Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009086.1 Hibiscus syriacus cultivar Beakdansim tig00112530_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: 1596699
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:445982 original size:33 final size:29
Alignment explanation
Indices: 445735--446019 Score: 197
Period size: 29 Copynumber: 9.6 Consensus size: 29
445725 GAGACAAAAC
445735 TTTGTTTCAAAAGAAACAAACTCAAAGATT
1 TTTGTTTCAAAAGAAAC-AACTCAAAGATT
* **
445765 TTGGTTTCAAAAGAAATGACTCAAAGATTT
1 TTTGTTTCAAAAGAAACAACTCAAAGA-TT
** * *
445795 TTTCACGAAATTGTCTTAAGAGA-AA--CAAA-A-C
1 TTT---G---TT-TCAAAAGAAACAACTCAAAGATT
* *
445826 TTTGGTTCAAAAGAAACAGACTCAAAGA-A
1 TTTGTTTCAAAAGAAACA-ACTCAAAGATT
445855 TTT-TTTCAAAAGAAACAACTCAAAGATT
1 TTTGTTTCAAAAGAAACAACTCAAAGATT
* *
445883 TTTATTTCAAAAGAAACAACTCACAGATT
1 TTTGTTTCAAAAGAAACAACTCAAAGATT
* * * *
445912 TTTATTTCAAAATAAACAACTCACAGACT
1 TTTGTTTCAAAAGAAACAACTCAAAGATT
*
445941 TTTGTTTCAAGAGAAACAAACTCAAAGATAGGT
1 TTTGTTTCAAAAGAAAC-AACTCAAAGAT---T
** *
445974 TTTGTTTCAAGGGAAACAATCTCAAAGATG
1 TTTGTTTCAAAAGAAACAA-CTCAAAGATT
* *
446004 TTTGTTTTAAGAGAAA
1 TTTGTTTCAAAAGAAA
446020 TTGTATTAAA
Statistics
Matches: 207, Mismatches: 28, Indels: 40
0.75 0.10 0.15
Matches are distributed among these distances:
24 7 0.03
25 2 0.01
26 1 0.00
27 9 0.04
28 21 0.10
29 78 0.38
30 42 0.20
31 3 0.01
32 2 0.01
33 28 0.14
34 4 0.02
36 3 0.01
37 7 0.03
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.30
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAACTCAAAGATT
Found at i:446164 original size:64 final size:64
Alignment explanation
Indices: 446015--446201 Score: 225
Period size: 64 Copynumber: 2.9 Consensus size: 64
446005 TTGTTTTAAG
* * ** * * * *
446015 AGAAATTGTATTAAAAGAGACAAACCTTTGTTTTCATAAAAAACATATTTAAAGATTTTTCTTCA
1 AGAAATTGTCTCAAAAGAGACAAAATTTTG-TTTCA-AAGAAACATACTCAAAGA-TTCTCTTCA
446080 AA
63 AA
*
446082 AGGAATTGTCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACATACTCAAAGATTCT-TTCAAA
1 AGAAATTGTCTCAAAAGAGACAAAATTTTGTTT-CAAAGAAACATACTCAAAGATTCTCTTCAAA
446146 AGAAACTT-TCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAGATT
1 AGAAA-TTGTCTCAAAAGAGACAAAATTTTGTT-TCAAAGAAACATACTCAAAGATT
446202 TTTTTTCATT
Statistics
Matches: 107, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
64 56 0.52
65 6 0.06
66 18 0.17
67 27 0.25
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.30
Consensus pattern (64 bp):
AGAAATTGTCTCAAAAGAGACAAAATTTTGTTTCAAAGAAACATACTCAAAGATTCTCTTCAAA
Found at i:446328 original size:30 final size:31
Alignment explanation
Indices: 446274--446332 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
446264 GAGACAAAGT
446274 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
*
446305 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
446333 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCC
Found at i:446717 original size:104 final size:104
Alignment explanation
Indices: 446441--446759 Score: 421
Period size: 106 Copynumber: 3.1 Consensus size: 104
446431 TGTTTTTTTT
446441 GAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAAAACAAATTCGAAATTTGTATCTC
1 GAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGT-AAAACAAATTCGAAATTTGTATCTC
*
446506 AAAGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAA
65 AAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAA
* * * * * * * *
446546 AAAAATAACAATCTCAAGTGAGATTAATTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTATAT
1 GAGAA-AACGATCTCAAGTGAGATCAACTTTGTTT-AATGTAAAACAAATTCGAAATTTGTATCT
* *
446610 CAAAGGAAAAAATGTCTCAAGCAAGACGAAGTTTGTTTT-AA
64 CAAAGG-AAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAA
* * *
446651 GAGAAAGCGATCCCAAATGAGATCAACTTTGTTTAATGTAAAACAAATTC-AAATTTTGTATCTC
1 GAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTAAAACAAATTCGAAA-TTTGTATCTC
* *
446715 AAAGGAAAAATGTCTCAAGTGAGACGAAATATGTTTTGAA
65 AAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAA
446755 -AGAAA
1 GAGAAA
446760 TTGTCTCAAG
Statistics
Matches: 182, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
103 38 0.21
104 50 0.27
105 35 0.19
106 57 0.31
107 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (104 bp):
GAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTAAAACAAATTCGAAATTTGTATCTCA
AAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAA
Found at i:448401 original size:12 final size:13
Alignment explanation
Indices: 448384--448466 Score: 53
Period size: 15 Copynumber: 5.8 Consensus size: 13
448374 CAATTTTTGT
448384 TCTTTGTTTTTTC
1 TCTTTGTTTTTTC
448397 T-TTTGTTCTTTT-
1 TCTTTGTT-TTTTC
448409 TCTTTGATTTTTCTC
1 TCTTTG-TTTTT-TC
*
448424 TCTTTGCTCTTTGTTTT
1 TCTTTG---TTT-TTTC
448441 TCTTTGATTCTTTTC
1 TCTTTG-TT-TTTTC
*
448456 TCTTTATTTTT
1 TCTTTGTTTTT
448467 ATTTGATCTT
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
12 7 0.12
13 15 0.27
14 5 0.09
15 16 0.29
16 1 0.02
17 10 0.18
18 2 0.04
ACGTcount: A:0.04, C:0.16, G:0.07, T:0.73
Consensus pattern (13 bp):
TCTTTGTTTTTTC
Found at i:448419 original size:19 final size:19
Alignment explanation
Indices: 448378--448419 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
448368 CTCGTTCAAT
**
448378 TTTTGTTCTTTGTTTTTTC
1 TTTTGTTCTTTGTTTTTGA
448397 TTTTGTTCTTT-TTCTTTGA
1 TTTTGTTCTTTGTT-TTTGA
448416 TTTT
1 TTTT
448420 TCTCTCTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.79
Consensus pattern (19 bp):
TTTTGTTCTTTGTTTTTGA
Found at i:448458 original size:25 final size:25
Alignment explanation
Indices: 448384--448476 Score: 81
Period size: 25 Copynumber: 3.9 Consensus size: 25
448374 CAATTTTTGT
*
448384 TCTTTGTTTTTTCTTTTGTTCTTTT-
1 TCTTTGATTTTTC-TTTGTTCTTTTC
* *
448409 TCTTTGATTTTTC--T-CTCTTTGC
1 TCTTTGATTTTTCTTTGTTCTTTTC
448431 TCTTTG-TTTTTCTTTGATTCTTTTC
1 TCTTTGATTTTTCTTTG-TTCTTTTC
* *
448456 TCTTT-ATTTTTATTTGATCTT
1 TCTTTGATTTTTCTTTGTTCTT
448477 CGCACTTGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
21 11 0.20
22 7 0.13
23 1 0.02
24 4 0.07
25 32 0.58
ACGTcount: A:0.05, C:0.15, G:0.08, T:0.72
Consensus pattern (25 bp):
TCTTTGATTTTTCTTTGTTCTTTTC
Found at i:452179 original size:30 final size:30
Alignment explanation
Indices: 452145--452217 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
452135 TAAATAGCAA
*
452145 AAAACATAAACTTTAGGGACTAAAATAAAT
1 AAAACATAAACTTTAGGGACCAAAATAAAT
* *
452175 AAAACAAAAACTTTAGGGACCAAAATAGAT
1 AAAACATAAACTTTAGGGACCAAAATAAAT
*
452205 AAAGCATAAACTT
1 AAAACATAAACTT
452218 AAATAACTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.56, C:0.12, G:0.11, T:0.21
Consensus pattern (30 bp):
AAAACATAAACTTTAGGGACCAAAATAAAT
Found at i:453717 original size:3 final size:3
Alignment explanation
Indices: 453711--453758 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
453701 GTATTTGTAT
*
453711 TAA TAA TAA TAGT TAA TAA -ATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
453757 TA
1 TA
453759 TTAAATAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 1 0.03
3 36 0.90
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:455299 original size:24 final size:22
Alignment explanation
Indices: 455267--455315 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
455257 TTACCATTAT
* *
455267 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
455291 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
455313 ATA
1 ATA
455316 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:456264 original size:6 final size:6
Alignment explanation
Indices: 456253--456277 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
456243 TCTCTCCGGT
456253 TCTGTC TCTGTC TCTGTC TCTGTC T
1 TCTGTC TCTGTC TCTGTC TCTGTC T
456278 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.16, T:0.52
Consensus pattern (6 bp):
TCTGTC
Found at i:456297 original size:13 final size:13
Alignment explanation
Indices: 456279--456303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
456269 TCTCTGTCTT
456279 TTTTTTTTTTCTG
1 TTTTTTTTTTCTG
456292 TTTTTTTTTTCT
1 TTTTTTTTTTCT
456304 TGTCGTTCTC
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTCTG
Found at i:456831 original size:3 final size:3
Alignment explanation
Indices: 456825--456890 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
456815 AATAATTATT
* *
456825 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
456870 TAA -ATT TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
456891 ATTTAAATGA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 47 0.89
4 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:456854 original size:27 final size:25
Alignment explanation
Indices: 456814--456890 Score: 120
