Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008166.1 Hibiscus syriacus cultivar Beakdansim tig00110747_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: 2544747
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2146712 original size:2 final size:2
Alignment explanation
Indices: 2146705--2146767 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
2146695 TTAGTCCCTA
2146705 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2146746 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2146768 GATGTTATGC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2148921 original size:27 final size:27
Alignment explanation
Indices: 2148883--2148938 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
2148873 TATATAACTC
2148883 TGCCAACTTTTCGGGAGACACGTTGTA
1 TGCCAACTTTTCGGGAGACACGTTGTA
2148910 TGCCAACTTTTCGGGAGACACGTTGTA
1 TGCCAACTTTTCGGGAGACACGTTGTA
2148937 TG
1 TG
2148939 ATAAGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (27 bp):
TGCCAACTTTTCGGGAGACACGTTGTA
Found at i:2152691 original size:59 final size:59
Alignment explanation
Indices: 2152591--2152709 Score: 145
Period size: 59 Copynumber: 2.0 Consensus size: 59
2152581 TTGCATACTT
* * * *
2152591 GGGTTAGAACTAAAGGATACCTAGTGGAGATTGTCTGCACGACTTTATTTGTTATATTC
1 GGGTTAGAACTAAAGGATACCTAGTGGAGAATGTCTGCACGACCTTATGTGTCATATTC
*
2152650 GGGTTAGCAA-TAAAGGATACCTAGTGTA-AATG-CTGGCCACGACCTTATGTGTCATATTC
1 GGGTTAG-AACTAAAGGATACCTAGTGGAGAATGTCT-G-CACGACCTTATGTGTCATATTC
2152709 G
1 G
2152710 ATTTAGCATT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
57 2 0.04
58 4 0.08
59 44 0.85
60 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (59 bp):
GGGTTAGAACTAAAGGATACCTAGTGGAGAATGTCTGCACGACCTTATGTGTCATATTC
Found at i:2153713 original size:16 final size:16
Alignment explanation
Indices: 2153692--2153729 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2153682 ACATGAAGTC
**
2153692 ATCCAAATAACCAAAT
1 ATCCAAATAAAAAAAT
2153708 ATCCAAATAAAAAAAT
1 ATCCAAATAAAAAAAT
2153724 ATCCAA
1 ATCCAA
2153730 TAATATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (16 bp):
ATCCAAATAAAAAAAT
Found at i:2155366 original size:20 final size:20
Alignment explanation
Indices: 2155313--2155392 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
2155303 TTGGTAATTG
*
2155313 ATGAACAATATCGATACTGAGA
1 ATGAACAATATCGATACT--GT
*
2155335 AAGAACAATATCGATACTGT
1 ATGAACAATATCGATACTGT
* *
2155355 ATGAACATTATCGATACTAT
1 ATGAACAATATCGATACTGT
* *
2155375 ATGAACATTACCGATACT
1 ATGAACAATATCGATACT
2155393 AAATACACTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 35 0.67
22 17 0.33
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (20 bp):
ATGAACAATATCGATACTGT
Found at i:2163340 original size:40 final size:40
Alignment explanation
Indices: 2163285--2163366 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2163275 TGCAGGTTTA
*
2163285 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
*
2163325 TAATACACTTCGGTGTATATGGTTGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
2163365 TA
1 TA
2163367 GCACTACGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
Found at i:2163518 original size:44 final size:47
Alignment explanation
Indices: 2163470--2163574 Score: 144
Period size: 44 Copynumber: 2.3 Consensus size: 47
2163460 GTAACCATGC
2163470 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATTGG-AA
1 AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATATTGGTAA
* * * *
2163514 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTACGGAA-TTAAATGGCAAGTATATTGGTAA
2163562 AAATAAGCTTATG
1 AAATAAGCTTATG
2163575 GGATAAATGG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 22 0.42
46 1 0.02
47 15 0.29
48 14 0.27
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATATTGGTAA
Found at i:2171713 original size:20 final size:21
Alignment explanation
Indices: 2171688--2171729 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
2171678 CACGTGAGGA
2171688 TTATCTTCTT-TTTATT-TTAT
1 TTATCTT-TTATTTATTGTTAT
2171708 TTATCTTTTATTTATTGTTAT
1 TTATCTTTTATTTATTGTTAT
2171729 T
1 T
2171730 ACCATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.10
20 13 0.65
21 5 0.25
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (21 bp):
TTATCTTTTATTTATTGTTAT
Found at i:2177345 original size:20 final size:21
Alignment explanation
Indices: 2177322--2177361 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2177312 TTATCTTCAT
2177322 TTTATT-TTATTTATC-TTTTA
1 TTTATTGTT-TTTATCATTTTA
2177342 TTTATTGTTTTTATCATTTT
1 TTTATTGTTTTTATCATTTT
2177362 TCATTGCCTT
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:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTATTGTTTTTATCATTTTA
Found at i:2193035 original size:29 final size:29
Alignment explanation
Indices: 2192988--2193061 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
2192978 AGTAAAATCC
2192988 CAAATTTT-AAA--TTA-TAACCAAAATA
1 CAAATTTTAAAAGTTTAGTAACCAAAATA
*
2193013 CAAATTTTAAAAGTTTAGTAACCAAAGTA
1 CAAATTTTAAAAGTTTAGTAACCAAAATA
* *
2193042 TAAACTTTGGAAAAGTTTAG
1 CAAA-TTT-TAAAAGTTTAG
2193062 GGACTAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.20
26 3 0.08
28 3 0.08
29 13 0.32
30 3 0.08
31 10 0.25
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (29 bp):
CAAATTTTAAAAGTTTAGTAACCAAAATA
Found at i:2202139 original size:24 final size:24
Alignment explanation
Indices: 2202112--2202160 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2202102 TGCATAACAT
*
2202112 TGTACATTGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
2202136 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
2202160 T
1 T
2202161 CATGAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:2208713 original size:15 final size:17
Alignment explanation
Indices: 2208682--2208713 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2208672 ATACGGGAGC
2208682 TTTATTTAACAATTAAT
1 TTTATTTAACAATTAAT
2208699 TTTA-TTAAC-ATTAAT
1 TTTATTTAACAATTAAT
2208714 ACAAACTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATTTAACAATTAAT
Found at i:2218062 original size:18 final size:19
Alignment explanation
Indices: 2218041--2218100 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
2218031 TCATCTCTCA
*
2218041 TTTTTTCTCTTTTTGTTTT
1 TTTTTTCTCTTTTTCTTTT
*
2218060 TTTCTTTTTCTTCTTTCTTTT
1 TTT-TTTCTCTT-TTTCTTTT
*
2218081 TGTTTTCT-TCTTTTCTTTT
1 TTTTTTCTCT-TTTTCTTTT
2218100 T
1 T
2218101 CTGTTTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 13 0.38
20 12 0.35
21 9 0.26
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTTCTCTTTTTCTTTT
Found at i:2218065 original size:14 final size:14
Alignment explanation
Indices: 2218041--2218094 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
2218031 TCATCTCTCA
2218041 TTTTTTCTCTTTTTG
1 TTTTTT-TCTTTTTG
2218056 TTTTTTTCTTTTT-
1 TTTTTTTCTTTTTG
* *
2218069 CTTCTTTCTTTTTG
1 TTTTTTTCTTTTTG
*
2218083 TTTTCTTCTTTT
1 TTTTTTTCTTTT
2218095 CTTTTTCTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
13 11 0.33
14 16 0.48
15 6 0.18
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTTCTTTTTG
Found at i:2218078 original size:27 final size:25
Alignment explanation
Indices: 2218043--2218123 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 25
2218033 ATCTCTCATT
*
2218043 TTTTCTCTTTTTGTTTTTTTCTTTTTC
1 TTTT-TCTTTTTGTTTTCTTC-TTTTC
2218070 TTCTTTCTTTTTGTTTTCTTCTTTTC
1 TT-TTTCTTTTTGTTTTCTTCTTTTC
*
2218096 TTTTTC-TGTT-TTTTCTTCTATTTC
1 TTTTTCTTTTTGTTTTCTTCT-TTTC
2218120 TTTT
1 TTTT
2218124 ATATATATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
23 9 0.18
24 11 0.22
25 4 0.08
26 7 0.14
27 17 0.34
28 2 0.04
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (25 bp):
TTTTTCTTTTTGTTTTCTTCTTTTC
Found at i:2218100 original size:14 final size:13
Alignment explanation
Indices: 2218042--2218123 Score: 62
Period size: 13 Copynumber: 6.3 Consensus size: 13
2218032 CATCTCTCAT
*
2218042 TTTTTCTCTTTTTGT
1 TTTTT-TCTTTTT-C
2218057 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
* *
