AATGACACGC
*
1575320 AATGTAAGTCATA
1 AATGCAAGTCATA
*
1575333 AATGTAAGTCATA
1 AATGCAAGTCATA
**
1575346 AATGCGTGTCATA
1 AATGCAAGTCATA
*
1575359 AATGCACGTCATA
1 AATGCAAGTCATA
1575372 GATTTATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (13 bp):
AATGCAAGTCATA
Found at i:1576785 original size:35 final size:33
Alignment explanation
Indices: 1576736--1576802 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 33
1576726 TTTTAACCTA
*
1576736 CAAGCTCTTACATTTATAGTTCACATGAATGTG
1 CAAGCTCTTACATTTACAGTTCACATGAATGTG
* *
1576769 CAAGCTCATATACATTTACGGTTCATATGAATGT
1 CAAGCTC-T-TACATTTACAGTTCACATGAATGT
1576803 ACAAAGAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 7 0.24
34 1 0.03
35 21 0.72
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (33 bp):
CAAGCTCTTACATTTACAGTTCACATGAATGTG
Found at i:1578864 original size:44 final size:44
Alignment explanation
Indices: 1578801--1578888 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
1578791 TCTTGGGCTT
1578801 GAGTACGACGCTTGTAGAGGTATATGAACGTTTATTGTCAAATG
1 GAGTACGACGCTTGTAGAGGTATATGAACGTTTATTGTCAAATG
*
1578845 GAGTACGACGTTTGTAGAGGTATATGAACGTTTATTGTCAAATG
1 GAGTACGACGCTTGTAGAGGTATATGAACGTTTATTGTCAAATG
1578889 ATTGAAAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (44 bp):
GAGTACGACGCTTGTAGAGGTATATGAACGTTTATTGTCAAATG
Found at i:1580004 original size:2 final size:2
Alignment explanation
Indices: 1579993--1580026 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1579983 TCAGAAACAA
1579993 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1580027 AGGTTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1580467 original size:22 final size:22
Alignment explanation
Indices: 1580450--1580492 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1580440 TTTAAACTTC
1580450 AAAAATATGTGTTTTAAATCTA
1 AAAAATATGTGTTTTAAATCTA
1580472 AAAAATATGTGTTTTAAATCT
1 AAAAATATGTGTTTTAAATCT
1580493 TGGTTAAAAT
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:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (22 bp):
AAAAATATGTGTTTTAAATCTA
Found at i:1581259 original size:20 final size:20
Alignment explanation
Indices: 1581231--1581281 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1581221 AATGATTTAT
1581231 GTGTCAAATCAACAATTAAC
1 GTGTCAAATCAACAATTAAC
*
1581251 GTGTTAAATCAACAATTAAC
1 GTGTCAAATCAACAATTAAC
*
1581271 GTGTCACATCA
1 GTGTCAAATCA
1581282 GTTTTATGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (20 bp):
GTGTCAAATCAACAATTAAC
Found at i:1585775 original size:21 final size:21
Alignment explanation
Indices: 1585749--1585788 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1585739 TCCAGATTCG
1585749 CAACGCGAACATCGACTATCA
1 CAACGCGAACATCGACTATCA
*
1585770 CAACGCGAACTTCGACTAT
1 CAACGCGAACATCGACTAT
1585789 TTTCCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (21 bp):
CAACGCGAACATCGACTATCA
Found at i:1585825 original size:21 final size:20
Alignment explanation
Indices: 1585799--1586064 Score: 220
Period size: 21 Copynumber: 12.8 Consensus size: 20
1585789 TTTCCAAATT
1585799 CGTTGCGATAGTCCAAGTTC
1 CGTTGCGATAGTCCAAGTTC
1585819 GCGTTGCGATAGTCCAAGTT-
1 -CGTTGCGATAGTCCAAGTTC
* * *
1585839 CGTTGCAATAATCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
*
1585859 GCGTTGCGATTTATTCCAAGTT-
1 -CGTTGCGA--TAGTCCAAGTTC
*
1585881 CGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
*
1585901 GCGTTGCGATTTATTCCAAGTT-
1 -CGTTGCGA--TAGTCCAAGTTC
*
1585923 CGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
*
1585943 GCGTTGCGATTTATTCCAAGTT-
1 -CGTTGCGA--TAGTCCAAGTTC
*
1585965 CGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
*
1585985 GCGTTGCGATTTATTCCAAGTT-
1 -CGTTGCGA--TAGTCCAAGTTC
*
1586007 CGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGTCCAAGTTC
* * *
1586027 ACGTTGCGATTTATTTCAAATT-
1 -CGTTGCGA--TAGTCCAAGTTC
1586049 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
1586065 AATCACAACG
Statistics
Matches: 199, Mismatches: 26, Indels: 42
0.75 0.10 0.16
Matches are distributed among these distances:
19 58 0.29
21 98 0.49
23 43 0.22
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCCAAGTTC
Found at i:1585896 original size:42 final size:42
Alignment explanation
Indices: 1585790--1586061 Score: 458
Period size: 42 Copynumber: 6.5 Consensus size: 42
1585780 TTCGACTATT
* *
1585790 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TA
1 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
* * *
1585830 GTCCAAGTTCGTTGCAATAATCGAAGTTCGCGTTGCGATTTA
1 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1585872 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1585914 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1585956 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
*
1585998 TTCCAAGTTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTA
1 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
* *
1586040 TTTCAAATTCGTTGCGATAGTC
1 TTCCAAGTTCGTTGCGATAGTC
1586062 CAAAATCACA
Statistics
Matches: 219, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 33 0.15
42 186 0.85
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (42 bp):
TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
Found at i:1586265 original size:4 final size:4
Alignment explanation
Indices: 1586256--1586280 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1586246 AATAGATATA
1586256 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1586281 TAAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1586451 original size:2 final size:2
Alignment explanation
Indices: 1586444--1586469 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1586434 ATTTAAACAA
1586444 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1586470 GACTAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1588325 original size:3 final size:3
Alignment explanation
Indices: 1588319--1588375 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
1588309 ATTATTTATT
* *
1588319 TAA TAA TAA TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1588364 TAAA TAA -AA TAA
1 T-AA TAA TAA TAA
1588376 ATGAAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.17
3 36 0.77
4 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1588377 original size:22 final size:21
Alignment explanation
Indices: 1588320--1588377 Score: 55
Period size: 25 Copynumber: 2.6 Consensus size: 21
1588310 TTATTTATTT
1588320 AATAATAAT-AATATAATAATA
1 AATAA-AATAAATATAATAATA
*
1588341 ATATTAAAACAAAATAATAATAATA
1 A-A-TAAAA-TAAAT-ATAATAATA
1588366 AATAAAATAAAT
1 AATAAAATAAAT
1588378 GAAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
21 1 0.03
22 7 0.23
23 8 0.27
24 4 0.13
25 10 0.33
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAAAATAAATATAATAATA
Found at i:1589199 original size:40 final size:40
Alignment explanation
Indices: 1589144--1589241 Score: 196
Period size: 40 Copynumber: 2.5 Consensus size: 40
1589134 TTGAACAAGC
1589144 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGT
1589184 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGT
1589224 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
1589242 TCTCTGGAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.48
Consensus pattern (40 bp):
TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGT
Found at i:1589201 original size:113 final size:113
Alignment explanation
Indices: 1588711--1589201 Score: 707
Period size: 113 Copynumber: 4.3 Consensus size: 113
1588701 ATTGAACAAG
* *
1588711 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGT
*
1588776 GATGAATTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
66 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* * ** * ** *
1588824 TTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTCTAGCTGGTAATAATGATCCAT-AGAA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCA-AG
*
1588888 TGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
65 TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * * **
1588937 TTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTTGAC-CTGGCAATGTTGATCCATCGGG
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT-TCTCTGGAAATGTTGATCCATCAAG
* * *
1589001 TGATGAATTAAAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTC
65 TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
1589050 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGT
* ** * *
1589115 GATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
66 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
*
1589163 TTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1589202 CTTCTTCATT
Statistics
Matches: 336, Mismatches: 38, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
112 2 0.01
113 334 0.99
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGT
GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