Period size: 24 Copynumber: 3.0 Consensus size: 25
456804 TTTGGGCTTG
456814 TAATAATTATTTAATAATAATATACTAA
1 TAATAA-TATTTAATAATAATA-A-TAA
456842 TAATAATATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
456867 TAATAA-ATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
456891 ATTTAAATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.37
25 9 0.18
26 1 0.02
27 15 0.31
28 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATAATATTTAATAATAATAATAA
Found at i:457146 original size:76 final size:76
Alignment explanation
Indices: 457015--458417 Score: 2673
Period size: 76 Copynumber: 18.5 Consensus size: 76
457005 GATGGAAATG
*
457015 TTTGAAAACATCATGCACTGAAAGG-CTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTG-AAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
*
457079 TCCTGAAGGCTT
65 TCCCGAAGGCTT
*
457091 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457156 CCCGAAGGCTT
66 CCCGAAGGCTT
457167 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457232 CCCGAAGGCTT
66 CCCGAAGGCTT
*
457243 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457308 CCCGAAGGCTT
66 CCCGAAGGCTT
*
457319 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457384 CCCGAAGGCTT
66 CCCGAAGGCTT
457395 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
457460 CTCGAAGGCTT
66 CCCGAAGGCTT
457471 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457536 CCCGAAGGCTT
66 CCCGAAGGCTT
457547 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457612 CCCGAAGGCTT
66 CCCGAAGGCTT
*
457623 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457688 CCCGAAGGCTT
66 CCCGAAGGCTT
457699 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
457764 CTCGAAGGCTT
66 CCCGAAGGCTT
457775 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457840 CCCGAAGGCTT
66 CCCGAAGGCTT
*
457851 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457916 CCCGAAGGCTT
66 CCCGAAGGCTT
*
457927 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
457992 CCCGAAGGCTT
66 CCCGAAGGCTT
458003 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
458068 CTCGAAGGCTT
66 CCCGAAGGCTT
458079 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
458144 CTCGAAGGCTT
66 CCCGAAGGCTT
458155 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
458220 CCCGAAGGCTT
66 CCCGAAGGCTT
458231 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
458296 CTCGAAGGCTT
66 CCCGAAGGCTT
458307 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
458372 CCCGAAGGCTT
66 CCCGAAGGCTT
458383 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
458418 TGGGAAATAG
Statistics
Matches: 1304, Mismatches: 22, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
75 4 0.00
76 1300 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:460021 original size:22 final size:22
Alignment explanation
Indices: 459993--460039 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
459983 GATTTCTGGG
* *
459993 CAAGGGGGAATCGGTACCCATT
1 CAAGGGGGAACCGATACCCATT
*
460015 CAA-GGGGAACCGATACCCCTT
1 CAAGGGGGAACCGATACCCATT
460036 CAAG
1 CAAG
460040 CAAATATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (22 bp):
CAAGGGGGAACCGATACCCATT
Found at i:460647 original size:18 final size:18
Alignment explanation
Indices: 460624--460658 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
460614 CTAGGAGATT
460624 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
460642 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
460659 CTAGAGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:461759 original size:22 final size:22
Alignment explanation
Indices: 461685--461751 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
461675 TTATGGACAT
461685 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
461707 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
461729 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
461751 A
1 A
461752 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:464908 original size:22 final size:22
Alignment explanation
Indices: 464880--464926 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
464870 GATTTCTGGG
* *
464880 CAAGGGGGAATCGGTACCCATT
1 CAAGGGGGAACCGATACCCATT
*
464902 CAA-GGGGAACCGATACCCCTT
1 CAAGGGGGAACCGATACCCATT
464923 CAAG
1 CAAG