2218070 TTCTTTCTTTTTG
1 TTTTTTCTTTTTC
2218083 TTTTCTTC-TTTTC
1 TTTT-TTCTTTTTC
*
2218096 -TTTTTCTGTTT-
1 TTTTTTCTTTTTC
* *
2218107 TTTCTTCTATTTC
1 TTTTTTCTTTTTC
2218120 TTTT
1 TTTT
2218124 ATATATATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 3 0.06
12 15 0.28
13 21 0.39
14 10 0.19
15 5 0.09
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:2218110 original size:23 final size:23
Alignment explanation
Indices: 2218043--2218123 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
2218033 ATCTCTCATT
2218043 TTTTCTCTTTT-TG-TTTTT-TTC
1 TTTTCT-TTTTCTGTTTTTTCTTC
*
2218064 TTTTTCTTCTTTCTTTTTGTTTTCTTC
1 -TTTTCTT-TTTC-TGTT-TTTTCTTC
2218091 TTTTCTTTTTCTGTTTTTTCTTC
1 TTTTCTTTTTCTGTTTTTTCTTC
2218114 TATTTCTTTT
1 T-TTTCTTTT
2218124 ATATATATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.02
22 9 0.18
23 9 0.18
24 12 0.24
25 5 0.10
26 11 0.22
27 3 0.06
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (23 bp):
TTTTCTTTTTCTGTTTTTTCTTC
Found at i:2218114 original size:18 final size:18
Alignment explanation
Indices: 2218064--2218120 Score: 51
Period size: 21 Copynumber: 2.9 Consensus size: 18
2218054 TGTTTTTTTC
*
2218064 TTTTTCTTCTTTCTTTTTGT
1 TTTTTCTTC-TT-TTTCTGT
2218084 TTTCTTCTTTTCTTTTTCTGT
1 TTT-TTC--TTCTTTTTCTGT
*
2218105 TTTTTCTTCTATTTCT
1 TTTTTCTTCTTTTTCT
2218121 TTTATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 9 0.28
20 6 0.19
21 12 0.38
22 2 0.06
23 3 0.09
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTTCTTCTTTTTCTGT
Found at i:2233467 original size:24 final size:24
Alignment explanation
Indices: 2233434--2233502 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
2233424 AAACGGAGAT
* * *
2233434 TCAGAAATCAAAACATAATTCAGG
1 TCAGATATCATAACAGAATTCAGG
*
2233458 TCAGATATCATAACAGAATCCAGG
1 TCAGATATCATAACAGAATTCAGG
*
2233482 TCAGGTATCATAACAGAATTC
1 TCAGATATCATAACAGAATTC
2233503 GTATCAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (24 bp):
TCAGATATCATAACAGAATTCAGG
Found at i:2233515 original size:24 final size:24
Alignment explanation
Indices: 2233434--2233515 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
2233424 AAACGGAGAT
* *
2233434 TCAGAAATCAAAACATAATTCAGG
1 TCAGAAATCATAACAGAATTCAGG
* *
2233458 TCAGATATCATAACAGAATCCAGG
1 TCAGAAATCATAACAGAATTCAGG
** *
2233482 TCAGGTATCATAACAGAATTC-GTA
1 TCAGAAATCATAACAGAATTCAG-G
2233506 TCAGAAATCA
1 TCAGAAATCA
2233516 GAAAAAAATC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (24 bp):
TCAGAAATCATAACAGAATTCAGG
Found at i:2237879 original size:28 final size:29
Alignment explanation
Indices: 2237848--2237916 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
2237838 AACTTTATAC
* *
2237848 TTTGGTC-CTTAACTTTCAAAATTTATGA
1 TTTGGTCACTAAACATTCAAAATTTATGA
* *
2237876 TTTGATCACTAAACATTCAAAATTTATGT
1 TTTGGTCACTAAACATTCAAAATTTATGA
2237905 TTTGGTCACTAA
1 TTTGGTCACTAA
2237917 CCAAATTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (29 bp):
TTTGGTCACTAAACATTCAAAATTTATGA
Found at i:2240340 original size:14 final size:14
Alignment explanation
Indices: 2240321--2240365 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2240311 TCGAAAGTGC
2240321 CTCGTAGGGTTGCA
1 CTCGTAGGGTTGCA
*
2240335 CTCGTA-AG-TGC-
1 CTCGTAGGGTTGCA
2240346 CTCGTAGGGTTGCA
1 CTCGTAGGGTTGCA
2240360 CTCGTA
1 CTCGTA
2240366 AGTGCCTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.23
12 4 0.15
13 4 0.15
14 12 0.46
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (14 bp):
CTCGTAGGGTTGCA
Found at i:2240351 original size:11 final size:11
Alignment explanation
Indices: 2240310--2240376 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 11
2240300 TAATACTACA
*
2240310 CTCGAAAGTGC
1 CTCGTAAGTGC
*
2240321 CTCGTAGGGTTGC
1 CTCGTA-AG-TGC
2240334 ACTCGTAAGTGC
1 -CTCGTAAGTGC
*
2240346 CTCGTAGGGTTGC
1 CTCGTA-AG-TGC
2240359 ACTCGTAAGTGC
1 -CTCGTAAGTGC
2240371 CTCGTA
1 CTCGTA
2240377 GAATTGCACC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
11 17 0.38
12 8 0.18
13 8 0.18
14 12 0.27
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (11 bp):
CTCGTAAGTGC
Found at i:2240385 original size:25 final size:25
Alignment explanation
Indices: 2240308--2240377 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
2240298 CTTAATACTA
*
2240308 CACTCGAAAGTGCCTCGTAGGGTTG
1 CACTCGTAAGTGCCTCGTAGGGTTG
2240333 CACTCGTAAGTGCCTCGTAGGGTTG
1 CACTCGTAAGTGCCTCGTAGGGTTG
2240358 CACTCGTAAGTGCCTCGTAG
1 CACTCGTAAGTGCCTCGTAG
2240378 AATTGCACCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (25 bp):
CACTCGTAAGTGCCTCGTAGGGTTG
Found at i:2247627 original size:20 final size:20
Alignment explanation
Indices: 2247602--2247641 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2247592 ATTAGCCGAT
2247602 GAATATGAAATATGAATCTG
1 GAATATGAAATATGAATCTG
* *
2247622 GAATATGAGATGTGAATCTG
1 GAATATGAAATATGAATCTG
2247642 AAGTGTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (20 bp):
GAATATGAAATATGAATCTG
Found at i:2254722 original size:44 final size:46
Alignment explanation
Indices: 2254614--2254723 Score: 143
Period size: 46 Copynumber: 2.4 Consensus size: 46
2254604 TTTATTAATC
* *
2254614 ATAAGCTTGTAAGCTTATTTTACCAAAATAATTACCATTTAATCCC
1 ATAAGCTCGTAAGCTTATTTTACCAAAATAATTACCATTTAATCCA
* * * * *
2254660 ATAAGCTCGTAAGTTTATTTTACCAATATACTTGCCA-TT-ATTCA
1 ATAAGCTCGTAAGCTTATTTTACCAAAATAATTACCATTTAATCCA
2254704 ATAAGCTCGTAAGCTTATTT
1 ATAAGCTCGTAAGCTTATTT
2254724 GCATGCTTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 22 0.39
45 2 0.04
46 32 0.57
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (46 bp):
ATAAGCTCGTAAGCTTATTTTACCAAAATAATTACCATTTAATCCA
Found at i:2254883 original size:40 final size:40
Alignment explanation
Indices: 2254828--2254988 Score: 279
Period size: 40 Copynumber: 4.0 Consensus size: 40
2254818 ACCGTAGTGC
2254828 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
* *
2254868 TACACATAAGGTCGTGCCCACCATATACACCGAAGTATAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
* *
2254908 TACACATAAGGTTGTGCCCACCATATACATCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
2254948 TACACATAAGGTCGTG-CCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
2254987 TA
1 TA
2254989 TAAACATGTA
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
39 24 0.21
40 89 0.79
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:2258483 original size:13 final size:14
Alignment explanation
Indices: 2258467--2258506 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
2258457 TGAATAAGAT
*
2258467 ATATGAATATG-GA
1 ATATGAAGATGTGA
2258480 ATATG-AGATGTGA
1 ATATGAAGATGTGA
2258493 ATATGAA-ATGTGA
1 ATATGAAGATGTGA
2258506 A
1 A
2258507 AGTATTGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 19 0.79
14 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (14 bp):
ATATGAAGATGTGA
Found at i:2259511 original size:21 final size:21
Alignment explanation
Indices: 2259487--2259528 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2259477 AAGGGTAAGG
*
2259487 GAAAGAAAATTGATAATGATA
1 GAAAGAAAATTGAGAATGATA
**
2259508 GAAAGAATGTTGAGAATGATA
1 GAAAGAAAATTGAGAATGATA
2259529 TTTACTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (21 bp):
GAAAGAAAATTGAGAATGATA
Found at i:2260047 original size:29 final size:29
Alignment explanation
Indices: 2260012--2260071 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
2260002 TATTATTTCC
*
2260012 ATATTTTAAAATGATATAAAATAATGTGG
1 ATATTTTAAAATGATAGAAAATAATGTGG
2260041 ATATTTTAAAATGATAGAAAATAATGTGG
1 ATATTTTAAAATGATAGAAAATAATGTGG
2260070 AT
1 AT
2260072 TATTGGATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (29 bp):
ATATTTTAAAATGATAGAAAATAATGTGG
Found at i:2263094 original size:13 final size:13
Alignment explanation
Indices: 2263076--2263103 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2263066 TACATTAGGC
2263076 TATGAATATGAAA
1 TATGAATATGAAA
2263089 TATGAATATGAAA
1 TATGAATATGAAA
2263102 TA
1 TA
2263104 AGAGATGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (13 bp):
TATGAATATGAAA
Found at i:2263103 original size:20 final size:20