Found at i:1589205 original size:153 final size:153
Alignment explanation
Indices: 1589028--1589359 Score: 601
Period size: 153 Copynumber: 2.2 Consensus size: 153
1589018 AGGTTGAACA
* *
1589028 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
1589093 TGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGA
66 TGGAAATGTTGATCCATCAAGTGACGGATTTGAGAAAAAGGTTGAACAAGCTCTTCTCATTATAA
1589158 ACTTCTTCTTCATTCTTCAGATG
131 ACTTCTTCTTCATTCTTCAGATG
1589181 AGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1589246 TGGAAATGTTGATCCATCAAGTGACGGATTTGAGAAAAAGGTTGAACAAGCTCTTCTCATTATAA
66 TGGAAATGTTGATCCATCAAGTGACGGATTTGAGAAAAAGGTTGAACAAGCTCTTCTCATTATAA
*
1589311 ACTTCTTCTTCCTTCTTCAGATG
131 ACTTCTTCTTCATTCTTCAGATG
*
1589334 AGTTCTTCTCATTATGAACTCCTTCT
1 AGTTCTTCTCATTATGAACTTCTTCT
1589360 GGAAATGTTG
Statistics
Matches: 172, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
153 172 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (153 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAATGTTGATCCATCAAGTGACGGATTTGAGAAAAAGGTTGAACAAGCTCTTCTCATTATAA
ACTTCTTCTTCATTCTTCAGATG
Found at i:1598094 original size:26 final size:28
Alignment explanation
Indices: 1598065--1598117 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
1598055 AAAATAAAAC
*
1598065 ATTAATAAAATAAT-A-TATATATAAAT
1 ATTAAGAAAATAATAAGTATATATAAAT
*
1598091 ATTAGGAAAATAATAAGTATATATAAA
1 ATTAAGAAAATAATAAGTATATATAAA
1598118 AATTTTGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 1 0.04
28 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (28 bp):
ATTAAGAAAATAATAAGTATATATAAAT
Found at i:1598659 original size:17 final size:18
Alignment explanation
Indices: 1598634--1598671 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1598624 TAAGAAAATC
1598634 TATTAATTTATATA-AAA
1 TATTAATTTATATAGAAA
* *
1598651 TATTTATTTATTTAGAAA
1 TATTAATTTATATAGAAA
1598669 TAT
1 TAT
1598672 CAGAAAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTAATTTATATAGAAA
Found at i:1600766 original size:3 final size:3
Alignment explanation
Indices: 1600760--1600812 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
1600750 ATTATTTATT
* *
1600760 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1600804 TAA TAA TAA
1 TAA TAA TAA
1600813 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1600782 original size:19 final size:18
Alignment explanation
Indices: 1600760--1600815 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
1600750 ATTATTTATT
1600760 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
1600779 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
1600798 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
1600816 AAACAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:1600785 original size:22 final size:21
Alignment explanation
Indices: 1600738--1600816 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
1600728 TGTAAAAATG
* * *
1600738 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
1600760 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
*
1600782 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
1600801 TAATAATAATAAATAA
1 TAATAATAATAAATAA
1600817 AACAAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:1600823 original size:22 final size:22
Alignment explanation
Indices: 1600760--1600823 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
1600750 ATTATTTATT
* *
1600760 TAATAAT-AATAATATAATATAA
1 TAATAATAAATAAAACAA-ATAA
*
1600782 TAATAATA-TTAAAACAAAATAA
1 TAATAATAAATAAAAC-AAATAA
1600804 TAATAATAAATAAAACAAAT
1 TAATAATAAATAAAACAAAT
1600824 GAAATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAAATAAAACAAATAA
Found at i:1617873 original size:17 final size:18
Alignment explanation
Indices: 1617839--1617877 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1617829 ATCATTTCGC
* *
1617839 TTTTTTGTTTCTTGTAAT
1 TTTTTTGTATATTGTAAT
1617857 TTTTTTGTATATT-TAAT
1 TTTTTTGTATATTGTAAT
1617874 TTTT
1 TTTT
1617878 CTTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (18 bp):
TTTTTTGTATATTGTAAT
Found at i:1621100 original size:24 final size:24
Alignment explanation
Indices: 1621068--1621114 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1621058 GGGTAGTTGG
1621068 ATTAGCTCAATTGGTTAGAGCGTT
1 ATTAGCTCAATTGGTTAGAGCGTT
*
1621092 ATTAGCTCAGTTGGTTAGAGCGT
1 ATTAGCTCAATTGGTTAGAGCGT
1621115 CGTGCTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (24 bp):
ATTAGCTCAATTGGTTAGAGCGTT
Found at i:1622663 original size:20 final size:20
Alignment explanation
Indices: 1622638--1622715 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
1622628 TTTGGTTCAC
* *
1622638 GGAATGGAAGATTATCGGTG
1 GGAATGGAAGATTACCAGTG
* *
1622658 GGAATGGAATATTACCAATG
1 GGAATGGAAGATTACCAGTG
1622678 GGAATGGAAGATTACCAGTG
1 GGAATGGAAGATTACCAGTG
*
1622698 GGAATGTAAGATTACCAG
1 GGAATGGAAGATTACCAG
1622716 GGAATAGGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.36, C:0.09, G:0.32, T:0.23
Consensus pattern (20 bp):
GGAATGGAAGATTACCAGTG
Found at i:1623889 original size:12 final size:13
Alignment explanation
Indices: 1623867--1623896 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1623857 AGAGGAAGTT
1623867 AATATAATAAATA
1 AATATAATAAATA
1623880 AATA-AATAAATA
1 AATATAATAAATA
1623892 AATAT
1 AATAT
1623897 TATTGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATATAATAAATA
Found at i:1626343 original size:20 final size:20
Alignment explanation
Indices: 1626318--1626362 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1626308 AGATTTCTAC
1626318 CCACCCAAACAATTGCTCCA
1 CCACCCAAACAATTGCTCCA
1626338 CCACCCAAACAATTGCTCCA
1 CCACCCAAACAATTGCTCCA
1626358 CCACC
1 CCACC
1626363 ACCAATTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.49, G:0.04, T:0.13
Consensus pattern (20 bp):
CCACCCAAACAATTGCTCCA
Found at i:1626627 original size:21 final size:21
Alignment explanation
Indices: 1626601--1626659 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1626591 ATTTACCGTG
1626601 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
* * *
1626622 ATTGCGGTCGTCGTGGACGCT
1 ATTGCGGCCGTCGCGGGCGCT
1626643 ATTGCGGCCGTCGCGGG
1 ATTGCGGCCGTCGCGGG
1626660 TAACTCGGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.07, C:0.29, G:0.42, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Found at i:1629073 original size:38 final size:38
Alignment explanation
Indices: 1628976--1629115 Score: 208
Period size: 38 Copynumber: 3.9 Consensus size: 38
1628966 TAGACCGCAT
1628976 TTGAAATCACACATAAAAGTCAAC--AT--ATGTGAAC
1 TTGAAATCACACATAAAAGTCAACATATGGATGTGAAC
1629010 TTG-AATCA-ATCAT---AGTCAACATATGGATGTGAAC
1 TTGAAATCACA-CATAAAAGTCAACATATGGATGTGAAC
1629044 TTGAAATCACACATAAAAGTCAACATATGGATGTGAAC
1 TTGAAATCACACATAAAAGTCAACATATGGATGTGAAC
1629082 TTGAAATCACACATAAAAGTCAACATATGGATGT
1 TTGAAATCACACATAAAAGTCAACATATGGATGT
1629116 AGAGTGCGCA
Statistics
Matches: 96, Mismatches: 0, Indels: 16
0.86 0.00 0.14
Matches are distributed among these distances:
30 7 0.07
32 3 0.03
33 8 0.08
34 14 0.15
35 8 0.08
36 1 0.01
38 55 0.57
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.26
Consensus pattern (38 bp):
TTGAAATCACACATAAAAGTCAACATATGGATGTGAAC
Found at i:1629674 original size:21 final size:20
Alignment explanation
Indices: 1629649--1629687 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1629639 TGTTTTGTGG
1629649 TACATCTTTATCTATCTTTGT
1 TACATCTTT-TCTATCTTTGT
* *
1629670 TACATGTTTTTTATCTTT
1 TACATCTTTTCTATCTTT
1629688 TTTTTATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.18, C:0.15, G:0.05, T:0.62
Consensus pattern (20 bp):
TACATCTTTTCTATCTTTGT
Found at i:1630901 original size:16 final size:16
Alignment explanation
Indices: 1630861--1630894 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1630851 TTCTCCTACA
1630861 ATTGAAAAATTAAATT
1 ATTGAAAAATTAAATT
1630877 ATTGAAAAATTAAATT
1 ATTGAAAAATTAAATT
1630893 AT
1 AT
1630895 CTTAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTGAAAAATTAAATT
Found at i:1636101 original size:22 final size:22
Alignment explanation
Indices: 1636076--1636147 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
1636066 CACCACATCT
1636076 CACATAATTTGTACTGAAGTG-C
1 CACATAATTTGTACTGAAG-GAC
*
1636098 CACAT-ATTTGTTCTGAAGGAC
1 CACATAATTTGTACTGAAGGAC
* *
1636119 CACATAGTTTTGT-CTCGAATGAC
1 CACATA-ATTTGTACT-GAAGGAC
1636142 CACATA
1 CACATA
1636148 GGATTATCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.02
21 18 0.42
22 7 0.16
23 17 0.40
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (22 bp):
CACATAATTTGTACTGAAGGAC
Found at i:1636142 original size:23 final size:22
Alignment explanation
Indices: 1636116--1636194 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
1636106 TGTTCTGAAG
*
1636116 GACCACATAGTTTTGTCTCGAA
1 GACCACATAGGTTTGTCTCGAA
* *
1636138 TGACCACATAGGATTATC-CTGAA
1 -GACCACATAGGTTTGTCTC-GAA