464927 CAAATATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (22 bp):
CAAGGGGGAACCGATACCCATT
Found at i:465534 original size:18 final size:18
Alignment explanation
Indices: 465511--465545 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
465501 CTAGGAGATT
465511 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
465529 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
465546 CTAGAGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:466644 original size:22 final size:22
Alignment explanation
Indices: 466570--466636 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
466560 TTATGGACAT
466570 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
*
466592 AATTCTACGGGCACTTCGATGC
1 AATTCTACGGGCACTTCGGTGC
466614 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
466636 A
1 A
466637 TTTATACGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:469815 original size:104 final size:105
Alignment explanation
Indices: 469693--469891 Score: 310
Period size: 104 Copynumber: 1.9 Consensus size: 105
469683 ACCAAATTAG
* * * *
469693 ATCAGGTAACTCAAAGAACACTTCCAGAAAATGCTCTTGAGTATCCTTATTTTTACTATGAGCAA
1 ATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCATCCTTATTTCTACTATGAGCAA
* *
469758 ATTCATCTTCCAAATTCAATGATT-GTTTTGTCCAACCAA
66 ATTCATCTTCAAAATCCAATGATTGGTTTTGTCCAACCAA
* *
469797 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACTATGAGCAA
1 ATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCATCCTTATTTCTACTATGAGCAA
*
469862 ATTCATCTTTAAAATCCAATGATTGGTTTT
66 ATTCATCTTCAAAATCCAATGATTGGTTTT
469892 TGGGGTTCAT
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
104 80 0.94
105 5 0.06
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (105 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCATCCTTATTTCTACTATGAGCAA
ATTCATCTTCAAAATCCAATGATTGGTTTTGTCCAACCAA
Found at i:470003 original size:84 final size:84
Alignment explanation
Indices: 469906--470212 Score: 553
Period size: 84 Copynumber: 3.7 Consensus size: 84
469896 GTTCATACCA
* * * *
469906 AACCAGATTAGATAACTCAAAGAACATTTCCAAAAGATGCTATTGAACACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
*
469971 TCAATGATTAG-TCTTGTTC
66 TCAATGATTAGTTC-TGTCC
469990 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
470055 TCAATGATTAGTTCTGTCC
66 TCAATGATTAGTTCTGTCC
470074 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
470139 TCAATGATTAGTTCTGTCC
66 TCAATGATTAGTTCTGTCC
470158 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
470213 ATTTGTTCCA
Statistics
Matches: 217, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
84 215 0.99
85 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (84 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
TCAATGATTAGTTCTGTCC
Found at i:477071 original size:24 final size:22
Alignment explanation
Indices: 477039--477087 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
477029 ACCATTATAT
* *
477039 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
477063 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
477085 ATA
1 ATA
477088 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:478031 original size:6 final size:6
Alignment explanation
Indices: 478020--478044 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
478010 TCTCTCCGGT
478020 TCTGTC TCTGTC TCTGTC TCTGTC T
1 TCTGTC TCTGTC TCTGTC TCTGTC T
478045 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.16, T:0.52
Consensus pattern (6 bp):
TCTGTC
Found at i:478597 original size:3 final size:3
Alignment explanation
Indices: 478591--478662 Score: 60
Period size: 3 Copynumber: 24.0 Consensus size: 3
478581 AATAATTATT
* * *
478591 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA -ATT
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A
*
478636 TAA TAA TAA -ATT TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA
478663 ATTTAAATGA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
2 4 0.07
3 47 0.85
4 4 0.07
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:478638 original size:18 final size:18
Alignment explanation
Indices: 478605--478668 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
478595 AATAATATAC
478605 TAATAATAATATTTAATAA
1 TAATAATAA-ATTTAATAA
478624 TAATAATAAA--T--T--
1 TAATAATAAATTTAATAA
478636 TAATAATAAATTTAATAA
1 TAATAATAAATTTAATAA