Alignment explanation
Indices: 2263076--2263128 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
2263066 TACATTAGGC
2263076 TATG-AATATGAAATATGAA
1 TATGAAATATGAAATATGAA
* * *
2263095 TATGAAATAAGAGATGTGAA
1 TATGAAATATGAAATATGAA
* *
2263115 TCTGAAATGTGAAA
1 TATGAAATATGAAA
2263129 GTATTGGTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.49, C:0.02, G:0.21, T:0.28
Consensus pattern (20 bp):
TATGAAATATGAAATATGAA
Found at i:2265293 original size:21 final size:21
Alignment explanation
Indices: 2265269--2265310 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2265259 AAGGGTAAGG
*
2265269 GAAAGAAAATTGATAATGATA
1 GAAAGAAAATTGAGAATGATA
* *
2265290 GAAAGCATATTGAGAATGATA
1 GAAAGAAAATTGAGAATGATA
2265311 TCGACTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.21, T:0.24
Consensus pattern (21 bp):
GAAAGAAAATTGAGAATGATA
Found at i:2271169 original size:10 final size:10
Alignment explanation
Indices: 2271154--2271189 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2271144 ATTCTAGTTG
2271154 CTTGTTGTTT
1 CTTGTTGTTT
2271164 CTTGTTG---
1 CTTGTTGTTT
2271171 CTTGTTGTTT
1 CTTGTTGTTT
2271181 CTTGTTGTT
1 CTTGTTGTT
2271190 GATCAATGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.30
10 16 0.70
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (10 bp):
CTTGTTGTTT
Found at i:2271170 original size:17 final size:17
Alignment explanation
Indices: 2271145--2271187 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
2271135 TCTCTCTTTA
*
2271145 TTCTAGTTGCTTGTTGT
1 TTCTTGTTGCTTGTTGT
2271162 TTCTTGTTGCTTGTTGT
1 TTCTTGTTGCTTGTTGT
2271179 TTCTTGTTG
1 TTCTTGTTG
2271188 TTGATCAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.02, C:0.12, G:0.23, T:0.63
Consensus pattern (17 bp):
TTCTTGTTGCTTGTTGT
Found at i:2271500 original size:44 final size:45
Alignment explanation
Indices: 2271405--2271509 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
2271395 TGCACACTAA
*
2271405 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGACT
* *
2271450 GAGTGCATCGATGCATAAAATTCATTCGATG-TTTGAAAATTA-ATT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAA--AGACT
2271495 G-GTGCATCGATGCAT
1 GAGTGCATCGATGCAT
2271510 GGATTGGTGC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
44 22 0.40
45 32 0.58
46 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.31
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGACT
Found at i:2273715 original size:13 final size:13
Alignment explanation
Indices: 2273687--2273725 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2273677 TTGGCAATGT
*
2273687 TTTGAAAA-ACTA
1 TTTGAAAATAATA
2273699 TTTGAAAATAATA
1 TTTGAAAATAATA
*
2273712 TTTGTAAATAATA
1 TTTGAAAATAATA
2273725 T
1 T
2273726 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:2274219 original size:20 final size:20
Alignment explanation
Indices: 2274194--2274246 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
2274184 ACCAGACGGA
2274194 TGCATCGATGCATGACCCTG
1 TGCATCGATGCATGACCCTG
2274214 TGCATCGATGCATGACCCTG
1 TGCATCGATGCATGACCCTG
2274234 TGCATCGATGCAT
1 TGCATCGATGCAT
2274247 ATTCAAGGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCATGACCCTG
Found at i:2282548 original size:116 final size:118
Alignment explanation
Indices: 2282360--2282578 Score: 293
Period size: 116 Copynumber: 1.9 Consensus size: 118
2282350 TAGTGGACAA
* * * * *
2282360 AATGTAAATTTTAAAAGTTTGATGGCTAAAGTATAAAATTAGGAAAAGTTTAAGGACCTAAGTGT
1 AATGCAAATATTAAAAGTTTGATGACCAAAGTATAAAATTAGGAAAAGTTTAAGGACCTAAGTGG
*
2282425 TAATTTTCCCAAAACGAATTTTT-TTCC-TAAACGGATTTGGTTATTGAGCAG
66 TAATTTTCCCAAAAAGAATTTTTATTCCATAAACGGATTTGGTTATTGAGCAG
*
2282476 AATGCAAATATTAAAAGTTT-AGTGACCAAAGTATAAAATT-GGTAAATGTTTAAGGACCTAAGT
1 AATGCAAATATTAAAAGTTTGA-TGACCAAAGTATAAAATTAGG-AAAAGTTTAAGGACCTAAGT
* * * *
2282539 GGTAGTTTTCTCAAAAAGATTTTTTATTCCATAAATGGAT
64 GGTAATTTTCCCAAAAAGAATTTTTATTCCATAAACGGAT
2282579 AATTTAATCT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
115 3 0.03
116 73 0.83
117 4 0.05
118 8 0.09
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (118 bp):
AATGCAAATATTAAAAGTTTGATGACCAAAGTATAAAATTAGGAAAAGTTTAAGGACCTAAGTGG
TAATTTTCCCAAAAAGAATTTTTATTCCATAAACGGATTTGGTTATTGAGCAG
Found at i:2285166 original size:39 final size:39
Alignment explanation
Indices: 2285068--2285182 Score: 176
Period size: 40 Copynumber: 2.9 Consensus size: 39
2285058 GCATATCGAT
*
2285068 TAAGCATTTCAGTGCATATGGTGGGCACGACCTTATGTG
1 TAAGCACTTCAGTGCATATGGTGGGCACGACCTTATGTG
*
2285107 TAATGCACTTCAGTGCATATGGTGGGCACTACCTTATGTG
1 TAA-GCACTTCAGTGCATATGGTGGGCACGACCTTATGTG
* * *
2285147 TAAGCACTTCAGTGAATATGGTGGGTACGAGCTTAT
1 TAAGCACTTCAGTGCATATGGTGGGCACGACCTTAT
2285183 AGGATAAATG
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
39 32 0.46
40 37 0.54
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (39 bp):
TAAGCACTTCAGTGCATATGGTGGGCACGACCTTATGTG
Found at i:2285899 original size:205 final size:204
Alignment explanation
Indices: 2285639--2286043 Score: 711
Period size: 205 Copynumber: 2.0 Consensus size: 204
2285629 ACAATCTTAT
* * *
2285639 TTATTTTTTTTTGAAAATAGAACATATTTTTCTATCACTCCTTGAAATTGATTTTGAATTGGTAA
1 TTATTTTTTTATGAAAATAGAACATAATTGTCTATCACTCCTTGAAATTGATTTTGAATTGGTAA
2285704 CCAACAATATTATTTTATGATTTTTCTCTGAATAATTATTTTATAATAATTGTTCAAGTTATGAA
66 CCAACAATATTATTTTATGATTTTTCTCTGAATAATTATTTTATAATAATTGTTCAAGTTATGAA
*
2285769 ACTTGAGATGTTTGAAGGAAATAAAATTTTACTCAGTTCAACTAAAGAAAGGTTTTGAATTTCTG
131 ACTTGAGATGTTTGAAGGAAACAAAATTTTACTCAGTTCAACTAAAGAAAGGTTTTGAATTTCTG
2285834 ATGTGTGCC
196 ATGTGTGCC
* * *
2285843 TTATTTATTTTATGAAAATATAACATAATTGTCTATCAGTTCTTGAAATTGATTTTGAATTGGTA
1 TTATTT-TTTTATGAAAATAGAACATAATTGTCTATCACTCCTTGAAATTGATTTTGAATTGGTA
* *
2285908 ACCAGCAATATTATTTTATGATTTTTCTCTGAATAATTCTTTTATAATAATTGTTCAAGTTATGA
65 ACCAACAATATTATTTTATGATTTTTCTCTGAATAATTATTTTATAATAATTGTTCAAGTTATGA
*
2285973 AACTTGAGATGTTTGAAGGAAACAAAATTTTACTCAGTTCAATTAAAGAAAGGTTTTGAATTTCT
130 AACTTGAGATGTTTGAAGGAAACAAAATTTTACTCAGTTCAACTAAAGAAAGGTTTTGAATTTCT
2286038 GATGTG
195 GATGTG
2286044 ACATCCATAA
Statistics
Matches: 190, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
204 6 0.03
205 184 0.97
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (204 bp):
TTATTTTTTTATGAAAATAGAACATAATTGTCTATCACTCCTTGAAATTGATTTTGAATTGGTAA
CCAACAATATTATTTTATGATTTTTCTCTGAATAATTATTTTATAATAATTGTTCAAGTTATGAA
ACTTGAGATGTTTGAAGGAAACAAAATTTTACTCAGTTCAACTAAAGAAAGGTTTTGAATTTCTG
ATGTGTGCC
Found at i:2292724 original size:13 final size:13
Alignment explanation
Indices: 2292703--2292733 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2292693 GTCACAACCC
2292703 GACCAGACCCGTT
1 GACCAGACCCGTT
*
2292716 GACCCGACCCGTT
1 GACCAGACCCGTT
2292729 GACCA
1 GACCA
2292734 TTGACCGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.42, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCAGACCCGTT
Found at i:2295087 original size:24 final size:24
Alignment explanation
Indices: 2295060--2295188 Score: 127
Period size: 24 Copynumber: 5.4 Consensus size: 24
2295050 ATTTGAATTA
2295060 TGATATGATACTTGACATGCATTC
1 TGATATGATACTTGACATGCATTC
*
2295084 TGATATGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGCATTC
* * * *
2295108 TGGTCTGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGCATTC
* * *
2295132 TGATCTGATACTTGACCT-CGATTT
1 TGATATGATACTTGACATGC-ATTC
* *
2295156 TGATATGATACTTGACATGAATTA
1 TGATATGATACTTGACATGCATTC
*
2295180 TGATTTGAT
1 TGATATGAT
2295189 TTTTTTGATA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
23 1 0.01
24 86 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (24 bp):
TGATATGATACTTGACATGCATTC
Found at i:2295118 original size:48 final size:48
Alignment explanation
Indices: 2295060--2295188 Score: 143
Period size: 48 Copynumber: 2.7 Consensus size: 48
2295050 ATTTGAATTA
* *
2295060 TGATATGATACTTGACATGCATTCTGATATGATA-TCTGACATGGATTC
1 TGATATGATACTTGACATGAATTCTGATATGATACT-TGACATCGATTC
* * * * * * *
2295108 TGGTCTGATACTTGACTTGGATTCTGATCTGATACTTGACCTCGATTT