*
1636161 GTACCATATAGGTTTGTCTCGAAA
1 G-ACCACATAGGTTTGTCTCG-AA
1636185 GACCACATAG
1 GACCACATAG
1636195 AACCCTCGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
22 2 0.04
23 39 0.87
24 4 0.09
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (22 bp):
GACCACATAGGTTTGTCTCGAA
Found at i:1636808 original size:17 final size:18
Alignment explanation
Indices: 1636775--1636808 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1636765 TCTTTTCTAT
1636775 GGTATCGATACCCATTTC
1 GGTATCGATACCCATTTC
1636793 GGTATCGATA-CCATTT
1 GGTATCGATACCCATTT
1636809 TGGCATTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (18 bp):
GGTATCGATACCCATTTC
Found at i:1645957 original size:61 final size:60
Alignment explanation
Indices: 1645892--1646047 Score: 172
Period size: 60 Copynumber: 2.6 Consensus size: 60
1645882 TATTTTGATG
1645892 AATTTGGGGATAAAATTGGAATGTTCAAAAAGTTTAAGGACTAATATAGAAT-GAAGGTCAT
1 AATTTGGGGATAAAATTGGAATGTTC-AAAAGTTTAAGGACTAATATAGAATGGAA-GTCAT
* * * * * * * *
1645953 AATTTGGGAATGAAATTGAAATGTTCAAAAGTTTGAGTATTAATTTAGAATGGTAGTCAT
1 AATTTGGGGATAAAATTGGAATGTTCAAAAGTTTAAGGACTAATATAGAATGGAAGTCAT
* * *
1646013 AGA-TTAGGGATAAAATTGGAATATTTAAAAGTTTA
1 A-ATTTGGGGATAAAATTGGAATGTTCAAAAGTTTA
1646048 TAGACCAATT
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
60 52 0.67
61 26 0.33
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (60 bp):
AATTTGGGGATAAAATTGGAATGTTCAAAAGTTTAAGGACTAATATAGAATGGAAGTCAT
Found at i:1646476 original size:13 final size:14
Alignment explanation
Indices: 1646448--1646476 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1646438 AAATCGACCT
1646448 TAAATTATATAAAA
1 TAAATTATATAAAA
1646462 TAAATTATA-AAAA
1 TAAATTATATAAAA
1646475 TA
1 TA
1646477 TTATATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATTATATAAAA
Found at i:1648165 original size:205 final size:200
Alignment explanation
Indices: 1647793--1648792 Score: 1188
Period size: 193 Copynumber: 5.0 Consensus size: 200
1647783 AGATATGTTT
* * * * *
1647793 AAAATTTTGTTAGGAATTATCGTTTATTGTATTCAAGGTGGAACACATCATACAAATCAAGCAAT
1 AAAAATTTGTTAGGAAATATCGTTCATTGTATTTAAGGTGGGACACATCATACAAATCAAGCAAT
* **
1647858 CTCAGTGATTGAAATATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAATTTAAAAAGTA
66 CTCAGTGACTGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAA-TTAAAAA-TA
* * *
1647923 TTTTTTTAAAAGTATATAAAAATAATTTGTTTTTAAAATCATTTATATCGTTCAAAATTTTAAAA
129 -TTTTTAAAAAGTATAT-AAAATAATTTATTTTTAAAATTATTTATATCGTTCAAAATTTTAAAA
* *
1647988 ATATATGTA
192 AAATATATA
* * * *
1647997 AAAACATTTGTTAAGAAATATAGTTCATTGTATTCAAGGTGGAACACATCATAACAAATCAAGCA
1 AAAA-ATTTGTTAGGAAATATCGTTCATTGTATTTAAGGTGGGACACATCAT-ACAAATCAAGCA
*
1648062 ATCT-ATGTGATTGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAAAATTAAAA
64 ATCTCA-GTGACTGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTT--AATTAAAA
* * * *
1648126 ATTATTTTTAAAAAGTATATAAAATAAATTATTTTTAAAATTATTTATTTCATTC-AAATTTAAA
126 A-TATTTTTAAAAAGTATATAAAATAATTTATTTTTAAAATTATTTATATCGTTCAAAATTT-TA
*
1648190 AAAAAATGTATA
189 AAAAAATATATA
* *
1648202 AAAAATTTTGTTAGGACATATCGTTCATTGTATTTAAGGTGGGACACATCATACAAATCAAACAA
1 AAAAA-TTTGTTAGGAAATATCGTTCATTGTATTTAAGGTGGGACACATCATACAAATCAAGCAA
* * * *
1648267 TCTTAATGACCGAAGGATGATTATTTATTTAATTATTGTTGTATTTA--TTTT--TT---AA-A-
65 TCTCAGTGACTGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAATTAAAAATAT
* **
1648323 -TTTAAAAAGTATATAAAAATAATTTATTTTTTAAATTATTTATATCGTTCAATTTTTTTAAAAA
130 TTTTAAAAAGTATAT-AAAATAATTTATTTTTAAAATTATTTATATCGTTCAA-AATTTTAAAAA
1648387 AATATATA
193 AATATATA
* * * *
1648395 AAAATTTGTGTTAGGACATATAGTTCATTGTATTTAAGGTGGGACACATCATACAAATCAAACAA
1 AAAAATT-TGTTAGGAAATATCGTTCATTGTATTTAAGGTGGGACACATCATACAAATCAAGCAA
* * **
1648460 TTTCAATGACCAAAGGATGATTATTTATTTAATTGTTGTTGTATTTA-TTTTT--TT---AA-A-
65 TCTCAGTGACTGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAATTAAAAATAT
*
1648517 -TTTAAAAAGTATATAAAATAATTTATTTTTAAAATTATTTATATCGTTC-AAATTTT-TAAAAA
130 TTTTAAAAAGTATATAAAATAATTTATTTTTAAAATTATTTATATCGTTCAAAATTTTAAAAAAA
1648579 -ATATA
195 TATATA
* * *
1648584 AAAAATTTGTTAGGAAATATCCTTAATTGTATTTAAGGTGGGACACATCATACAAATCAAGTAAT
1 AAAAATTTGTTAGGAAATATCGTTCATTGTATTTAAGGTGGGACACATCATACAAATCAAGCAAT
1648649 CTCAGTGACT-AGAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAAATTTAAAAAT
66 CTCAGTGACTGA-AGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTT-AA-TTAAAAAT
* * * * *
1648713 ATTTTTTAATAGTATATAAAGTAATTTATTTTTAAATTTATTTATATCATT-AAAATTTTTGAAA
128 ATTTTTAAAAAGTATATAAAATAATTTATTTTTAAAATTATTTATATCGTTCAAAA-TTTT-AAA
*
1648777 AATATATATA
191 AAAATATATA
1648787 AAAAAT
1 AAAAAT
1648793 AATTTATTTT
Statistics
Matches: 703, Mismatches: 63, Indels: 61
0.85 0.08 0.07
Matches are distributed among these distances:
187 1 0.00
188 93 0.13
189 16 0.02
190 5 0.01
191 18 0.03
192 34 0.05
193 153 0.22
194 26 0.04
195 2 0.00
196 2 0.00
197 1 0.00
198 2 0.00
199 46 0.07
200 4 0.01
202 8 0.01
203 11 0.02
204 64 0.09
205 129 0.18
206 77 0.11
207 9 0.01
208 2 0.00
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.43
Consensus pattern (200 bp):
AAAAATTTGTTAGGAAATATCGTTCATTGTATTTAAGGTGGGACACATCATACAAATCAAGCAAT
CTCAGTGACTGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAATTAAAAATATT
TTTAAAAAGTATATAAAATAATTTATTTTTAAAATTATTTATATCGTTCAAAATTTTAAAAAAAT
ATATA
Found at i:1648667 original size:381 final size:389
Alignment explanation
Indices: 1647793--1648711 Score: 1153
Period size: 381 Copynumber: 2.3 Consensus size: 389
1647783 AGATATGTTT
* * * * *
1647793 AAAATTTTGTTAGGAATTATCGTTTATTGTATTCAAGGTGGAACACATCATACAAATCAAGCAAT
1 AAAAATTTGTTAGGAAATATCGTTAATTGTATTTAAGGTGGGACACATCATACAAATCAAGCAAT
* **
1647858 CTCAGTGA-TTGAAATATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAATTTAAAAAGT
66 CTCAGTGACTAGAAGGATGATTATTTATTTAATTGTTGTTGTATTTA---TTT--TTT---AA--
* *
1647922 ATTTTTTTAAAAGTATATAAAAATAATTTGTTTTTAAAATCATTTATATCGTTCAAAATTTTAAA
121 A---TTTAAAAAGTATATAAAAATAATTTATTTTTAAAATCATTTATATCGTTCAAAATTTTAAA
* *
1647987 AATATATGTAAAAACATTTGTTAAGAAATATAGTTCATTGTATTCAAGGTGGAACACATCATAAC
183 AAAATATATAAAAACATTTGTTAAGAAATATAGTTCATTGTATTCAAGGTGGAACACATCATAAC
* * ***
1648052 AAATCAAGCAATCTATGTGATTGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTA
248 AAATCAAACAATCTATATGACCAAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTT-
*
1648117 AAATTAAAAATTATTTTTAAAAAGTATATAAAATAAATTATTTTTAAAATTATTTATTTCATTCA
312 --ATT--AAA-TA-TTTTAAAAAGTATATAAAATAAATTATTTTTAAAATTATTTATATCATTCA
1648182 AATTTAAAAAAAAATGTATA
371 AATTTAAAAAAAAA-GTATA
* * *
1648202 AAAAATTTTGTTAGGACATATCGTTCATTGTATTTAAGGTGGGACACATCATACAAATCAAACAA
1 AAAAA-TTTGTTAGGAAATATCGTTAATTGTATTTAAGGTGGGACACATCATACAAATCAAGCAA
* * * *
1648267 TCTTAATGAC-CGAAGGATGATTATTTATTTAATTATTGTTGTATTTATTTTTTAAATTTAAAAA
65 TCTCAGTGACTAGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAAATTTAAAAA
* * **
1648331 GTATATAAAAATAATTTATTTTTTAAATTATTTATATCGTTCAATTTTTTTAAAAAAATATATAA
130 GTATATAAAAATAATTTATTTTTAAAATCATTTATATCGTTCAA-AATTTTAAAAAAATATATAA
* * * * *
1648396 AAA-TTTGTGTTAGGACATATAGTTCATTGTATTTAAGGTGGGACACATCAT-ACAAATCAAACA
194 AAACATT-TGTTAAGAAATATAGTTCATTGTATTCAAGGTGGAACACATCATAACAAATCAAACA
*
1648459 ATTTCA-ATGACCAAAGGATGATTATTTATTTAATTGTTGTTGTATTTA-TTTTT-TT-AA-A-T
258 ATCT-ATATGACCAAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTATTAAATATT
* * **
1648518 TTAAAAAGTATATAAAATAATTTATTTTTAAAATTATTTATATCGTTCAAATTT-TTAAAAAA-T
322 TTAAAAAGTATATAAAATAAATTATTTTTAAAATTATTTATATCATTCAAATTTAAAAAAAAAGT
1648581 ATA
387 ATA
* *
1648584 AAAAATTTGTTAGGAAATATCCTTAATTGTATTTAAGGTGGGACACATCATACAAATCAAGTAAT
1 AAAAATTTGTTAGGAAATATCGTTAATTGTATTTAAGGTGGGACACATCATACAAATCAAGCAAT
1648649 CTCAGTGACTAG-AGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAAATTTAAAAA
66 CTCAGTGACTAGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAAATTTAAAAA
1648712 TATTTTTTAA
Statistics
Matches: 458, Mismatches: 46, Indels: 40
0.84 0.08 0.07
Matches are distributed among these distances:
381 112 0.24
382 10 0.02
384 6 0.01
385 52 0.11
387 1 0.00
389 2 0.00
392 2 0.00
396 5 0.01
397 102 0.22
398 60 0.13
400 1 0.00
402 2 0.00
405 3 0.01
407 3 0.01
409 4 0.01
410 93 0.20
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.43
Consensus pattern (389 bp):
AAAAATTTGTTAGGAAATATCGTTAATTGTATTTAAGGTGGGACACATCATACAAATCAAGCAAT
CTCAGTGACTAGAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTAAATTTAAAAAG
TATATAAAAATAATTTATTTTTAAAATCATTTATATCGTTCAAAATTTTAAAAAAATATATAAAA
ACATTTGTTAAGAAATATAGTTCATTGTATTCAAGGTGGAACACATCATAACAAATCAAACAATC
TATATGACCAAAGGATGATTATTTATTTAATTGTTGTTGTATTTATTTTTTATTAAATATTTTAA
AAAGTATATAAAATAAATTATTTTTAAAATTATTTATATCATTCAAATTTAAAAAAAAAGTATA
Found at i:1649232 original size:17 final size:17
Alignment explanation
Indices: 1649210--1649258 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1649200 ATACAAACAT