478654 TAATAATAAATTTAA
1 TAATAATAAATTTAA
478669 ATGAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
12 10 0.26
14 2 0.05
16 2 0.05
18 16 0.41
19 9 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATAATAAATTTAATAA
Found at i:478665 original size:30 final size:31
Alignment explanation
Indices: 478580--478668 Score: 125
Period size: 30 Copynumber: 3.0 Consensus size: 31
478570 TTTGGGCTTG
*
478580 TAATAATTATTTAATAATAAT-AT--A-CTAA
1 TAATAA-TATTTAATAATAATAATAAATTTAA
478608 TAATAATATTTAATAATAATAATAAATTTAA
1 TAATAATATTTAATAATAATAATAAATTTAA
478639 TAATAA-ATTTAATAATAATAATAAATTTAA
1 TAATAATATTTAATAATAATAATAAATTTAA
478669 ATGAAAAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
27 14 0.25
28 8 0.14
30 25 0.45
31 9 0.16
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (31 bp):
TAATAATATTTAATAATAATAATAAATTTAA
Found at i:484032 original size:32 final size:32
Alignment explanation
Indices: 483961--484039 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 32
483951 AATTAATTGA
*
483961 TTAATATTTTT-ATTTTTTATTTATTTTATAT
1 TTAATATTTTTAATTTTTAATTTATTTTATAT
*
483992 TATTATATTTTTAATTTTTAATTT-TTATTACT-T
1 T-TAATATTTTTAATTTTTAATTTATT-TTA-TAT
484025 TTAATATTTTATAAT
1 TTAATATTTT-TAAT
484040 AAACTTATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 1 0.03
32 19 0.47
33 19 0.47
34 1 0.03
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (32 bp):
TTAATATTTTTAATTTTTAATTTATTTTATAT
Found at i:484578 original size:14 final size:14
Alignment explanation
Indices: 484561--484591 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
484551 GAAAATAAAT
484561 TTTCTATTTTTCAA
1 TTTCTATTTTTCAA
484575 TTTCTATTTTTCAA
1 TTTCTATTTTTCAA
484589 TTT
1 TTT
484592 GGTTTACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTCTATTTTTCAA
Found at i:488279 original size:30 final size:30
Alignment explanation
Indices: 488243--488300 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
488233 AATGACCACT
*
488243 ATAGGTCTTCAGGAGCATACAGCGACCTCC
1 ATAGGTCTTCAGGAGCACACAGCGACCTCC
488273 ATAGGTCTTCAGGAGCACACAGCGACCT
1 ATAGGTCTTCAGGAGCACACAGCGACCT
488301 ATGGAGCACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (30 bp):
ATAGGTCTTCAGGAGCACACAGCGACCTCC
Found at i:488989 original size:16 final size:17
Alignment explanation
Indices: 488968--489002 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
488958 TTTTTATTTA
488968 TTTTATTTGTTAA-TGT
1 TTTTATTTGTTAATTGT
*
488984 TTTTATTTTTTAATTGT
1 TTTTATTTGTTAATTGT
489001 TT
1 TT
489003 GAATTGTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTAATTGT
Found at i:493626 original size:2 final size:2
Alignment explanation
Indices: 493619--493644 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
493609 AACTTAATCA
493619 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
493645 GATAGTAAAT
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:498948 original size:18 final size:16
Alignment explanation
Indices: 498918--498967 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
498908 TGCAACGTTT
498918 ATATTTTTAAAAAATAAA
1 ATATTTTT-AAAAAT-AA
*
498936 ATATTATTTAAAAATAT
1 ATATT-TTTAAAAATAA
*
498953 ATATTTTTTAAAATA
1 ATATTTTTAAAAATA
498968 TGAGTGTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 9 0.31
17 6 0.21
18 11 0.38
19 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTTTTAAAAATAA
Found at i:501659 original size:479 final size:479
Alignment explanation
Indices: 500762--501721 Score: 1875
Period size: 479 Copynumber: 2.0 Consensus size: 479
500752 AAATTACATC
500762 ATTCGTCACTCAACTATCTTCTCACTCATATTTTGGTCATTAATTTTTTTAATTTAATCACTTAA
1 ATTCGTCACTCAACTATCTTCTCACTCATATTTTGGTCATTAATTTTTTTAATTTAATCACTTAA
*
500827 CTTTCAAATTACTTCTATTTTAATCACTCTAATTTATTTTATTATTAATAAAAAAAAATTTTACT
66 CTTTCAAATCACTTCTATTTTAATCACTCTAATTTATTTTATTATTAATAAAAAAAAATTTTACT
*
500892 AATATTTTATATGATGTGGTATCCTTTTAATTATTATTTTATTAATGTATGAATAAAATAAAAAA
131 AATATTTTATATGATGTGGTATCCTTTTAATTATTATTTTATTAATATATGAATAAAATAAAAAA
500957 GGGAAGGGACGAGTTCGAGAGGTCAAAAAGAGTGAGTTGTGAGCGTGGGGTGAGTGATTTGTGAT
196 GGGAAGGGACGAGTTCGAGAGGTCAAAAAGAGTGAGTTGTGAGCGTGGGGTGAGTGATTTGTGAT
501022 TTAGGATTTGTGGTATAATTTTTGGGTTTAAGTATAATTTTAAATTTAATTTTTTATTTAAATTA
261 TTAGGATTTGTGGTATAATTTTTGGGTTTAAGTATAATTTTAAATTTAATTTTTTATTTAAATTA
*