1 TGATATGATACTTGACATGAATTCTGATATGATACTTGACATCGATTC
* *
2295156 TGATATGATACTTGACATGAATTATGATTTGAT
1 TGATATGATACTTGACATGAATTCTGATATGAT
2295189 TTTTTTGATA
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
48 65 0.98
49 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.40
Consensus pattern (48 bp):
TGATATGATACTTGACATGAATTCTGATATGATACTTGACATCGATTC
Found at i:2297424 original size:117 final size:117
Alignment explanation
Indices: 2297247--2297465 Score: 307
Period size: 117 Copynumber: 1.9 Consensus size: 117
2297237 GGTTAGTGAA
* * * *
2297247 CAAAATGTAAATTTTGAAAGTTTGATGGCCAAAGTAGAAAATTAGGAAACATTTAAGGACCTATA
1 CAAAATGCAAATATTGAAAGTTTAATAGCCAAAGTAGAAAATTAGGAAACATTTAAGGACCTA-A
2297312 -TGGTAATTTTC-TCAAAAAAAAATTTTATTCCATAAATGTATTTTCTTATGAC
65 GTGGTAATTTTCAT-AAAAAAAAATTTTATTCCATAAATGTATTTTCTTATGAC
* * ** *
2297364 CAAAATGCAAATATTGAGAGTTTAATAGCCAAAGTATAAAATTAGGAAAGTTTTAGGGACCTAAG
1 CAAAATGCAAATATTGAAAGTTTAATAGCCAAAGTAGAAAATTAGGAAACATTTAAGGACCTAAG
* *
2297429 TGGTAATTTTCATAAAAATAATTTTTATTCCATAAAT
66 TGGTAATTTTCATAAAAAAAAATTTTATTCCATAAAT
2297466 AGATAGTTTA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
116 1 0.01
117 87 0.98
118 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (117 bp):
CAAAATGCAAATATTGAAAGTTTAATAGCCAAAGTAGAAAATTAGGAAACATTTAAGGACCTAAG
TGGTAATTTTCATAAAAAAAAATTTTATTCCATAAATGTATTTTCTTATGAC
Found at i:2300090 original size:40 final size:39
Alignment explanation
Indices: 2300031--2300206 Score: 181
Period size: 40 Copynumber: 4.5 Consensus size: 39
2300021 GCGTATCGAT
* *
2300031 TAAGCACTTTAGTGCATATGGTGGGCACGACCTTATGTG
1 TAAGCACTTTGGTGCATATGGTGGGCACAACCTTATGTG
* * *
2300070 TAATCCACTTTGGTGCATATGGTGGGAATAACCTTATGTG
1 TAA-GCACTTTGGTGCATATGGTGGGCACAACCTTATGTG
* ** * ** *
2300110 TAATTCACTTCAGTGTATATAATGGGCACGACCTTATGTG
1 TAA-GCACTTTGGTGCATATGGTGGGCACAACCTTATGTG
* * * *
2300150 TAAGAACTTCGGTGTATATGGTGGGCACAACCTTATTTG
1 TAAGCACTTTGGTGCATATGGTGGGCACAACCTTATGTG
*
2300189 TAAGCACTATGGTGCATA
1 TAAGCACTTTGGTGCATA
2300207 AATTTGACTC
Statistics
Matches: 111, Mismatches: 25, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
39 46 0.41
40 65 0.59
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (39 bp):
TAAGCACTTTGGTGCATATGGTGGGCACAACCTTATGTG
Found at i:2303425 original size:19 final size:20
Alignment explanation
Indices: 2303396--2303433 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2303386 TATTTCTTAA
2303396 ATTATTACCTTATAAGATTT
1 ATTATTACCTTATAAGATTT
*
2303416 ATTA-TACCTTGTAAGATT
1 ATTATTACCTTATAAGATT
2303434 ATAAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (20 bp):
ATTATTACCTTATAAGATTT
Found at i:2306139 original size:40 final size:40
Alignment explanation
Indices: 2306095--2306226 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 40
2306085 ATTGATTAAG
* *
2306095 CACTTCAGTGCATATGGTGAGCATGACCTTATGTGTAATT
1 CACTTCAGTGCATATGGTGGGCATAACCTTATGTGTAATT
* * * *
2306135 CACTTCGGTGCATATGGTGGGCACAACCTTATGTTTAA-G
1 CACTTCAGTGCATATGGTGGGCATAACCTTATGTGTAATT
* * *
2306174 GACTTCGGTG-ATATGGTGGGCATCACCTTATGTGT-ATT
1 CACTTCAGTGCATATGGTGGGCATAACCTTATGTGTAATT
*
2306212 CACTACAGTGCATAT
1 CACTTCAGTGCATAT
2306227 ATTTAACTCA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
37 1 0.01
38 29 0.38
39 13 0.17
40 33 0.43
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (40 bp):
CACTTCAGTGCATATGGTGGGCATAACCTTATGTGTAATT
Found at i:2322275 original size:22 final size:22
Alignment explanation
Indices: 2322227--2322268 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2322217 GACTTTTTTT
*
2322227 GTCAAAGTCAACCGTCAGACCA
1 GTCAAAGTCAACAGTCAGACCA
*
2322249 GTCAAAGTCAACAGTTAGAC
1 GTCAAAGTCAACAGTCAGAC
2322269 TGATCAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (22 bp):
GTCAAAGTCAACAGTCAGACCA
Found at i:2322339 original size:20 final size:20
Alignment explanation
Indices: 2322291--2322344 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
2322281 CAGGTTAACG
2322291 GGTCGGGTTGACACGATTCA
1 GGTCGGGTTGACACGATTCA
** * * *
2322311 GGTTAGGTTGACTCGGTTTA
1 GGTCGGGTTGACACGATTCA
2322331 GGTCGGGTTGACAC
1 GGTCGGGTTGACAC
2322345 AAATCGGGTC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.37, T:0.30
Consensus pattern (20 bp):
GGTCGGGTTGACACGATTCA
Found at i:2324024 original size:17 final size:17
Alignment explanation
Indices: 2324004--2324046 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2323994 ATTCATGCAT
2324004 TTAGTTCATTAAT-AAA
1 TTAGTTCATTAATCAAA
*
2324020 GTTAGTTTATTAATCAAA
1 -TTAGTTCATTAATCAAA
*
2324038 CTAGTTCAT
1 TTAGTTCAT
2324047 CTATTAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (17 bp):
TTAGTTCATTAATCAAA
Found at i:2324069 original size:17 final size:17
Alignment explanation
Indices: 2324028--2324070 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2324018 AAGTTAGTTT
* *
2324028 ATTAATCAAACTAGTTC
1 ATTAATTAAACTAGTGC
2324045 ATCT-ATTAAACTAGTGC
1 AT-TAATTAAACTAGTGC
2324062 ATTAATTAA
1 ATTAATTAA
2324071 GTAATTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (17 bp):
ATTAATTAAACTAGTGC
Found at i:2324113 original size:32 final size:30
Alignment explanation
Indices: 2324077--2324138 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2324067 TTAAGTAATT
2324077 CTTTAATTATTTGTCATGCATATTTCATTTAA
1 CTTTAATT-TTTGTCATGCAT-TTTCATTTAA
* * *
2324109 CTTTAATTTTTTTGATGGATTTTCATTTAA
1 CTTTAATTTTTGTCATGCATTTTCATTTAA
2324139 GTTTGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 10 0.37
31 9 0.33
32 8 0.30
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (30 bp):
CTTTAATTTTTGTCATGCATTTTCATTTAA
Found at i:2327685 original size:41 final size:41
Alignment explanation
Indices: 2327640--2327737 Score: 115
Period size: 41 Copynumber: 2.4 Consensus size: 41
2327630 ATCCATAATT
* *
2327640 CAATTCAATTTGGTCATGGAAACATGCATTTATTCACAAAA
1 CAATTCAATTTGATCATGGAAACATGCATTAATTCACAAAA
* * * * **
2327681 CAATTCAATTAGATCATGGTACCATGTATTAATTCACAATC
1 CAATTCAATTTGATCATGGAAACATGCATTAATTCACAAAA
*
2327722 CAATTCAATTTAATCA
1 CAATTCAATTTGATCA
2327738 AGGTAAAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (41 bp):
CAATTCAATTTGATCATGGAAACATGCATTAATTCACAAAA
Found at i:2334237 original size:44 final size:44
Alignment explanation
Indices: 2334181--2334272 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
2334171 TAATATTACT
2334181 TTTGAGTATTATTAGAATTATAAATGTTAGAAAGTATAATAACA
1 TTTGAGTATTATTAGAATTATAAATGTTAGAAAGTATAATAACA
* * *
2334225 TTTGAGTGTTATTAGAATTATTAATGTTAGAAAGTATACTAACA
1 TTTGAGTATTATTAGAATTATAAATGTTAGAAAGTATAATAACA
2334269 TTTG
1 TTTG
2334273 TATTGTAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.41
Consensus pattern (44 bp):
TTTGAGTATTATTAGAATTATAAATGTTAGAAAGTATAATAACA
Found at i:2334556 original size:55 final size:55
Alignment explanation
Indices: 2334482--2334748 Score: 401
Period size: 55 Copynumber: 4.9 Consensus size: 55
2334472 TTACCGAAAG
* * *
2334482 GGCACTAGGTGTGCAACCTCAAGAAATTCATAATGAGATTATGAATTTGCGTATT
1 GGCACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
* *
2334537 GGAACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATTAATTTCCGTATT
1 GGCACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
*
2334592 GGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
*
2334647 GGCACTATGTGTGCAACCTCATGAAATTCATAATGAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
* * * * * *
2334702 GGTACTATGTGTACAACCCCACA-TAATTCATAATAAGTTTGTGAATT
1 GGCACTATGTGTGCAACCTCA-AGAAATTCATAATGAGTTTATGAATT
2334749 ATGGTATCGA
Statistics
Matches: 195, Mismatches: 16, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
55 195 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (55 bp):
GGCACTATGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
Found at i:2338170 original size:65 final size:63
Alignment explanation
Indices: 2338053--2338259 Score: 179
Period size: 65 Copynumber: 3.2 Consensus size: 63
2338043 TTTCAAAGTG
* * * **
2338053 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGCAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCACCAA-CCATGCATCAATGCACTCA-G--GTATTTTGAAACATCGAATGCATT