1649210 AAAATTTAATATATATG
1 AAAATTTAATATATATG
* *
1649227 AAAATTTTATATGATATT
1 AAAATTTAATAT-ATATG
*
1649245 AAAA-ATAATATATA
1 AAAATTTAATATATA
1649259 GTTTATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.11
17 16 0.59
18 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
AAAATTTAATATATATG
Found at i:1649322 original size:6 final size:6
Alignment explanation
Indices: 1649311--1649352 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1649301 AACTTACTTC
* * *
1649311 AATTAA AATTAA CATTAA AATT-A AATTAA AGTTAT AATTAA A
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA A
1649353 GAGTTAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (6 bp):
AATTAA
Found at i:1649338 original size:17 final size:17
Alignment explanation
Indices: 1649311--1649352 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
1649301 AACTTACTTC
1649311 AATTAAAATTAACA-TTAA
1 AATT-AAATTAA-AGTTAA
*
1649329 AATTAAATTAAAGTTAT
1 AATTAAATTAAAGTTAA
1649346 AATTAAA
1 AATTAAA
1649353 GAGTTAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.77
18 4 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AATTAAATTAAAGTTAA
Found at i:1649353 original size:12 final size:11
Alignment explanation
Indices: 1649311--1649352 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
1649301 AACTTACTTC
1649311 AATTAAAATTA
1 AATTAAAATTA
1649322 ACATTAAAATTA
1 A-ATTAAAATTA
*
1649334 AATTAAAGTTA
1 AATTAAAATTA
1649345 TAATTAAA
1 -AATTAAA
1649353 GAGTTAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (11 bp):
AATTAAAATTA
Found at i:1653162 original size:30 final size:31
Alignment explanation
Indices: 1653122--1653190 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
1653112 AAATTATCTC
*
1653122 TTTA-TTTTTGTTTTAACTTATTAAATAT-T
1 TTTATTTTTTGTCTTAACTTATTAAATATAT
*
1653151 TTTATTTTTTGTCTTAATTTATTAAATATAT
1 TTTATTTTTTGTCTTAACTTATTAAATATAT
*
1653182 TTTGTTTTT
1 TTTATTTTT
1653191 ATTTAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 4 0.11
30 22 0.63
31 9 0.26
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (31 bp):
TTTATTTTTTGTCTTAACTTATTAAATATAT
Found at i:1653306 original size:29 final size:29
Alignment explanation
Indices: 1653274--1653335 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1653264 ATATATTTAA
*
1653274 ATATTTTATTATTAATTT-AATATAAAAAT
1 ATATTTTACTATTAATTTAAAT-TAAAAAT
* *
1653303 ATATTTTACTCTTATTTTAAATTAAAAAT
1 ATATTTTACTATTAATTTAAATTAAAAAT
1653332 ATAT
1 ATAT
1653336 AATATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (29 bp):
ATATTTTACTATTAATTTAAATTAAAAAT
Found at i:1653350 original size:34 final size:34
Alignment explanation
Indices: 1653303--1653369 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1653293 ATATAAAAAT
*
1653303 ATATTTTACTCTTAT-TTTAAATTAAAAATATATA
1 ATATTTTACTCTTATCTTT-AATCAAAAATATATA
* *
1653337 ATATTTTATTCTTATCTTTACTCAAAAATATAT
1 ATATTTTACTCTTATCTTTAATCAAAAATATAT
1653370 TAAAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (34 bp):
ATATTTTACTCTTATCTTTAATCAAAAATATATA
Found at i:1653416 original size:31 final size:31
Alignment explanation
Indices: 1653378--1653528 Score: 97
Period size: 31 Copynumber: 4.7 Consensus size: 31
1653368 ATTAAAATAT
1653378 TATATATTTTTAAATGAAAATAAGAGTAAAA
1 TATATATTTTTAAATGAAAATAAGAGTAAAA
* * * *
1653409 TATATATTTTTTATATTAAATTAATAGTAAAA
1 TATATA-TTTTTAAATGAAAATAAGAGTAAAA
* ** * * * ** *
1653441 TATTTAAATATATATCAAGTTAAGATATTTAAAA
1 TATATATTTTTAAATGAAAATAAG--A-GTAAAA
* *
1653475 AATATATTTTTAAATGAAGATAA-AGATAAAA
1 TATATATTTTTAAATGAAAATAAGAG-TAAAA
* *
1653506 TATATATTTTTACATTAAAATAA
1 TATATATTTTTAAATGAAAATAA
1653529 AAAATATATT
Statistics
Matches: 90, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
31 43 0.48
32 26 0.29
33 1 0.01
34 20 0.22
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (31 bp):
TATATATTTTTAAATGAAAATAAGAGTAAAA
Found at i:1653438 original size:32 final size:33
Alignment explanation
Indices: 1653370--1653443 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
1653360 AAAAATATAT
1653370 TAAAATATTATATATTTTTAAATGAAAATAAGAG
1 TAAAATA-TATATATTTTTAAATGAAAATAAGAG
* * * *
1653404 TAAAATATATAT-TTTTTATATTAAATTAATAG
1 TAAAATATATATATTTTTAAATGAAAATAAGAG
1653436 TAAAATAT
1 TAAAATAT
1653444 TTAAATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 24 0.67
33 5 0.14
34 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (33 bp):
TAAAATATATATATTTTTAAATGAAAATAAGAG
Found at i:1653548 original size:26 final size:26
Alignment explanation
Indices: 1653495--1653587 Score: 73
Period size: 26 Copynumber: 3.4 Consensus size: 26
1653485 TAAATGAAGA
* * *
1653495 TAAAGATAAAATATATATTT-TTACAT
1 TAAA-ATAAAAAATATATTTAATAAAT
1653521 TAAAATAAAAAATATATTTAATAAAT
1 TAAAATAAAAAATATATTTAATAAAT
*
1653547 TAAGAA-AAAAAATAAAATCATTTAATAAGT
1 TAA-AATAAAAAAT---AT-ATTTAATAAAT
*
1653577 TAAAACAAAAA
1 TAAAATAAAAA
1653588 TAAAGAGATA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
25 14 0.25
26 18 0.32
27 2 0.04
29 4 0.07
30 18 0.32
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (26 bp):
TAAAATAAAAAATATATTTAATAAAT
Found at i:1655913 original size:12 final size:12
Alignment explanation
Indices: 1655896--1655930 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1655886 AGCCTCCAAC
*
1655896 TGCTCCGGCAGT
1 TGCTCCAGCAGT
1655908 TGCTCCAGCAGT
1 TGCTCCAGCAGT
1655920 TGCTCCAGCAG
1 TGCTCCAGCAG
1655931 ATGAAGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.34, G:0.29, T:0.23
Consensus pattern (12 bp):
TGCTCCAGCAGT
Found at i:1658611 original size:21 final size:20
Alignment explanation
Indices: 1658585--1658623 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1658575 ACCAAGGGTA
*
1658585 GAGTATCGATACTCCTCATAG
1 GAGTATCGAT-CTACTCATAG
1658606 GAGTATCGATCTACTCAT
1 GAGTATCGATCTACTCAT
1658624 CTTCTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (20 bp):
GAGTATCGATCTACTCATAG
Found at i:1659787 original size:15 final size:17
Alignment explanation
Indices: 1659761--1659792 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1659751 AGAAATTATA
1659761 ATATAGAATTTA-ATTT
1 ATATAGAATTTATATTT
1659777 ATATA-AATTTATATTT
1 ATATAGAATTTATATTT
1659793 TAATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATAGAATTTATATTT
Found at i:1660709 original size:31 final size:30
Alignment explanation
Indices: 1660673--1660753 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 30
1660663 TGATATTTTT
1660673 ATCTAAAATTAATAAGGT-AAATTAATATTTA
1 ATCTAAAATT--TAAGGTCAAATTAATATTTA
* *
1660704 ATCTAAAATTTAGGGTCAAATTAATATTTT
1 ATCTAAAATTTAAGGTCAAATTAATATTTA
*
1660734 GTCTAAAATTTAAGGATCAA
1 ATCTAAAATTTAAGG-TCAA
1660754 GTGAATATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.11
30 25 0.57
31 14 0.32
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (30 bp):
ATCTAAAATTTAAGGTCAAATTAATATTTA
Found at i:1666383 original size:2 final size:2
Alignment explanation
Indices: 1666376--1666412 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1666366 CAGAAAACAT
1666376 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1666413 GTTGTGATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1671946 original size:20 final size:21
Alignment explanation
Indices: 1671909--1671948 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1671899 AAATTAAGTT
1671909 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1671930 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1671949 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1672203 original size:19 final size:19
Alignment explanation
Indices: 1672179--1672217 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1672169 TCGAATGCAT
1672179 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1672198 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1672217 T
1 T
1672218 GAATATTTTC
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:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1672318 original size:64 final size:65
Alignment explanation
Indices: 1672165--1672325 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
1672155 GAATTAATTG
* * *** *
1672165 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
1672230 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
1672293 A
65 A
1672294 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1672326 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1672340 original size:64 final size:64
Alignment explanation
Indices: 1672165--1672345 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
1672155 GAATTAATTG
* * * *
1672165 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
1672230 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
1672294 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
1672346 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 48 0.48