501087 TATATTAAAAATAATAAAAATTACACATCACAAAAATATTAATTAAATCAATTAGAGCGATTAAA
326 TATATTAAAAATAATAAAAATTACACATCACAAAAATATTAATTAAATCAATTAGAACGATTAAA
501152 ATATGAGTAATTTAAAAGTTAAGTAGTTTAATTGAATCTTTTTAAACTTTAACAGTCAAAATAAG
391 ATATGAGTAATTTAAAAGTTAAGTAGTTTAATTGAATCTTTTTAAACTTTAACAGTCAAAATAAG
501217 ATTGAGAATATATAGTGATAAATG
456 ATTGAGAATATATAGTGATAAATG
501241 ATTCGTCACTCAACTATCTTCTCACTCATATTTTGGTCATTAATTTTTTTAATTTAATCACTTAA
1 ATTCGTCACTCAACTATCTTCTCACTCATATTTTGGTCATTAATTTTTTTAATTTAATCACTTAA
**
501306 CTTTCAAATCACTTCTATTTTAATCACTCTAATTTATTTTATTATTAATAAAAAATTATTTTACT
66 CTTTCAAATCACTTCTATTTTAATCACTCTAATTTATTTTATTATTAATAAAAAAAAATTTTACT
501371 AATATTTTATATGATGTGGTATCCTTTTAATTATTATTTTATTAATATATGAATAAAATAAAAAA
131 AATATTTTATATGATGTGGTATCCTTTTAATTATTATTTTATTAATATATGAATAAAATAAAAAA
501436 GGGAAGGGACGAGTTCGAGAGGTCAAAAAGAGTGAGTTGTGAGCGTGGGGTGAGTGATTTGTGAT
196 GGGAAGGGACGAGTTCGAGAGGTCAAAAAGAGTGAGTTGTGAGCGTGGGGTGAGTGATTTGTGAT
501501 TTAGGATTTGTGGTATAATTTTTGGGTTTAAGTATAATTTTAAATTTAATTTTTTATTTAAATTA
261 TTAGGATTTGTGGTATAATTTTTGGGTTTAAGTATAATTTTAAATTTAATTTTTTATTTAAATTA
501566 TATATTAAAAATAATAAAAATTACACATCACAAAAATATTAATTAAATCAATTAGAACGATTAAA
326 TATATTAAAAATAATAAAAATTACACATCACAAAAATATTAATTAAATCAATTAGAACGATTAAA
501631 ATATGAGTAATTTAAAAGTTAAGTAGTTTAATTGAATCTTTTTAAACTTTAACAGTCAAAATAAG
391 ATATGAGTAATTTAAAAGTTAAGTAGTTTAATTGAATCTTTTTAAACTTTAACAGTCAAAATAAG
501696 ATTGAGAATATATAGTGATAAATG
456 ATTGAGAATATATAGTGATAAATG
501720 AT
1 AT
501722 GTAATTTATC
Statistics
Matches: 476, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
479 476 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (479 bp):
ATTCGTCACTCAACTATCTTCTCACTCATATTTTGGTCATTAATTTTTTTAATTTAATCACTTAA
CTTTCAAATCACTTCTATTTTAATCACTCTAATTTATTTTATTATTAATAAAAAAAAATTTTACT
AATATTTTATATGATGTGGTATCCTTTTAATTATTATTTTATTAATATATGAATAAAATAAAAAA
GGGAAGGGACGAGTTCGAGAGGTCAAAAAGAGTGAGTTGTGAGCGTGGGGTGAGTGATTTGTGAT
TTAGGATTTGTGGTATAATTTTTGGGTTTAAGTATAATTTTAAATTTAATTTTTTATTTAAATTA
TATATTAAAAATAATAAAAATTACACATCACAAAAATATTAATTAAATCAATTAGAACGATTAAA
ATATGAGTAATTTAAAAGTTAAGTAGTTTAATTGAATCTTTTTAAACTTTAACAGTCAAAATAAG
ATTGAGAATATATAGTGATAAATG
Found at i:504998 original size:18 final size:18
Alignment explanation
Indices: 504975--505010 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
504965 ATATTGTTGA
504975 GTCCTTCTACGAAGATGC
1 GTCCTTCTACGAAGATGC
504993 GTCCTTCTACGAAGATGC
1 GTCCTTCTACGAAGATGC
505011 TAAGCTTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (18 bp):
GTCCTTCTACGAAGATGC
Found at i:508975 original size:6 final size:6
Alignment explanation
Indices: 508964--509187 Score: 151
Period size: 6 Copynumber: 37.3 Consensus size: 6
508954 TTATAAAATA
* * * *
508964 ATATAC ATATAC ATATAC ACATAC ATATAC ACATAC ACATAC ACATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
* * * * * * * *
509012 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
* * * * * * * *
509060 ACATAC ACATAC ACATAC ACATAC ACATAC ATACAC ATACAC ATACAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
* * * * * * * *
509108 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
* * * * *
509156 ATACAC ATACAC ATACAC ATACAC ATACAC AT
1 ATATAC ATATAC ATATAC ATATAC ATATAC AT
509188 GTAATGCTGT
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 213 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (6 bp):
ATATAC
Found at i:508989 original size:18 final size:18
Alignment explanation
Indices: 508966--509187 Score: 403
Period size: 18 Copynumber: 12.4 Consensus size: 18
508956 ATAAAATAAT
* *
508966 ATACATATACATATACAC
1 ATACACATACACATACAC
*
508984 ATACATATACACATACAC
1 ATACACATACACATACAC
509002 ATACACATACACATACAC
1 ATACACATACACATACAC
509020 ATACACATACACATACAC
1 ATACACATACACATACAC
509038 ATACACATACACATACAC
1 ATACACATACACATACAC
509056 ATACACATACACATACAC
1 ATACACATACACATACAC
509074 ATACACATACACAT--AC
1 ATACACATACACATACAC
509090 ATACACATACACATACAC
1 ATACACATACACATACAC
509108 ATACACATACACATACAC
1 ATACACATACACATACAC
509126 ATACACATACACATACAC
1 ATACACATACACATACAC
509144 ATACACATACACATACAC
1 ATACACATACACATACAC
509162 ATACACATACACATACAC
1 ATACACATACACATACAC
509180 ATACACAT
1 ATACACAT
509188 GTAATGCTGT
Statistics
Matches: 200, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
16 16 0.08
18 184 0.92
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (18 bp):
ATACACATACACATACAC