2338116 TC
62 TC
* * ** *
2338118 ATGCATCGATGCA-TATACTATGCATCAATGCACTCAGAGT-TTTATGAAAACATTAAATCCATT
1 ATGCATCGATGCACCA-ACCATGCATCAATGCACTCAG-GTATTT-TG-AAACATCGAATGCATT
*
2338181 TG
62 TC
* * * *
2338183 ATGCATAGATGCACCAGCCATGCATCGATGCACTCAGGTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACCAACCATGCATCAATGCACTCAGGTATTTTGAAACATCGAATGCATTTC
2338246 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2338260 TCTTACTATA
Statistics
Matches: 114, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
62 1 0.01
63 31 0.27
64 20 0.18
65 61 0.54
66 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (63 bp):
ATGCATCGATGCACCAACCATGCATCAATGCACTCAGGTATTTTGAAACATCGAATGCATTTC
Found at i:2343736 original size:43 final size:40
Alignment explanation
Indices: 2343638--2343738 Score: 103
Period size: 43 Copynumber: 2.4 Consensus size: 40
2343628 TTTTTGTGCT
* *
2343638 TAATGCATCGATGCATCCTTAAATGTGCATCGATACACCG
1 TAATGCATCGATGCAGCCTTAAATGTGCATCGATACAACG
* * *
2343678 TGAAGGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGG
1 T-AA--TGCATCGATGCA-GCCTTAAATGTGCATCGAT--ACAACG
2343724 TAATGCATCGATGCA
1 TAATGCATCGATGCA
2343739 TCGGTCGGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
40 1 0.02
41 2 0.04
43 22 0.45
44 17 0.35
45 2 0.04
46 5 0.10
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (40 bp):
TAATGCATCGATGCAGCCTTAAATGTGCATCGATACAACG
Found at i:2346495 original size:65 final size:64
Alignment explanation
Indices: 2346372--2346578 Score: 215
Period size: 65 Copynumber: 3.2 Consensus size: 64
2346362 TTTCAATGTG
* * * ** *
2346372 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AATATCGAATGCATT
1 ATGCATCGATGCACCAA-CTATGCATCGATGCACTCA--GACTATTTTGAAACATCGAATGCATT
2346435 TC
63 TC
* *
2346437 ATGCATCGATGCA-CATACTATGCATCGATGCACTCAGAGT-TTTATGAAAACATTGAATGCATT
1 ATGCATCGATGCACCA-ACTATGCATCGATGCACTCAGACTATTT-TG-AAACATCGAATGCATT
*
2346500 TG
63 TC
* * * *
2346502 ATGCATCGATACACCAGCTATGCATCGATGCACTCAGTCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACCAACTATGCATCGATGCACTCAGACTATTTTGAAACATCGAATGCATTTC
2346566 ATGCATCGATGCA
1 ATGCATCGATGCA
2346579 TTCTTAGTGC
Statistics
Matches: 120, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 45 0.38
65 64 0.53
66 5 0.04
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACCAACTATGCATCGATGCACTCAGACTATTTTGAAACATCGAATGCATTTC
Found at i:2346594 original size:19 final size:17
Alignment explanation
Indices: 2346557--2346597 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
2346547 GAAACATCGA
*
2346557 ATGCATTTTATGCATCG
1 ATGCATTTTATGCACCG
2346574 ATGCATTCTTAGTGCACCG
1 ATGCATT-TTA-TGCACCG
2346593 ATGCA
1 ATGCA
2346598 CTAAGGGTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 3 0.14
19 11 0.52
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (17 bp):
ATGCATTTTATGCACCG
Found at i:2348977 original size:47 final size:44
Alignment explanation
Indices: 2348877--2349002 Score: 144
Period size: 47 Copynumber: 2.8 Consensus size: 44
2348867 TATAAAATCC
* *
2348877 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATT
1 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
2348922 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCA-TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
2348969 CTTGCCATTATTCCGTAAGATCATAAGCTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
2349003 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 37 0.52
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2349151 original size:40 final size:40
Alignment explanation
Indices: 2349107--2349228 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
2349097 ACCGTAGGGC
2349107 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2349147 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2349187 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2349227 TA
1 TA
2349229 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2353062 original size:6 final size:6
Alignment explanation
Indices: 2353046--2353163 Score: 73
Period size: 6 Copynumber: 19.3 Consensus size: 6
2353036 TGTCTCATTT
* * * *
2353046 TTTTCTC TTTTTC -TTTTC TTTCTC GTTTTC ATTTTT- TTTTTC TTCTTG
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
* * *
2353094 GTTTTC ATTTTC ATTTTC TTTTTC TATATTTTC TTTTTC TATTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC --T-TTTTC TTTTTC T-TTTTC TTTTTC
* *
2353145 TTCTTC TATTT- TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TT
2353164 CTTATAATAT
Statistics
Matches: 87, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
5 18 0.21
6 50 0.57
7 13 0.15
8 1 0.01
9 5 0.06
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:2353067 original size:17 final size:17
Alignment explanation
Indices: 2353040--2353083 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2353030 TTTTCATGTC
*
2353040 TCATTTTTTTCTCTTTT
1 TCATTTTTTTCTCGTTT
2353057 TC-TTTTCTTTCTCGTTT
1 TCATTTT-TTTCTCGTTT
2353074 TCATTTTTTT
1 TCATTTTTTT
2353084 TTTCTTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (17 bp):
TCATTTTTTTCTCGTTT
Found at i:2353110 original size:27 final size:26
Alignment explanation
Indices: 2353080--2353146 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
2353070 GTTTTCATTT
*
2353080 TTTTTTTCTTCTTGGTTTTCATTTTC-A
1 TTTTTTT-TTCTT-ATTTTCATTTTCTA
*
2353107 TTTTCTTTTTCTATATTTTCTTTTTCTA
1 TTTT-TTTTTCT-TATTTTCATTTTCTA
2353135 TTTTTTTTTCTT
1 TTTTTTTTTCTT
2353147 CTTCTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 1 0.03
27 25 0.71
28 9 0.26
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTCTTATTTTCATTTTCTA
Found at i:2353115 original size:17 final size:16
Alignment explanation
Indices: 2353025--2353115 Score: 55
Period size: 17 Copynumber: 5.6 Consensus size: 16
2353015 CAAGTGAAAT
*
2353025 ATTTTTTTTCATGTCTC
1 ATTTTTTTTCAT-TTTC
*
2353042 ATTTTTTTCTCTTTTTC
1 ATTTTTTT-TCATTTTC
*
2353059 -TTTTCTTTCTCGTTTTC
1 ATTTT-TTT-TCATTTTC
2353076 ATTTTTTTT--TTCTTC
1 ATTTTTTTTCATT-TTC
**
2353091 -TTGGTTTTCATTTTC
1 ATTTTTTTTCATTTTC
2353106 ATTTTCTTTT
1 ATTTT-TTTT
2353116 TCTATATTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
14 8 0.14
15 6 0.10
16 9 0.15
17 29 0.49
18 7 0.12
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.73
Consensus pattern (16 bp):
ATTTTTTTTCATTTTC
Found at i:2353132 original size:33 final size:33
Alignment explanation
Indices: 2353095--2353165 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2353085 TTCTTCTTGG
*
2353095 TTTTC-ATTTTCATTTTCTTTTTCTATATTTTCT
1 TTTTCTATTTT-ATTTTCTTCTTCTATATTTTCT
*
2353128 TTTTCTATTTTTTTTTCTTCTTCTAT-TTTT-T
1 TTTTCTATTTTATTTTCTTCTTCTATATTTTCT
2353159 TTCTTCT
1 TT-TTCT
2353166 TATAATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 3 0.09
32 8 0.24
33 18 0.53
34 5 0.15
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (33 bp):
TTTTCTATTTTATTTTCTTCTTCTATATTTTCT
Found at i:2353148 original size:15 final size:16
Alignment explanation
Indices: 2353106--2353165 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 16
2353096 TTTCATTTTC
*
2353106 ATTTTCTTT-TTCTAT
1 ATTTTTTTTCTTCTAT
*
2353121 ATTTTCTTT-TTCTAT
1 ATTTTTTTTCTTCTAT
*
2353136 -TTTTTTTTCTTCTTCT
1 ATTTTTTTTCTTC-TAT
2353152 ATTTTTTTTCTTCT
1 ATTTTTTTTCTTCT
2353166 TATAATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.17
15 18 0.45
16 3 0.08
17 12 0.30
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTTTTTCTTCTAT
Found at i:2353156 original size:17 final size:18
Alignment explanation
Indices: 2353122--2353166 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
2353112 TTTTTCTATA
*
2353122 TTTTCTTTTTCTATTTTT
1 TTTTCTTCTTCTATTTTT
2353140 TTTTCTTCTTCTA-TTTT
1 TTTTCTTCTTCTATTTTT
2353157 TTTTCTTCTT
1 TTTTCTTCTT
2353167 ATAATATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTCTTCTATTTTT
Found at i:2356101 original size:47 final size:45
Alignment explanation
Indices: 2356026--2356151 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