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:1678153 original size:44 final size:44
Alignment explanation
Indices: 1678097--1678198 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
1678087 TTTGTGCTTC
* * *
1678097 ATGCACCGATGCATTTAACA-ATGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATGCATTCAACAGATGCACCGATGCATCCC-TTGAAT
* * *
1678141 ATGTATCGATGCA-TCACCATGATGCACCGATGCATGCCTTGAAT
1 ATGCATCGATGCATTCAACA-GATGCACCGATGCATCCCTTGAAT
1678185 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1678199 AAGAACATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
43 4 0.08
44 29 0.60
45 15 0.31
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
ATGCATCGATGCATTCAACAGATGCACCGATGCATCCCTTGAAT
Found at i:1678627 original size:11 final size:10
Alignment explanation
Indices: 1678610--1678634 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1678600 ATTTCGAATT
1678610 TAAAAAAAAA
1 TAAAAAAAAA
1678620 TAAAAAAAAA
1 TAAAAAAAAA
1678630 TAAAA
1 TAAAA
1678635 TTAAGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:1679485 original size:20 final size:21
Alignment explanation
Indices: 1679448--1679487 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1679438 AAATTAAGTT
1679448 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1679469 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1679488 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1679742 original size:19 final size:19
Alignment explanation
Indices: 1679718--1679756 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1679708 TCGAATGCAT
1679718 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1679737 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1679756 T
1 T
1679757 GAATATTTTC
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:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1679884 original size:64 final size:64
Alignment explanation
Indices: 1679704--1679866 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
1679694 GAATTAATTG
* * * *
1679704 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** *
1679769 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGACTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*
1679833 AACATCGAATGCATTTCATGCATCGATACACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
1679867 TGGTGCACCT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:1682733 original size:2 final size:2
Alignment explanation
Indices: 1682726--1682754 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1682716 GCAAGGGAGA
1682726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1682755 AATGTTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1691265 original size:31 final size:31
Alignment explanation
Indices: 1691230--1691312 Score: 118
Period size: 31 Copynumber: 2.7 Consensus size: 31
1691220 TGATGGATTA
1691230 TTGTAAATTGTATTAAGGATTTC-TAACACAT
1 TTGTAAATTGTATTAAGGATTTCAT-ACACAT
1691261 TTGTAAATTGTATTAAGGATTTCATACACAT
1 TTGTAAATTGTATTAAGGATTTCATACACAT
*
1691292 TTGTTTAATT-TATT-AGGATTT
1 TTG-TAAATTGTATTAAGGATTT
1691313 TTAATTGGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
30 7 0.14
31 36 0.73
32 6 0.12
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (31 bp):
TTGTAAATTGTATTAAGGATTTCATACACAT
Found at i:1693331 original size:120 final size:123
Alignment explanation
Indices: 1693059--1693333 Score: 317
Period size: 120 Copynumber: 2.2 Consensus size: 123
1693049 TGAAAAGTGC
* * *
1693059 GATACCCCTTTA-CTATTGC-TAGTTAGTCTCTTTATGAAATGATATCTGATATTGCTATAATTA
1 GATACCCC-TTAGCTATTGCTTA-TTATTCTCGTCATGAAATGATATCTGATATTGCTATAATTA
* * * * *
1693122 TTTTTCGATTAGGAGATTGTATTTTTTTTAAGAACTAAATTGAGAACAAGATGAGATTGTAG
64 TTTTT--ATTAGGAGAATGTATTCTTTTTAAGAACTAAATTGAGAAAAAGAAGAGATTGGAG
* * * * **
1693184 GATACCCCTTAGCTATTACTGAATATTCTCGTCATGTAATGATATCTGATATTGCTATTGTTA-T
1 GATACCCCTTAGCTATTGCTTATTATTCTCGTCATGAAATGATATCTGATATTGCTATAATTATT
* ** *
1693248 TTT-TTAGGAGAATGTA-TCTTTTTCATTATTAAATTGAGAAAAAGAAGAGATTGGAG
66 TTTATTAGGAGAATGTATTCTTTTTAAGAACTAAATTGAGAAAAAGAAGAGATTGGAG
1693304 GATACCCCTTAGCTATTGCTTATTATTCTC
1 GATACCCCTTAGCTATTGCTTATTATTCTC
1693334 TTCAGTTTTC
Statistics
Matches: 127, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
120 59 0.46
121 12 0.09
124 7 0.06
125 48 0.38
126 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.41
Consensus pattern (123 bp):
GATACCCCTTAGCTATTGCTTATTATTCTCGTCATGAAATGATATCTGATATTGCTATAATTATT
TTTATTAGGAGAATGTATTCTTTTTAAGAACTAAATTGAGAAAAAGAAGAGATTGGAG
Found at i:1698606 original size:21 final size:21
Alignment explanation
Indices: 1698560--1698617 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1698550 GATCCCTTTT
*
1698560 CAAAAGGATCAATCCCTCAGG
1 CAAAAGGATCGATCCCTCAGG
* *
1698581 AAAAATGATCGATCCCTC-GAG
1 CAAAAGGATCGATCCCTCAG-G
1698602 CAAAAGGATCGATCCC
1 CAAAAGGATCGATCCC
1698618 AAACTTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.16
Consensus pattern (21 bp):
CAAAAGGATCGATCCCTCAGG
Found at i:1702096 original size:37 final size:37
Alignment explanation
Indices: 1702023--1702097 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1702013 GTTGAAAAAT
* *
1702023 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
1702060 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
1702097 A
1 A
1702098 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1723422 original size:16 final size:17
Alignment explanation
Indices: 1723389--1723424 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1723379 TTTAAATCAT
*
1723389 AATTTTAAATACATAAA
1 AATTTTAAATAAATAAA
1723406 AATTTTAAA-AAATAAA
1 AATTTTAAATAAATAAA
1723422 AAT
1 AAT
1723425 CCAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTTAAATAAATAAA
Found at i:1734521 original size:18 final size:19
Alignment explanation
Indices: 1734498--1734534 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1734488 TAGAGGTTTT
*
1734498 TAAAAAAA-TCAACGGTCA
1 TAAAAAAAGTCAACAGTCA
1734516 TAAAAAAAGTCAACAGTCA
1 TAAAAAAAGTCAACAGTCA
1734535 AAGTCAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (19 bp):
TAAAAAAAGTCAACAGTCA
Found at i:1738736 original size:2 final size:2
Alignment explanation
Indices: 1738729--1738754 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1738719 TAGTTTTACA
1738729 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1738755 GCAGTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1738891 original size:30 final size:30
Alignment explanation
Indices: 1738831--1738892 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1738821 TTAGCTGTAC
*
1738831 AAAAAGTGAAGCTATATAAATCGGTGTAAA
1 AAAAAGTGAAGCTATATAAATCGGTCTAAA
*
1738861 AAAAAGTGAAGCTATATATA-CTGGTCTAAA
1 AAAAAGTGAAGCTATATAAATC-GGTCTAAA
1738891 AA
1 AA
1738893 TTGAGAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.24
Consensus pattern (30 bp):
AAAAAGTGAAGCTATATAAATCGGTCTAAA
Found at i:1740101 original size:21 final size:22
Alignment explanation
Indices: 1740069--1740125 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
1740059 TAGATATAAT
1740069 TTGAATCAAAT-CAAACTTAAA
1 TTGAATCAAATCCAAACTTAAA
*
1740090 TTGAATGC-AATCCAAATTTAAA
1 TTGAAT-CAAATCCAAACTTAAA
* * *
1740112 ATGATTCAACTCCA
1 TTGAATCAAATCCA
1740126 GGCTTATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.30
Consensus pattern (22 bp):
TTGAATCAAATCCAAACTTAAA
Found at i:1742165 original size:16 final size:16
Alignment explanation
Indices: 1742144--1742178 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1742134 TGAACTCTCA
*
1742144 TAATTTTAATAATTTT
1 TAATTTTAATAATTCT
*
1742160 TAATTTTTATAATTCT
1 TAATTTTAATAATTCT
1742176 TAA
1 TAA
1742179 AATATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTTTAATAATTCT
Found at i:1764144 original size:19 final size:19
Alignment explanation
Indices: 1764108--1764144 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1764098 CATTAAGATA
*
1764108 AAATATTTAAAATTATAAT
1 AAATATTTAAAATCATAAT
*
1764127 AAATATTTATAATCATAA
1 AAATATTTAAAATCATAA
1764145 ATAGGTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATTTAAAATCATAAT
Found at i:1765371 original size:14 final size:15
Alignment explanation
Indices: 1765352--1765380 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1765342 TGATGTGTTA
1765352 AAAATT-ATATTTTT
1 AAAATTAATATTTTT
1765366 AAAATTAATATTTTT
1 AAAATTAATATTTTT
1765381 TAAACTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAAATTAATATTTTT
Found at i:1765865 original size:31 final size:31
Alignment explanation
Indices: 1765829--1765887 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1765819 AACTTAAAAG
* *
1765829 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
*
1765860 AGTTTTATAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
1765888 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:1765933 original size:26 final size:26
Alignment explanation