Found at i:518357 original size:2 final size:2
Alignment explanation
Indices: 518350--518381 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
518340 AAGACTTTGT
518350 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
518382 GTTCAGCCTT
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:519033 original size:25 final size:25
Alignment explanation
Indices: 518991--519043 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
518981 ATTCTGACAC
* *
518991 ATCACATAAACATGTTAGAAGTTTT
1 ATCACATAAACATATTAGAAGTCTT
* * *
519016 ATCACATAAGCCTATTAGAGGTCTT
1 ATCACATAAACATATTAGAAGTCTT
519041 ATC
1 ATC
519044 TATAAGTTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (25 bp):
ATCACATAAACATATTAGAAGTCTT
Found at i:529600 original size:7 final size:7
Alignment explanation
Indices: 529588--529631 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
529578 AGGAACAGCT
529588 GGTTAAG
1 GGTTAAG
529595 GGTTAAG
1 GGTTAAG
529602 GGTTAAG
1 GGTTAAG
529609 GGTTAAG
1 GGTTAAG
529616 GGTTAAG
1 GGTTAAG
529623 GGTTAAG
1 GGTTAAG
529630 GG
1 GG
529632 GGGAGCAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.27, C:0.00, G:0.45, T:0.27
Consensus pattern (7 bp):
GGTTAAG
Found at i:541262 original size:2 final size:2
Alignment explanation
Indices: 541255--541283 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
541245 ATTAATCTTA
541255 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
541284 AAAATAAAAA
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:547459 original size:12 final size:14
Alignment explanation
Indices: 547426--547459 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
547416 GCTTTAGTTT
547426 CCATATATGAAAAA
1 CCATATATGAAAAA
547440 CCATATATGAAAAA
1 CCATATATGAAAAA
*
547454 CAATAT
1 CCATAT
547460 CTATGAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (14 bp):
CCATATATGAAAAA
Found at i:550547 original size:30 final size:29
Alignment explanation
Indices: 550506--550577 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 29
550496 TGGTTTTTCG
*
550506 GAAAATAAATTACTGAAATTTGAATTACTA
1 GAAAATGAATTACTGAAATTTGAATT-CTA
* *
550536 GAAAATGAATTACTGGAATTTGAATTCTG
1 GAAAATGAATTACTGAAATTTGAATTCTA
550565 GAAAATGAATTAC
1 GAAAATGAATTAC
550578 ATTTTTAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (29 bp):
GAAAATGAATTACTGAAATTTGAATTCTA
Found at i:550573 original size:14 final size:15
Alignment explanation
Indices: 550505--550577 Score: 78
Period size: 15 Copynumber: 4.9 Consensus size: 15
550495 CTGGTTTTTC
*
550505 GGAAAATAAATTACT
1 GGAAAATGAATTACT
*
550520 -GAAATTTGAATTACT
1 GGAAA-ATGAATTACT
*
550535 AGAAAATGAATTACT
1 GGAAAATGAATTACT
**
550550 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
550564 GGAAAATGAATTAC
1 GGAAAATGAATTAC
550578 ATTTTTAGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
14 16 0.34
15 27 0.57
16 4 0.09
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:550970 original size:25 final size:26
Alignment explanation
Indices: 550915--550971 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
550905 ATATTTTCAA
* *
550915 AATATTAATTAGTATTTTAAATATCT
1 AATATTAAATAGTATTTTAAATATAT
* *
550941 -TTATTAAATATTA-TTTAAATATAT
1 AATATTAAATAGTATTTTAAATATAT
550965 AATATTA
1 AATATTA
550972 TTCATTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
AATATTAAATAGTATTTTAAATATAT
Found at i:550973 original size:28 final size:27
Alignment explanation
Indices: 550941--551018 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 27
550931 TTAAATATCT
* *
550941 TTATTAAATATTATTTAAATATATAATA
1 TTATT-AATATTATTTAAATATAAAAAA
*
550969 TTATT--CATTA-TTAATATATAAAAAA
1 TTATTAATATTATTTAA-ATATAAAAAA
550994 TTATTATATATTA-TTAAA-ATAAAAA
1 TTATTA-ATATTATTTAAATATAAAAA
551019 TATATATCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 4 0.10
25 17 0.40
26 7 0.17
27 1 0.02
28 13 0.31
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TTATTAATATTATTTAAATATAAAAAA
Found at i:551017 original size:25 final size:25
Alignment explanation
Indices: 550941--551093 Score: 75
Period size: 28 Copynumber: 5.8 Consensus size: 25
550931 TTAAATATCT
* * *
550941 TTATTAAATATTATTTAAATATATAA
1 TTATTATATATTATTAAAATA-AAAA
550967 -TATTAT-TCATTATTAATATATAAAAAA
1 TTATTATAT-ATTATTAA-A-AT-AAAAA
550994 TTATTATATATTATTAAAATAAAAA
1 TTATTATATATTATTAAAATAAAAA