2356016 TATAAAATCC
* *
2356026 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
* *
2356071 CTTACCATTTAAATTCCATAAGCTCTTAAGCTTATTTTACCCAAATA
1 CTTACCATTT--ATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
* *
2356118 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTT
2356152 GCATGGTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 38 0.52
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:2356299 original size:40 final size:40
Alignment explanation
Indices: 2356255--2356336 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
2356245 ACCGTAGTGC
2356255 TACACATAAGGTCGTGCCCACCAAATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCAAATACACCGAAGTGTAT
*
2356295 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCAAATACACCGAAGTGTAT
2356335 TA
1 TA
2356337 TAAACCTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCAAATACACCGAAGTGTAT
Found at i:2364488 original size:29 final size:29
Alignment explanation
Indices: 2364456--2364550 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
2364446 AAATATTTAC
2364456 ATAAATTAAAATTAAGGACAAAACATTTT
1 ATAAATTAAAATTAAGGACAAAACATTTT
* *
2364485 ATAAATTAAAATTAAGGATAAAACCTTTT
1 ATAAATTAAAATTAAGGACAAAACATTTT
* * *
2364514 ATAATTTAAAA-T-AGAGACCACAACTTTTT
1 ATAAATTAAAATTAAG-GA-CAAAACATTTT
2364543 ATAAATTA
1 ATAAATTA
2364551 CATTAAAGGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 2 0.04
28 3 0.05
29 52 0.91
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (29 bp):
ATAAATTAAAATTAAGGACAAAACATTTT
Found at i:2366819 original size:16 final size:16
Alignment explanation
Indices: 2366785--2366819 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2366775 GAATTTAGAT
*
2366785 AAAAATAAATAAAGCA
1 AAAAATAAATAAAGAA
*
2366801 AAAAATAAATAAATAA
1 AAAAATAAATAAAGAA
2366817 AAA
1 AAA
2366820 GAAGGATTAA
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:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (16 bp):
AAAAATAAATAAAGAA
Found at i:2368136 original size:17 final size:17
Alignment explanation
Indices: 2368107--2368170 Score: 76
Period size: 17 Copynumber: 3.7 Consensus size: 17
2368097 GATGGATCAT
*
2368107 TTAA-TAAATCTAGTCCA
1 TTAATTAAA-CTAGTTCA
2368124 TTAATTAAACTAGTTCA
1 TTAATTAAACTAGTTCA
* *
2368141 TTTATTTAAATTAGTTCA
1 -TTAATTAAACTAGTTCA
2368159 TTAATTAAACTA
1 TTAATTAAACTA
2368171 TCTCCTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 21 0.52
18 19 0.47
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.44
Consensus pattern (17 bp):
TTAATTAAACTAGTTCA
Found at i:2368142 original size:35 final size:35
Alignment explanation
Indices: 2368103--2368170 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
2368093 GTATGATGGA
2368103 TCATTTA-ATAAATCTAGTCCATTAATTAAACTAGT
1 TCATTTATATAAAT-TAGTCCATTAATTAAACTAGT
* *
2368138 TCATTTATTTAAATTAGTTCATTAATTAAACTA
1 TCATTTATATAAATTAGTCCATTAATTAAACTA
2368171 TCTCCTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (35 bp):
TCATTTATATAAATTAGTCCATTAATTAAACTAGT
Found at i:2371859 original size:41 final size:41
Alignment explanation
Indices: 2371812--2371910 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 41
2371802 TATACTTAAT
*
2371812 ATATATATATATATAATACATTTTAAAACTATATA-ATTTCAAA
1 ATATATATATATAT-ATACA-TATAAAA-TATATATATTTCAAA
* * * *
2371855 ATATAT-TATATATATACATATATAATATATATGTTTTAAT
1 ATATATATATATATATACATATAAAATATATATATTTCAAA
2371895 ATATATATATATATAT
1 ATATATATATATATAT
2371911 TAGAAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 6 0.12
40 16 0.33
41 14 0.29
42 7 0.14
43 6 0.12
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (41 bp):
ATATATATATATATATACATATAAAATATATATATTTCAAA
Found at i:2371860 original size:2 final size:2
Alignment explanation
Indices: 2371855--2371910 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
2371845 TAATTTCAAA
* * *
2371855 AT AT AT -T AT AT AT AT AC AT AT AT A- AT AT AT AT GT -T TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2371893 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2371911 TAGAAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 4 0.09
2 42 0.91
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2375259 original size:41 final size:41
Alignment explanation
Indices: 2375202--2375283 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
2375192 AATTTCCTTG
2375202 GAGGAGTTGGCGATGCAACCATTATAGCCTCTGGTCCTGAA
1 GAGGAGTTGGCGATGCAACCATTATAGCCTCTGGTCCTGAA
2375243 GAGGAGTTGGCGATGCAACCATTATAGCCTCTGGTCCTGAA
1 GAGGAGTTGGCGATGCAACCATTATAGCCTCTGGTCCTGAA
2375284 ACGGTACCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (41 bp):
GAGGAGTTGGCGATGCAACCATTATAGCCTCTGGTCCTGAA
Found at i:2377550 original size:19 final size:19
Alignment explanation
Indices: 2377498--2377552 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
2377488 TATATATATA
* *
2377498 TATATACTTTTAATTCTTTT
1 TATATA-TTTTTATTATTTT
**
2377518 TCATATATCATTATTATTTT
1 T-ATATATTTTTATTATTTT
2377538 TATATATTTTTATTA
1 TATATATTTTTATTA
2377553 CTATAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 12 0.43
20 11 0.39
21 5 0.18
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATATTTTTATTATTTT
Found at i:2377557 original size:16 final size:15
Alignment explanation
Indices: 2377538--2377593 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
2377528 TTATTATTTT
2377538 TATATATTTTTATTA
1 TATATATTTTTATTA
* *
2377553 CTATA-ATTATATGTTA
1 -TATATATT-TTTATTA
*
2377569 TATATATTTATTATTT
1 TATATATTT-TTATTA
2377585 TATATATTT
1 TATATATTT
2377594 CATTTTATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
TATATATTTTTATTA
Found at i:2377616 original size:15 final size:15
Alignment explanation
Indices: 2377596--2377649 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
2377586 ATATATTTCA
2377596 TTTTATCTTTTATTT
1 TTTTATCTTTTATTT
2377611 TTTTATCTTTTATTT
1 TTTTATCTTTTATTT
* *
2377626 TTGTAT-TGTTATTGT
1 TTTTATCTTTTATT-T
*
2377641 TATTATCTT
1 TTTTATCTT
2377650 CTTTATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 6 0.19
15 25 0.78
16 1 0.03
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTATCTTTTATTT
Found at i:2377688 original size:33 final size:32
Alignment explanation
Indices: 2377618--2377694 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
2377608 TTTTTTTATC
*
2377618 TTTTATTTTTGTATTGTTATTGTTATTATCTT
1 TTTTATTTTTGTATTGTTATTGTTATTATATT
*
2377650 CTTTATTTTATGTATT-TTATT-TATATATATATT
1 TTTTATTTT-TGTATTGTTATTGT-TAT-TATATT
*
2377683 TTTTATATTTGT
1 TTTTATTTTTGT
2377695 TTTTGTGCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
31 1 0.03
32 19 0.50
33 18 0.47
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (32 bp):
TTTTATTTTTGTATTGTTATTGTTATTATATT
Found at i:2388221 original size:9 final size:9
Alignment explanation
Indices: 2388209--2388243 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2388199 TGAAAAAATT
2388209 GAAAAAAGA
1 GAAAAAAGA
2388218 GAAAAAAGAA
1 GAAAAAAG-A
*
2388228 CAAAAAAGA
1 GAAAAAAGA
2388237 GAAAAAA
1 GAAAAAA
2388244 CAAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (9 bp):
GAAAAAAGA
Found at i:2389438 original size:110 final size:110
Alignment explanation
Indices: 2389241--2389439 Score: 299
Period size: 110 Copynumber: 1.8 Consensus size: 110
2389231 GTTTCAGAGC
* *
2389241 CAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAACGAAG
* *
2389306 GGGCGACTAATTGTGAACAAACAACTTTTCAGTTTCATTCAAAGT
66 GGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGT
* * * *
2389351 CAATTTCAACTTCACAGCGAATGATATTGAACTCGAGACAACACAAGCTCAACTTCATAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAACGAAG
* * *
2389416 GGGCGGCTGACTGTCAATAAACAA
66 GGGCGACTAACTGTCAACAAACAA
2389440 TTTCTAGAGC
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 78 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (110 bp):
CAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCACAACGAAG
GGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGT
Found at i:2390974 original size:2 final size:2
Alignment explanation