Indices: 1765904--1765958 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 26
1765894 AACTACAATA
1765904 ATATTTTTTTTAAAATAAATCAAT-T
1 ATATTTTTTTTAAAATAAATCAATCT
*
1765929 -TA--TATTTTAAAATAAATCAATCT
1 ATATTTTTTTTAAAATAAATCAATCT
1765952 ATATTTT
1 ATATTTT
1765959 AAAATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
22 18 0.75
23 1 0.04
24 4 0.17
26 1 0.04
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATTTTTTTTAAAATAAATCAATCT
Found at i:1766637 original size:23 final size:22
Alignment explanation
Indices: 1765911--1766646 Score: 798
Period size: 22 Copynumber: 33.5 Consensus size: 22
1765901 ATAATATTTT
**
1765911 TTTTAAAATAAATCAATTTATA
1 TTTTAAAATAAATCAATCCATA
*
1765933 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*** *
1765955 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
* *
1765977 TTTTAAAATAAATCAATTCGTA
1 TTTTAAAATAAATCAATCCATA
* *** *
1765999 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
1766021 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
1766043 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*** *
1766065 TTTTAAAATAAATTTTTTTCATA
1 TTTTAAAATAAA-TCAATCCATA
1766088 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
1766110 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
1766132 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
1766154 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
1766176 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
**
1766198 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
1766220 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
1766242 TTTTAAAAT--ATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
1766262 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *** **
1766284 CTTTAAAAT-AATTTTTTTATA
1 TTTTAAAATAAATCAATCCATA
*
1766305 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1766327 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
1766349 TTTTAAAATAAATTTGTCCATA
1 TTTTAAAATAAATCAATCCATA
1766371 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
1766393 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
1766415 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*** *
1766437 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
1766459 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1766481 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* * * *** *
1766503 TTTAAAAACAATTTTTTTTCATA
1 TTTTAAAATAA-ATCAATCCATA
1766526 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1766548 TTTTAAAATAAAT-TTTCTCATA
1 TTTTAAAATAAATCAATC-CATA
*
1766570 TTTTAAAATAAATCAATCCGTA
1 TTTTAAAATAAATCAATCCATA
*
1766592 TTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAATCCATA
* **
1766614 TTTTAAAAATTAATCAATATATA
1 TTTT-AAAATAAATCAATCCATA
1766637 TTTTAAAATA
1 TTTTAAAATA
1766647 GATTTAAATG
Statistics
Matches: 592, Mismatches: 112, Indels: 20
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.03
21 22 0.04
22 497 0.84
23 56 0.09
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1768471 original size:30 final size:32
Alignment explanation
Indices: 1768413--1768471 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1768403 TTGTTTTATC
* *
1768413 TATATTTTTTATCTTGATATTTATTAAAAATA
1 TATATGTTTTATCTTGATATTTAGTAAAAATA
*
1768445 TATATGTTTTAT-TTTATATTT-GTAAAA
1 TATATGTTTTATCTTGATATTTAGTAAAA
1768472 TTAATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.21
31 8 0.33
32 11 0.46
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (32 bp):
TATATGTTTTATCTTGATATTTAGTAAAAATA
Found at i:1769437 original size:606 final size:608
Alignment explanation
Indices: 1768278--1769489 Score: 2284
Period size: 606 Copynumber: 2.0 Consensus size: 608
1768268 TTCTTTTTGT
* *
1768278 TTGTTACATTACTTTCTCTTATTCTATCTTTTATGTTTTTTATTGTAATTTCTACACAATAAAAT
1 TTGTTACATTACTTTCTCTTATTATATCTCTTATGTTTTTTATTGTAATTTCTACACAATAAAAT
1768343 AAAAATTAAATATAATATAATAAATTCAAGTAGATTAAATATTTTTTATGTTATTTATGATTGTT
66 AAAAATTAAATATAATATAATAAATTCAAGTAGATTAAATATTTTTTATGTTATTTATGATTGTT
*
1768408 TTATCTATATTTTTTATCTTGATATTTATTAAAAATATATATGTTTTATTTTATATTTGTAAAAT
131 TTATCTATACTTTTTATCTTGATATTTATTAAAAATATATATGTTTTATTTTATATTTGTAAAAT
*
1768473 TAATATTATAATAGTTAAATATTGTGAATAAAGTAAAGTCGGTGGTAATGTAAAGATAGTGCTCG
196 TAATATTATAATAATTAAATATTGTGAATAAAGTAAAGTCGGTGGTAATGTAAAGATAGTGCTCG
* *
1768538 AGATGAATTATTGTTTCATCTTTAGAGTAGAGATAGAAATTTTGTAGAGTAGAGATGAGAGTTAA
261 AGATGAATTATTGTTTCATCTTTAGAGTAGAGATAGAAATTCTATAGAGTAGAGATGAGAGTTAA
* *
1768603 AGATAACCTTAGTACGTAGAGTCTGTCACACAGTTTAGTACTATCAATCACTTTTATTGAATCTA
326 AGATAACCTTAATACATAGAGTCTGTCACACAGTTTAGTACTATCAATCACTTTTATTGAATCTA
1768668 CCGTTTGAAATTTATAAGCATTTGGATTAAATTTATAAATACTTCTTAAAAAATATCAGATACGT
391 CCGTTTGAAATTTATAAGCATTTGGATTAAATTTATAAATACTTCTTAAAAAATATCAGATACGT
1768733 AAATTTCCTTTTTCCTCCTCCTTTTAACGTTTTAAGTTAATTGTTGCAATTTTATTTAAAATAAT
456 AAATTTCCTTTTTCCTCCTCCTTTTAACGTTTTAAGTTAATTGTTGCAATTTTATTTAAAATAAT
1768798 AGGAATACACTTACTCTTTTAAGGAGCCAAATGCATC-G-CTCTACTTAACAAGTGTCGTTAAAG
521 AGGAATACACTTACTCTTTTAAGGAGCCAAATGCATCAGCCTCTACTTAACAAGTGTCGTTAAAG
1768861 ACCGAAAGATTGTGATATCATTG
586 ACCGAAAGATTGTGATATCATTG
* *
1768884 TTGTTATATTACTTTCTCTTATTATTTCTCTTATGTTTTTTATTGTAATTTCTACACAATAAAAT
1 TTGTTACATTACTTTCTCTTATTATATCTCTTATGTTTTTTATTGTAATTTCTACACAATAAAAT
1768949 AAAAATTAAATATAATATAATAAATTCAAGTAGATTAAATATTTTTTATGTTATTTATGATTGTT
66 AAAAATTAAATATAATATAATAAATTCAAGTAGATTAAATATTTTTTATGTTATTTATGATTGTT
*
1769014 TTATCTATACTTTTTATCTTGATATTTATTAAAAATGTATATGTTTTATTTTATATTTGTAAAAT
131 TTATCTATACTTTTTATCTTGATATTTATTAAAAATATATATGTTTTATTTTATATTTGTAAAAT
1769079 TAATATTATAATAATTAAATATTGTGAATAAAGTAAAGTCGGTGGTAATGTAAAGATAGTGCTCG
196 TAATATTATAATAATTAAATATTGTGAATAAAGTAAAGTCGGTGGTAATGTAAAGATAGTGCTCG
* *
1769144 AGATGAATTATTGTTTCATCTTTAGAGTAGAGATAGAGATTCTATAGAGTAGATATGAGAGTTAA
261 AGATGAATTATTGTTTCATCTTTAGAGTAGAGATAGAAATTCTATAGAGTAGAGATGAGAGTTAA
1769209 AGATAACCTTAATACATAGAGTCTGTCACACAGTTTAGTACTATCAATCACTTTTATTGAATCTA
326 AGATAACCTTAATACATAGAGTCTGTCACACAGTTTAGTACTATCAATCACTTTTATTGAATCTA
*
1769274 CCGTTTGAAATTTATAAGCATTTGGATTAAATTTGTAAATACTTCTTAAAAAATATCAGATACGT
391 CCGTTTGAAATTTATAAGCATTTGGATTAAATTTATAAATACTTCTTAAAAAATATCAGATACGT
1769339 AAATTTCCTTTTTCCTCCTCCTTTTAACGTTTTAAGTTAATTGTTGCAATTTTATTTAAAATAAT
456 AAATTTCCTTTTTCCTCCTCCTTTTAACGTTTTAAGTTAATTGTTGCAATTTTATTTAAAATAAT
1769404 AGGAATACACTTACTCTTTTAAGGAGCCAAATGCATCAGCCTCTACTTAACAAGTGTCGTTAAAG
521 AGGAATACACTTACTCTTTTAAGGAGCCAAATGCATCAGCCTCTACTTAACAAGTGTCGTTAAAG
1769469 ACCGAAAGATTGTGATATCAT
586 ACCGAAAGATTGTGATATCAT
1769490 CTGTCATGCG
Statistics
Matches: 590, Mismatches: 14, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
606 543 0.92
607 1 0.00
608 46 0.08
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (608 bp):
TTGTTACATTACTTTCTCTTATTATATCTCTTATGTTTTTTATTGTAATTTCTACACAATAAAAT
AAAAATTAAATATAATATAATAAATTCAAGTAGATTAAATATTTTTTATGTTATTTATGATTGTT
TTATCTATACTTTTTATCTTGATATTTATTAAAAATATATATGTTTTATTTTATATTTGTAAAAT
TAATATTATAATAATTAAATATTGTGAATAAAGTAAAGTCGGTGGTAATGTAAAGATAGTGCTCG
AGATGAATTATTGTTTCATCTTTAGAGTAGAGATAGAAATTCTATAGAGTAGAGATGAGAGTTAA
AGATAACCTTAATACATAGAGTCTGTCACACAGTTTAGTACTATCAATCACTTTTATTGAATCTA
CCGTTTGAAATTTATAAGCATTTGGATTAAATTTATAAATACTTCTTAAAAAATATCAGATACGT
AAATTTCCTTTTTCCTCCTCCTTTTAACGTTTTAAGTTAATTGTTGCAATTTTATTTAAAATAAT
AGGAATACACTTACTCTTTTAAGGAGCCAAATGCATCAGCCTCTACTTAACAAGTGTCGTTAAAG
ACCGAAAGATTGTGATATCATTG
Found at i:1774376 original size:13 final size:13
Alignment explanation
Indices: 1774360--1774384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1774350 AATATTTTAG
1774360 TTTAAAAAAATAT
1 TTTAAAAAAATAT
1774373 TTTAAAAAAATA
1 TTTAAAAAAATA
1774385 AATATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAAAAAAATAT
Found at i:1774913 original size:21 final size:20
Alignment explanation
Indices: 1774887--1774929 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1774877 AATTCAAAAT
*
1774887 CATCAAAACATATGGAATAAA
1 CATC-AAACATATGCAATAAA
*
1774908 CATCAAAGATATGCAATAAA
1 CATCAAACATATGCAATAAA
1774928 CA
1 CA
1774930 ACAAGTGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (20 bp):
CATCAAACATATGCAATAAA
Found at i:1776654 original size:45 final size:45
Alignment explanation
Indices: 1776586--1776699 Score: 155
Period size: 44 Copynumber: 2.6 Consensus size: 45
1776576 TCATTAGTTA
*
1776586 ATTTTTGAT--AAAAATAATATTTTAAATAGCACTT-AATATTAAT
1 ATTTTTGATAAAAAAATATTATTTTAAATAGC-CTTAAATATTAAT
*
1776629 ATTTTTGATAAAAAAATATTATTTT-AATAGCGTTAAATATTAAT
1 ATTTTTGATAAAAAAATATTATTTTAAATAGCCTTAAATATTAAT
*
1776673 ATTTTCGATAAAATAAATATTATTTTA
1 ATTTTTGATAAAA-AAATATTATTTTA
1776700 GGTGACGCTC
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
43 11 0.17
44 27 0.43
45 25 0.40
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (45 bp):
ATTTTTGATAAAAAAATATTATTTTAAATAGCCTTAAATATTAAT
Found at i:1786699 original size:3 final size:3