Indices: 2390924--2390955 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2390914 ATTCTATCGT
2390924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2390956 CTTTATCTTT
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):
TA
Found at i:2391065 original size:15 final size:15
Alignment explanation
Indices: 2391045--2391076 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2391035 ATATATTTCA
*
2391045 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
2391060 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
2391075 TT
1 TT
2391077 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:2391093 original size:20 final size:20
Alignment explanation
Indices: 2391046--2391099 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
2391036 TATATTTCAT
*
2391046 TTTATCTTTTATTTTTTTATC
1 TTTAT-TTTTATTTTTGTATC
2391067 TTCTATTTTTATTTTTGTAT-
1 TT-TATTTTTATTTTTGTATC
*
2391087 TGTTATTGTTATT
1 T-TTATTTTTATT
2391100 ATCTTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 10 0.34
21 16 0.55
22 3 0.10
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTATTTTTATTTTTGTATC
Found at i:2392722 original size:2 final size:2
Alignment explanation
Indices: 2392715--2392764 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2392705 AAGTATTGCA
2392715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2392757 AT AT AT AT
1 AT AT AT AT
2392765 CAAGGTACCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2394060 original size:39 final size:39
Alignment explanation
Indices: 2394006--2394083 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
2393996 ACTTCCTCAA
* ** *
2394006 CACCATTTCCTTTGTCGTTTTTGTTCCATGTTTATTCAG
1 CACCAATTCCTTTGTCAATTTGGTTCCATGTTTATTCAG
*
2394045 CACCAATTCCTTTGTCAATTTGGTTCCATGTTTCTTCAG
1 CACCAATTCCTTTGTCAATTTGGTTCCATGTTTATTCAG
2394084 TCGAATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.15, C:0.24, G:0.13, T:0.47
Consensus pattern (39 bp):
CACCAATTCCTTTGTCAATTTGGTTCCATGTTTATTCAG
Found at i:2395198 original size:21 final size:21
Alignment explanation
Indices: 2395172--2395213 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2395162 ACAGATTGCT
2395172 CAAA-GGGAACCGATTCTCCCC
1 CAAAGGGGAACCGATTC-CCCC
*
2395193 CAAAGGGGTACCGATTCCCCC
1 CAAAGGGGAACCGATTCCCCC
2395214 TGAATGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.26, C:0.38, G:0.21, T:0.14
Consensus pattern (21 bp):
CAAAGGGGAACCGATTCCCCC
Found at i:2400646 original size:22 final size:22
Alignment explanation
Indices: 2400589--2400647 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
2400579 TTAGTGCTGA
* *
2400589 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
* * *
2400611 GGGAACCGGTTTCCCCTTTGAAT
1 GGGAACC-GATTCCCCCTTGAAG
2400634 GGGAACCGATTCCC
1 GGGAACCGATTCCC
2400648 TAGGGGAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:2406091 original size:6 final size:5
Alignment explanation
Indices: 2406080--2406109 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2406070 TTCAATTTCA
2406080 TCTTT TCTTTT TCTTT TCTTT TCTTT TCTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTT
2406110 AAAAAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:2408048 original size:26 final size:26
Alignment explanation
Indices: 2407983--2408048 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
2407973 ATTGCACTTA
**
2407983 AAAGTGCCACATGCCACTTCCACTCG
1 AAAGTGCCACATATCACTTCCACTCG
** * *
2408009 AAAGTATCACATATCACTTGCATTCG
1 AAAGTGCCACATATCACTTCCACTCG
*
2408035 AAAGTGCCATATAT
1 AAAGTGCCACATAT
2408049 ATATAAAAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (26 bp):
AAAGTGCCACATATCACTTCCACTCG
Found at i:2411561 original size:21 final size:22
Alignment explanation
Indices: 2411537--2411582 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2411527 ACTAATGATC
*
2411537 ATGCCAAGGCATAA-AATTCAT
1 ATGCCAAGGCAAAACAATTCAT
2411558 ATGCCAAGGCAAAAGCAATTCAT
1 ATGCCAAGGCAAAA-CAATTCAT
2411581 AT
1 AT
2411583 TCCTGCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
23 9 0.41
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (22 bp):
ATGCCAAGGCAAAACAATTCAT
Found at i:2415417 original size:40 final size:40
Alignment explanation
Indices: 2415373--2415453 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
2415363 TGTCATGACA
2415373 TTGAATTTCATTGACTGTACATAAATAATAATTTTATTCT
1 TTGAATTTCATTGACTGTACATAAATAATAATTTTATTCT
2415413 TTGAATTTCATTGACTGTACATAAATAATAATTTTATTCT
1 TTGAATTTCATTGACTGTACATAAATAATAATTTTATTCT
2415453 T
1 T
2415454 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (40 bp):
TTGAATTTCATTGACTGTACATAAATAATAATTTTATTCT
Found at i:2426148 original size:26 final size:26
Alignment explanation
Indices: 2426104--2426178 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
2426094 CTACCAAATA
* *
2426104 TTGCACTC-AAAATTGCCACATGTCAC
1 TTGCACTCGAAAGTT-CCACATATCAC
2426130 TTGCACTCGAAAGTTCCACATATCAC
1 TTGCACTCGAAAGTTCCACATATCAC
*
2426156 TTGCACTCGAAAGTGCCACATAT
1 TTGCACTCGAAAGTTCCACATAT
2426179 ATATACAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 40 0.89
27 5 0.11
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
TTGCACTCGAAAGTTCCACATATCAC
Found at i:2442096 original size:20 final size:20
Alignment explanation
Indices: 2442068--2442105 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2442058 TAAGAATTTT
*
2442068 TTTATATTATTAAATATATTA
1 TTTATATTAGTAAA-ATATTA
2442089 TTTA-ATTAGTAAAATAT
1 TTTATATTAGTAAAATAT
2442106 AAAATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 8 0.50
21 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTATATTAGTAAAATATTA
Found at i:2443095 original size:22 final size:20
Alignment explanation
Indices: 2443054--2443094 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2443044 AATTAAATTT
*
2443054 TATTTTTAAGATTATAATAA
1 TATTTTTAAAATTATAATAA
*
2443074 TATTTTTAAAACTAT-ATAA
1 TATTTTTAAAATTATAATAA
2443093 TA
1 TA
2443095 AATGATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTTTTAAAATTATAATAA
Found at i:2457560 original size:12 final size:12
Alignment explanation
Indices: 2457523--2457585 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
2457513 ATTTGATACT
2457523 TGACATGGATTC
1 TGACATGGATTC
*
2457535 TGATAT-GATATC
1 TGACATGGAT-TC
2457547 TGACATGGATTC
1 TGACATGGATTC
* *
2457559 TGATAT-GATAC
1 TGACATGGATTC
*
2457570 TTGACTTGGATTC
1 -TGACATGGATTC
2457583 TGA
1 TGA
2457586 TCTGATAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:2457639 original size:24 final size:24
Alignment explanation
Indices: 2457508--2457622 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
2457498 TCGATTTGAT
*
2457508 TTCTGATTTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
2457532 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
*
2457556 TTCTGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* * *
2457580 TTCTGATCTGATAGTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
2457604 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
2457623 GTGAATTATG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:2458606 original size:15 final size:15
Alignment explanation
Indices: 2458586--2458629 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2458576 TTATGAATAC
2458586 AATGAATTCAATCTA
1 AATGAATTCAATCTA
* *
2458601 AATGAATGTAAAACTA
1 AATGAAT-TCAATCTA
2458617 ATATGAATTCAAT
1 A-ATGAATTCAAT
2458630 TATATATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (15 bp):
AATGAATTCAATCTA
Found at i:2459137 original size:47 final size:47
Alignment explanation
Indices: 2459030--2459142 Score: 140
Period size: 47 Copynumber: 2.4 Consensus size: 47
2459020 GATTGTTTTG
* * *
2459030 AGGGTTAGTTCACTTGGGAGTATTCAAACCATTTAGAGATTTCTCTG
1 AGGGTGAGTTCACTTGGGAGTATTCAAACCATTTAAAGATTTCTCTA
* * *
2459077 AGGGTGAATTCACTTGGGA-TCATTCAAACCCTTTAAAGATTTCTTTA
1 AGGGTGAGTTCACTTGGGAGT-ATTCAAACCATTTAAAGATTTCTCTA
*
2459124 AGGGTGAGCTCAC-TGGGAG
1 AGGGTGAGTTCACTTGGGAG
2459143 CACTTAAATC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 6 0.11
47 50 0.89
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (47 bp):
AGGGTGAGTTCACTTGGGAGTATTCAAACCATTTAAAGATTTCTCTA
Found at i:2459295 original size:48 final size:48
Alignment explanation
Indices: 2459192--2459317 Score: 137
Period size: 48 Copynumber: 2.6 Consensus size: 48
2459182 TTTGAGAGAG
* * ** *
2459192 CTCATACCCTTTGTAGATTTTTGTTGAAAGCAGACTCGTTTGGTAACG
1 CTCAGACCCTTTGTAGATTTTCGTTGAGGGCAGACTCGTTTGGTAACA
* * * *
2459240 CTTAGACCCTTTGTAGATTTTCGTTGAGGGCGGGCTCGCTTTGG-AGCA
1 CTCAGACCCTTTGTAGATTTTCGTTGAGGGCAGACTCG-TTTGGTAACA
*
2459288 CTCAGACCCCTTCGTAGATTTTCGTTGAGG
1 CTCAGA-CCCTTTGTAGATTTTCGTTGAGG
2459318 ACAAGCTTAC
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 38 0.58
49 27 0.42
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.35
Consensus pattern (48 bp):
CTCAGACCCTTTGTAGATTTTCGTTGAGGGCAGACTCGTTTGGTAACA
Found at i:2459344 original size:49 final size:49
Alignment explanation
Indices: 2459246--2459345 Score: 110
Period size: 49 Copynumber: 2.0 Consensus size: 49
2459236 AACGCTTAGA
* * ** * * *
2459246 CCCTTTGTAGATTTTCGTTGAGGGCGGGCTCGCTTTGGAGCACTCAGAC
1 CCCTTCGTAGATTTTCGTTGAGGACAAGCTCACTTGGGAGCACTAAGAC
* **
2459295 CCCTTCGTAGATTTTCGTTGAGGACAAGCTTACTTGGGAGTGCTAAGAC
1 CCCTTCGTAGATTTTCGTTGAGGACAAGCTCACTTGGGAGCACTAAGAC
2459344 CC
1 CC
2459346 TTTATGATGG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.30
Consensus pattern (49 bp):
CCCTTCGTAGATTTTCGTTGAGGACAAGCTCACTTGGGAGCACTAAGAC
Found at i:2473564 original size:22 final size:21
Alignment explanation
Indices: 2473524--2473589 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 21
2473514 TATGAAATCA
2473524 TTATAAAAATATATATTTATAATT
1 TTATAAAAA-A-ATATTTAT-ATT
2473548 TTATAAAAAAATATTTAT-TT
1 TTATAAAAAAATATTTATATT
**
2473568 TT-TAAAACTATATTTATTATT
1 TTATAAAAAAATATTTA-TATT
2473589 T
1 T
2473590 ATTTGAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 12 0.32
20 5 0.13
21 3 0.08
22 8 0.21
23 1 0.03
24 9 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATAAAAAAATATTTATATT
Found at i:2484598 original size:194 final size:193
Alignment explanation
Indices: 2484252--2484600 Score: 511
Period size: 194 Copynumber: 1.8 Consensus size: 193
2484242 TATGGTAACG
* * *
2484252 TTATGCATAATCATCATTCATAATATTATTAGGTAATGATATATTATGTCACTAAAAATGTGACA
1 TTATGCATAAACACCATTCATAATATTATTAAGTAATGATATATTATGTCACTAAAAATGTGACA
* * * *
2484317 ATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGACAATATAAATTATTAATA
66 ATATCTCTTTCATCACATATAAGTTGATTTTAATGCATTATCTGTGACAATATAAATCATCAATA
** *
2484382 ACGAAATCTTATTTAGTTTAGTGACGTAACCAACTGTCATAGAATATAAATTATAACGTGACA
131 ACGAAATCTTACATAATTTAGTGACGTAACCAACTGTCATAGAATATAAATTATAACGTGACA
* * *
2484445 TTATGCATAAACACCATTCATAATATTATTAAGTAACAT-TTATATTATGTCACTAAACATTTGA
1 TTATGCATAAACACCATTCATAATATTATTAAGT-A-ATGATATATTATGTCACTAAAAATGTGA
* * *
2484509 CAATATCTCTTTCATCACATATAGGTTGATTTTAATGTATTATCTGTGACGATATAAATCATCAA
64 CAATATCTCTTTCATCACATATAAGTTGATTTTAATGCATTATCTGTGACAATATAAATCATCAA
* *
2484574 TAATGAAATTTTACATAATTTAGTGAC
129 TAACGAAATCTTACATAATTTAGTGAC
2484601 ATAATTAGTT
Statistics
Matches: 136, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
193 31 0.23
194 103 0.76
195 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (193 bp):
TTATGCATAAACACCATTCATAATATTATTAAGTAATGATATATTATGTCACTAAAAATGTGACA
ATATCTCTTTCATCACATATAAGTTGATTTTAATGCATTATCTGTGACAATATAAATCATCAATA
ACGAAATCTTACATAATTTAGTGACGTAACCAACTGTCATAGAATATAAATTATAACGTGACA
Found at i:2485497 original size:19 final size:19
Alignment explanation
Indices: 2485473--2485513 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2485463 TACAATGAAT
2485473 GGGAGGGCCTCCTTATATG
1 GGGAGGGCCTCCTTATATG
2485492 GGGAGGGCCTCCTTATATG
1 GGGAGGGCCTCCTTATATG
2485511 GGG
1 GGG
2485514 TTTGGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.15, C:0.20, G:0.41, T:0.24
Consensus pattern (19 bp):
GGGAGGGCCTCCTTATATG
Found at i:2487860 original size:20 final size:20
Alignment explanation
Indices: 2487837--2487886 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2487827 GTGTCAAAAT
2487837 TAGCGATACTAACCCTTGGG
1 TAGCGATACTAACCCTTGGG
2487857 TAGCGATACTAACCCTTGGG
1 TAGCGATACTAACCCTTGGG
*
2487877 TATCGATACT
1 TAGCGATACT
2487887 CACCTGAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (20 bp):
TAGCGATACTAACCCTTGGG
Found at i:2491011 original size:17 final size:17
Alignment explanation
Indices: 2490969--2491005 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2490959 GTAACTTGGC
*
2490969 CAACAGTGCCGTAAGGT
1 CAACAGTGCCGTAAGCT
2490986 CAACAGTGCCGTAAGCT
1 CAACAGTGCCGTAAGCT
2491003 CAA
1 CAA
2491006 TGGTGCTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.16
Consensus pattern (17 bp):
CAACAGTGCCGTAAGCT
Found at i:2491730 original size:21 final size:21
Alignment explanation
Indices: 2491704--2491757 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
2491694 AAATGCCTTG
2491704 GTATCGATACTCCTATGGATA
1 GTATCGATACTCCTATGGATA
2491725 GTATCGATACTCCTATGGATA
1 GTATCGATACTCCTATGGATA
* *
2491746 ATCTCGATACTC
1 GTATCGATACTC
2491758 TACCTGGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (21 bp):
GTATCGATACTCCTATGGATA
Found at i:2526818 original size:49 final size:49
Alignment explanation
Indices: 2526746--2526904 Score: 237
Period size: 49 Copynumber: 3.2 Consensus size: 49
2526736 CCAAAATAAA
* * *
2526746 TGCATAACGGTGCATTTTGGCATAAAGGGTTCCACTAAAGAAAGTTAAG
1 TGCATAACGGTGCATTTTGGCATAAAAGGTGCCACTAATGAAAGTTAAG
* * *
2526795 TGCATAACGGTGCATTTTGGCATAAAAGGTGCAACTAATGAAAATTAAA
1 TGCATAACGGTGCATTTTGGCATAAAAGGTGCCACTAATGAAAGTTAAG
* **
2526844 TGCATAACGATGCATTTCAGCATAAAAGGTGCCACTAATGAAAGTTAAG
1 TGCATAACGGTGCATTTTGGCATAAAAGGTGCCACTAATGAAAGTTAAG
2526893 TGCATAACGGTG
1 TGCATAACGGTG
2526905 TCATAAAAGG
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 97 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (49 bp):
TGCATAACGGTGCATTTTGGCATAAAAGGTGCCACTAATGAAAGTTAAG
Found at i:2529167 original size:20 final size:20
Alignment explanation
Indices: 2529134--2529172 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2529124 TTAATTATTT
2529134 AATTATTATATTTATTTAGG
1 AATTATTATATTTATTTAGG
2529154 AATTAGTTAT-TTTATTTAG
1 AATTA-TTATATTTATTTAG
2529173 TAACAACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
AATTATTATATTTATTTAGG
Found at i:2530004 original size:28 final size:26
Alignment explanation
Indices: 2529973--2530030 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
2529963 TTCTACTTTA
* *
2529973 TTTATTTTCTTATAATTTTTCATTTATT
1 TTTATTTTATTATAA-CTTTCA-TTATT
*
2530001 TTTATTTTATTATTACTTTCATTATT
1 TTTATTTTATTATAACTTTCATTATT
2530027 TTTA
1 TTTA
2530031 ACCCCCCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
27 5 0.19
28 13 0.48
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTATTTTATTATAACTTTCATTATT
Found at i:2539004 original size:21 final size:20
Alignment explanation
Indices: 2538980--2539031 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
2538970 AAATACCTCG
2538980 GTATCGATACTGACCCTCTAA
1 GTATCGATACTGACCC-CTAA
* * ** *
2539001 GTATTGATATTGGTCCCTGA
1 GTATCGATACTGACCCCTAA
2539021 GTATCGATACT
1 GTATCGATACT
2539032 CCTTGAAGGG
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (20 bp):
GTATCGATACTGACCCCTAA
Found at i:2542261 original size:45 final size:45
Alignment explanation
Indices: 2542172--2542302 Score: 158
Period size: 45 Copynumber: 2.9 Consensus size: 45
2542162 GGTAATCATG
* * * *
2542172 AAATAAGCTCATGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTAACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
*
2542216 AAATAAGCTAACGAGCTTATGAAATAAATGGTAAGTATTTTGGTA
1 AAATAAGCTAACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
* * *
2542261 AAATAAGC-ATACAAGCTTATGGGATAAATGTTAAGTGATTTT
1 AAATAAGCTA-ACGAGCTTATGGAATAAATGGTAAGT-ATTTT
2542303 ATCTTATTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 23 0.31
45 47 0.63
46 5 0.07
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTAACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
Done.