Alignment explanation
Indices: 1786675--1786736 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
1786665 TGTAAATATT
* * * *
1786675 ATA A-A ATA ATA TTA TTA TTA ATA ATA ATA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1786722 ATA ATA ATT ATA ATA
1 ATA ATA ATA ATA ATA
1786737 TTTTTAAGCC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:1786992 original size:37 final size:37
Alignment explanation
Indices: 1786910--1787710 Score: 468
Period size: 37 Copynumber: 21.3 Consensus size: 37
1786900 GTCGGACTCG
** **
1786910 AGATTGATTTATTTCACTACTCTTTAGTGAA-GCTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*
1786946 AGATTGATTTGCTTCACTACTCTTTGGTGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* *
1786983 AGATAGATTTGCTTCACTACTCTTCGGTGAAGACTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*
1787020 AGATTGATTTG-TTCCACTACTCTTCGATGAAGGCTTA
1 AGATTGATTTGCTT-CACTACTCTTCGGTGAAGGCTTA
**** **** * * *
1787057 AGA-TGGCCCGGAGGACTTAATCATCATGCTCGGAAGGCTTA
1 AGATTGATTTGCTTCAC-TACTCTTC--GGT--GAAGGCTTA
* *
1787098 CTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1 -AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*
1787136 AGATTGATTTGCTTCACTACTCTTTGGTGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* ** **** * * * *
1787173 AGA-TGGTCCGGAGGATTTAATCGTCATGCTCGAAAGGCTTA
1 AGATTGATTTGCTTCA-CTACTCTTC--GGT-G-AAGGCTTA
* * *
1787214 CTGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTA
1 -AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* **
1787252 AGATGGATTTGCTTCACTACTC-TCAATGAAGGCTTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGC-TTA
* *
1787289 A-ATTGATTTGCTTCACTATTCTTCAGTGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* *
1787325 AGA-TGGTTTGCTTCACT-CTTCTTCGGTGAAGGTTTA
1 AGATTGATTTGCTTCACTAC-TCTTCGGTGAAGGCTTA
** * *
1787361 AGATT-ACCCTGAGGACTT-AATCATCATGTTC-G-GAAGGCTTA
1 AGATTGA---T-TTG-CTTCACT-A-C-TCTTCGGTGAAGGCTTA
* * * *
1787402 CTGATGGATTTGTTTCACTACTCTTCTGTGAAGGCTTA
1 -AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*
1787440 AGATTGATTTACTTCACTACTCTTCGGTGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * ** *** * * * *
1787477 AGATGGCTCAG-AGGACTTAATCATCATGCTCGGAAGGTTTA
1 AGATTGATTTGCTTCAC-TACTCTTC--GGT--GAAGGCTTA
* *
1787518 CTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1 -AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * *
1787556 AGATTGATTTGCTTCACTACTCTCCAGTGAAGGCTTC
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * * * * *
1787593 TGA-TGGTTTGTTTCACTATTCTCCGGTGAAGGTTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * * *
1787629 GGA-TG--GTGCTTCACTCCTCTTTGGTGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * *
1787663 AGATTGA-TTGCTTCACAACTCTTCAGTGAAAGCTTA
1 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*
1787699 AGATTGACTTGC
1 AGATTGATTTGC
1787711 CCCAATCTCA
Statistics
Matches: 579, Mismatches: 141, Indels: 89
0.72 0.17 0.11
Matches are distributed among these distances:
34 24 0.04
35 2 0.00
36 168 0.29
37 242 0.42
38 37 0.06
39 11 0.02
40 11 0.02
41 36 0.06
42 32 0.06
43 16 0.03
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (37 bp):
AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
Found at i:1787128 original size:116 final size:116
Alignment explanation
Indices: 1786974--1787286 Score: 488
Period size: 116 Copynumber: 2.7 Consensus size: 116
1786964 ACTCTTTGGT
* * *
1786974 GAAGGCTTA-AGATAGATTTGCTTCACTACTCTTCGGTGAAGACTTAAGATTGATTTG-TTCCAC
1 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTT-CAC
1787037 TACTCTTCGATGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTCG
65 TACTCTTCGATGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTCG
1787089 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
1 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
* * * * *
1787154 ACTCTTTGGTGAAGGCTTAAGATGGTCCGGAGGATTTAATCGTCATGCTCG
66 ACTCTTCGATGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTCG
* * *
1787205 AAAGGCTTACTGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGATTTGCTTCACT
1 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
*
1787270 ACTC-TCAATGAAGGCTT
66 ACTCTTCGATGAAGGCTT
1787287 TAAATTGATT
Statistics
Matches: 182, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
115 19 0.10
116 161 0.88
117 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (116 bp):
GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
ACTCTTCGATGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTCG
Found at i:1787400 original size:188 final size:189
Alignment explanation
Indices: 1787104--1787462 Score: 535
Period size: 188 Copynumber: 1.9 Consensus size: 189
1787094 CTTACTGATG
* *
1787104 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTTGGTGAAGG
1 GATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGG
** * *
1787169 CTTAAGATGGTCCGGAGGATTTAATCGTCATGCTCGAAAGGCTTACTGATGGATTTGCTTCACTA
66 CTTAAGATGACCCGGAGGACTTAATCATCATGCTCGAAAGGCTTACTGATGGATTTGCTTCACTA
*
1787234 CTCTT-TGGTGAAGGCTTAAGATGGATTTGCTTCACTACTCTCAATGAAGGCTTTAAATT
131 CTCTTCT-GTGAAGGCTTAAGATGGATTTACTTCACTACTCTCAATGAAGGCTTTAAATT
* *
1787293 GATTTGCTTCACTATTCTTCAGTGAAGGCTTAAGA-TGGTTTGCTTCACT-CTTCTTCGGTGAAG
1 GATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTAC-TCTTCGGTGAAG
* * * * * *
1787356 GTTTAAGATTACCCTGAGGACTTAATCATCATGTTCGGAAGGCTTACTGATGGATTTGTTTCACT
65 GCTTAAGATGACCCGGAGGACTTAATCATCATGCTCGAAAGGCTTACTGATGGATTTGCTTCACT
*
1787421 ACTCTTCTGTGAAGGCTTAAGATTGATTTACTTCACTACTCT
130 ACTCTTCTGTGAAGGCTTAAGATGGATTTACTTCACTACTCT
1787463 TCGGTGAAGG
Statistics
Matches: 152, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
187 1 0.01
188 117 0.77
189 34 0.22
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (189 bp):
GATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGG
CTTAAGATGACCCGGAGGACTTAATCATCATGCTCGAAAGGCTTACTGATGGATTTGCTTCACTA
CTCTTCTGTGAAGGCTTAAGATGGATTTACTTCACTACTCTCAATGAAGGCTTTAAATT
Found at i:1787472 original size:304 final size:303
Alignment explanation
Indices: 1786922--1787667 Score: 1049
Period size: 304 Copynumber: 2.5 Consensus size: 303
1786912 ATTGATTTAT
* **
1786922 TTCACTACTCTTTAGTGAA-GCTTAAGATTGATTTGCTTCACTACTCTTTGGTGAAGGC-TTAAG
1 TTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTACTC-TCAGTGAAGGCTTTAA-
* * * * *
1786985 ATAGATTTGCTTCACTACTCTTCGGTGAAGACTTAAGATTGATTTG-TTCCACTACTCTTCGATG
64 ATTGATTTGCTTCACTATTCTTCGGTGAAGGCTTAAGA-TGGTTTGCTT-CACT-CTCTTCGGTG
**
1787049 AAGGCTTAAGATGGCCCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTC
126 AAGGCTTAAGATTACCCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTC
* *
1787114 ACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGG
191 ACTACTCTTCGGTGAAGGCTTAAGATTGATTTACTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* * *
1787179 -TCCGGAGGATTTAATCGTCATGCTCGAAAGGCTTACTGATGGATTTGC
256 CT-CAGAGGACTTAATCATCATGCTCGAAAGGCTTACTGATGGATTTGC
* *
1787227 TTCACTACTCTTTGGTGAAGGCTTAAGATGGATTTGCTTCACTACTCTCAATGAAGGCTTTAAAT
1 TTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTCAGTGAAGGCTTTAAAT
*
1787292 TGATTTGCTTCACTATTCTTCAGTGAAGGCTTAAGATGGTTTGCTTCACTCTTCTTCGGTGAAGG
66 TGATTTGCTTCACTATTCTTCGGTGAAGGCTTAAGATGGTTTGCTTCACTC-TCTTCGGTGAAGG
* * * *
1787357 TTTAAGATTACCCTGAGGACTTAATCATCATGTTCGGAAGGCTTACTGATGGATTTGTTTCACTA
130 CTTAAGATTACCCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTA
*
1787422 CTCTTCTGTGAAGGCTTAAGATTGATTTACTTCACTACTCTTCGGTGAAGGCTTAAGATGGCTCA
195 CTCTTCGGTGAAGGCTTAAGATTGATTTACTTCACTACTCTTCGGTGAAGGCTTAAGATGGCTCA
* *
1787487 GAGGACTTAATCATCATGCTCGGAAGGTTTACTGATGGATTTGC
260 GAGGACTTAATCATCATGCTCGAAAGGCTTACTGATGGATTTGC
* *
1787531 TTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTCCAGTGAAGGCTTCT-G
1 TTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCT-CAGTGAAGGCTT-TAA
* * * * * *
1787595 A-TGGTTTGTTTCACTATTCTCCGGTGAAGGTTTAGGATGG--TGCTTCACTCCTCTTTGGTGAA
64 ATTGATTTGCTTCACTATTCTTCGGTGAAGGCTTAAGATGGTTTGCTTCACT-CTCTTCGGTGAA
1787657 GGCTTAAGATT
128 GGCTTAAGATT
1787668 GATTGCTTCA
Statistics
Matches: 396, Mismatches: 37, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
302 29 0.07
303 2 0.01
304 259 0.65
305 75 0.19
306 31 0.08
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (303 bp):
TTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTCAGTGAAGGCTTTAAAT
TGATTTGCTTCACTATTCTTCGGTGAAGGCTTAAGATGGTTTGCTTCACTCTCTTCGGTGAAGGC
TTAAGATTACCCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTAC
TCTTCGGTGAAGGCTTAAGATTGATTTACTTCACTACTCTTCGGTGAAGGCTTAAGATGGCTCAG
AGGACTTAATCATCATGCTCGAAAGGCTTACTGATGGATTTGC
Found at i:1787598 original size:116 final size:116
Alignment explanation
Indices: 1787293--1787591 Score: 440
Period size: 116 Copynumber: 2.6 Consensus size: 116
1787283 GCTTTAAATT
* *
1787293 GATTTGCTTCACTATTCTTCAGTGAAGGCTTAAGA-TGGTTTGCTTCACT-CTTCTTCGGTGAAG
1 GATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTAC-TCTTCGGTGAAG
* ** * *
1787356 GTTTAAGATTACCCTGAGGACTTAATCATCATGTTCGGAAGGCTTACTGATG
65 GCTTAAGATGGCCCAGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATG
* * *
1787408 GATTTGTTTCACTACTCTTCTGTGAAGGCTTAAGATTGATTTACTTCACTACTCTTCGGTGAAGG
1 GATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGG
* *
1787473 CTTAAGATGGCTCAGAGGACTTAATCATCATGCTCGGAAGGTTTACTGATG
66 CTTAAGATGGCCCAGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATG
* * *
1787524 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTCCAGTGAAGG
1 GATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGG
1787589 CTT
66 CTT
1787592 CTGATGGTTT
Statistics
Matches: 165, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
115 32 0.19
116 132 0.80
117 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (116 bp):
GATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTGAAGG
CTTAAGATGGCCCAGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATG
Found at i:1787678 original size:70 final size:72
Alignment explanation
Indices: 1786922--1787705 Score: 186
Period size: 79 Copynumber: 10.4 Consensus size: 72
1786912 ATTGATTTAT
*** * ***
1786922 TTCACTACTCTTTAGTGAA-GCTTAAGATTGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGA
1 TTCACTACTCTCCGGTGAAGGCTTAAGATTGA-GTGCTTCACTACTCTCCAGTGAAGGCTTAAGA
*
1786986 TAGATTTGC
65 TGGA-TTGC
* * * *
1786995 TTCACTACTCTTCGGTGAAGACTTAAGATTGATTTG-TTCCACTACTCTTC-GATGAAGGCTTAA
1 TTCACTACTCTCCGGTGAAGGCTTAAGATTGA-GTGCTT-CACTACTCTCCAG-TGAAGGCTTAA
*** *
1787058 GATGGCCCGG
63 GATGGATTGC
*** * * * * * * * *
1787068 AGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGC
1 TTCAC-TACTC-TC-CGGT--GAAGGCTTA-AGATTGA-GTGCTTCACTACTCTCCAGTGAAGGC
*
1787133 TTAAGATTGATTTGC
59 TTAAGATGGA-TTGC
** * *
1787148 TTCACTACTCTTTGGTGAAGGCTTAAGATGGTCCGGAG-GATT---TAATCGT-CATGCTCGAAA
1 TTCACTACTCTCCGGTGAAGGCTTAAGAT--T---GAGTGCTTCACTACTC-TCCA-G-T-G-AA
*
1787208 GGCTTACTGATGGATTTGC
56 GGCTTA-AGATGGA-TTGC
** * * *
1787227 TTCACTACTCTTTGGTGAAGGCTTAAGATGGATTTGCTTCACTACTCT-CAATGAAGGCTTTAA-
1 TTCACTACTCTCCGGTGAAGGCTTAAGATTGA-GTGCTTCACTACTCTCCAGTGAAGGC-TTAAG
*
1787290 ATTGATTTGC
64 ATGGA-TTGC
* * * * ** * * *
1787300 TTCACTATTCTTCAGTGAAGGCTTAAGATGGTTTGCTTCACT-CTTCTTCGGTGAAGGTTTAAGA
1 TTCACTACTCTCCGGTGAAGGCTTAAGATTGAGTGCTTCACTAC-TCTCCAGTGAAGGCTTAAGA
* *
1787364 T-TACCCTG-
65 TGGA--TTGC
*** * * * * * * * * *
1787372 AGGACTTAATCATCATGTTCGGAAGGCTTACTGATGGATTTGTTTCACTACTCTTCTGTGAAGGC
1 TTCAC-TACTC-TC-CGGT--GAAGGCTTA-AGATTGA-GTGCTTCACTACTCTCCAGTGAAGGC
* *
1787437 TTAAGATTGATTTAC
59 TTAAGATGGA-TTGC
* *
1787452 TTCACTACTCTTCGGTGAAGGCTTAAGATGGCTCAGAG-GACTT-AAT-CATCATGCTC-G-GAA
1 TTCACTACTCTCCGGTGAAGGCTTAAGAT---T--GAGTG-CTTCACTAC-TC-T-C-CAGTGAA
* *
1787512 GGTTTACTGATGGATTTGC
56 GGCTTA-AGATGGA-TTGC
* * **
1787531 TTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTCCAGTGAAGGCTTCTGA
1 TTCACTACTCTCCGGTGAAGGCTTAAGATTGA-GTGCTTCACTACTCTCCAGTGAAGGCTTAAGA
* *
1787596 TGGTTTGT
65 TGGATTGC
* * * * ***
1787604 TTCACTATTCTCCGGTGAAGGTTTAGGA-TG-GTGCTTCACTCCTCTTTGGTGAAGGCTTAAGAT
1 TTCACTACTCTCCGGTGAAGGCTTAAGATTGAGTGCTTCACTACTCTCCAGTGAAGGCTTAAGAT
*
1787667 TGATTGC
66 GGATTGC
* * * *
1787674 TTCACAACTCTTCAGTGAAAGCTTAAGATTGA
1 TTCACTACTCTCCGGTGAAGGCTTAAGATTGA
1787706 CTTGCCCCAA
Statistics
Matches: 533, Mismatches: 116, Indels: 125
0.69 0.15 0.16
Matches are distributed among these distances:
70 51 0.10
71 3 0.01
72 22 0.04
73 103 0.19
74 73 0.14
75 37 0.07
76 14 0.03
77 24 0.05
78 37 0.07
79 158 0.30
80 11 0.02
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (72 bp):
TTCACTACTCTCCGGTGAAGGCTTAAGATTGAGTGCTTCACTACTCTCCAGTGAAGGCTTAAGAT
GGATTGC
Found at i:1796346 original size:30 final size:30
Alignment explanation
Indices: 1796287--1796388 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
1796277 CCCGAAGGAC
* * *
1796287 CTATCCAAAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1796316 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1796346 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1796376 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1796389 CCGAAGAACC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 18 0.27
30 49 0.73
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1796405 original size:60 final size:59
Alignment explanation
Indices: 1796287--1796405 Score: 139
Period size: 60 Copynumber: 2.0 Consensus size: 59
1796277 CCCGAAGGAC
* * *
1796287 CTATCCAAAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAAAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAA
* * * * * * *
1796346 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAAAGGTCACAAAGA-CCCCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAA
1796406 ACTGTCCATA
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
59 18 0.37
60 31 0.63
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (59 bp):
CTATCCAAAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAA
Found at i:1797370 original size:19 final size:19
Alignment explanation
Indices: 1797304--1797377 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 19
1797294 AATGAAGGTA
1797304 TGCATCGATGCACTACACAG
1 TGCATCGATGCACTAC-CAG
* * *
1797324 TGGATCGATGCATTCCCTATCGG
1 TGCATCGATGCA----CTACCAG
*
1797347 TGCATCGATGCACTACCTG
1 TGCATCGATGCACTACCAG
*
1797366 TGCATCGGTGCA
1 TGCATCGATGCA
1797378 TAAAATACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.37
20 11 0.26
23 13 0.30
24 3 0.07
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTACCAG
Found at i:1800587 original size:26 final size:26
Alignment explanation
Indices: 1800540--1800589 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1800530 ATTTCTACTA
*
1800540 ACATATCACATATAAGCATCCTACCC
1 ACATATCACATATAAGAATCCTACCC
*
1800566 ACATAT-ACATATAATAATTCCTAC
1 ACATATCACATATAAGAA-TCCTAC
1800590 TATGCACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.42, C:0.28, G:0.02, T:0.28
Consensus pattern (26 bp):
ACATATCACATATAAGAATCCTACCC
Found at i:1800990 original size:30 final size:30
Alignment explanation
Indices: 1800889--1800979 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 30
1800879 CCCGAAGGAC
* *
1800889 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1800918 CTATCCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1800948 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1800978 CT
1 CT
1800980 GTCTATAGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 19 0.33
30 38 0.67
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1803170 original size:20 final size:21
Alignment explanation
Indices: 1803118--1803178 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
1803108 TTCCCCTGTG
1803118 GGGGGAATCGGTTCTCCTTCAAA
1 GGGGGAATCGGTTC-CC-TCAAA
*
1803141 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
1803161 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1803179 TACACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 2 0.06
23 14 0.40
ACGTcount: A:0.16, C:0.25, G:0.33, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1807020 original size:22 final size:21
Alignment explanation
Indices: 1806978--1807017 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1806968 GAGTTTATTT
*
1806978 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1806999 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1807018 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1810705 original size:21 final size:21
Alignment explanation
Indices: 1810652--1810707 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1810642 CAATGCGAAG
*
1810652 TGGTCTTCATGCCTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
*
1810673 GGGTCTTCATGTCTTTATGAA
1 TGGTCTTCATGTCTTTATGAA
1810694 TGGTCTTCATGTCT
1 TGGTCTTCATGTCT
1810708 CCCGATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (21 bp):
TGGTCTTCATGTCTTTATGAA
Found at i:1814380 original size:18 final size:18
Alignment explanation
Indices: 1814359--1814423 Score: 105
Period size: 18 Copynumber: 3.6 Consensus size: 18
1814349 TCTAATCCGG
1814359 GTCTTGGGCTTGAACCAA
1 GTCTTGGGCTTGAACCAA
1814377 GTCTTGGGCTTGAACCAA
1 GTCTTGGGCTTGAACCAA
1814395 GTCTTGGGCTTGAACCGAA
1 GTCTTGGGCTTGAACC-AA
*
1814414 -TCTTGAGCTT
1 GTCTTGGGCTT
1814424 ATTGTAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
18 43 0.96
19 2 0.04
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.31
Consensus pattern (18 bp):
GTCTTGGGCTTGAACCAA
Found at i:1815324 original size:16 final size:16
Alignment explanation
Indices: 1815300--1815330 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1815290 TTCTAAATTT
*
1815300 TTTTTGAGTTCAAGTC
1 TTTTCGAGTTCAAGTC
1815316 TTTTCGAGTTCAAGT
1 TTTTCGAGTTCAAGT
1815331 TTCAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTCGAGTTCAAGTC
Done.