* * * *
551019 TATATATCTTATATTACTATAAT-ATAA
1 T-TAT-T-ATATATTATTAAAATAAAAA
*
551046 TTGATTAT-T-TTATATAATATTAAAAA
1 TT-ATTATATATTAT-TAA-AATAAAAA
551072 -TATTATATTATTATTATAAATA
1 TTATTATA-TATTATTA-AAATA
551094 TTAATAAATA
Statistics
Matches: 97, Mismatches: 13, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
23 3 0.03
24 9 0.09
25 22 0.23
26 17 0.18
27 18 0.19
28 27 0.28
29 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (25 bp):
TTATTATATATTATTAAAATAAAAA
Found at i:551031 original size:28 final size:29
Alignment explanation
Indices: 550957--551110 Score: 84
Period size: 28 Copynumber: 5.4 Consensus size: 29
550947 AATATTATTT
550957 AAATATATAATATTATTCATTATTAATATATAA
1 AAATATAT-AT-TTA-T-ATTATTAATATATAA
550990 AAA-AT-TATTATATATTATTAA-A-ATAA
1 AAATATATATT-TATATTATTAATATATAA
* *
551016 AAATATATATCTTATATTACT-ATA-ATAT
1 AAATATATAT-TTATATTATTAATATATAA
*
551044 AATTGAT-TATTT-TA-TA-TAATAT-TAA
1 AAAT-ATATATTTATATTATTAATATATAA
*
551069 AAATAT-TATATTATTATTATAAATAT-TAA
1 AAATATATAT-TTA-TATTATTAATATATAA
551098 TAAATATAT-TTTA
1 -AAATATATATTTA
551111 AATATTTTAA
Statistics
Matches: 100, Mismatches: 6, Indels: 34
0.71 0.04 0.24
Matches are distributed among these distances:
24 6 0.06
25 12 0.12
26 9 0.09
27 8 0.08
28 31 0.31
29 16 0.16
30 11 0.11
31 2 0.02
32 2 0.02
33 3 0.03
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (29 bp):
AAATATATATTTATATTATTAATATATAA
Found at i:551108 original size:53 final size:53
Alignment explanation
Indices: 550955--551110 Score: 131
Period size: 53 Copynumber: 2.8 Consensus size: 53
550945 TAAATATTAT
* * * *
550955 TTAAATATATAATATTATTCATTATTAATATATAAAAAATTATTATATATTATTAAA
1 TTAAAAATATTATATTATT-ATTATAAATAT-TAATAAATTATT-T-TATTATTAAA
* * **
551012 ATAAAAATATATATCTTA-TATTACTATAATA-TAATTGATTATTTTA-TA-TAATA
1 TTAAAAATAT-TATATTATTATTA-TA-AATATTAATAAATTATTTTATTATTAA-A
551065 TTAAAAATATTATATTATTATTATAAATATTAATAAATATATTTTA
1 TTAAAAATATTATATTATTATTATAAATATTAATAAAT-TATTTTA
551111 AATATTTTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
51 4 0.05
52 17 0.21
53 24 0.30
54 2 0.03
55 1 0.01
56 13 0.16
57 10 0.12
58 9 0.11
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (53 bp):
TTAAAAATATTATATTATTATTATAAATATTAATAAATTATTTTATTATTAAA
Found at i:551360 original size:27 final size:27
Alignment explanation
Indices: 551325--551378 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
551315 CGAATTACAT
**
551325 GAAACAAACAAGGGAAAATATTTTCCG
1 GAAACAAACAAGAAAAAATATTTTCCG
* *
551352 GAAATAAACACGAAAAAATATTTTCCG
1 GAAACAAACAAGAAAAAATATTTTCCG
551379 AAAAACGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (27 bp):
GAAACAAACAAGAAAAAATATTTTCCG
Found at i:556721 original size:31 final size:33
Alignment explanation
Indices: 556674--556752 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 33
556664 TTTAAATAGC
*
556674 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAATAATATTTATATAAA
*
556706 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATATTTATATAAA
*
556740 TATTATTTATTTA
1 TATTATTTTTTTA
556753 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:556914 original size:17 final size:17
Alignment explanation
Indices: 556892--556945 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
556882 AATGTTAATA
556892 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
556909 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
556926 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
556943 TTT
1 TTT
556946 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:558506 original size:21 final size:21
Alignment explanation
Indices: 558476--558523 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
558466 GCAGGGGTAC
* *
558476 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
558497 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
558518 ATGCCA
1 ATGCCA
558524 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:558553 original size:21 final size:21
Alignment explanation
Indices: 558527--558599 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
558517 TATGCCATCT
*
558527 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
558548 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
558569 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
558590 CCGCAGGGTT
1 CCGCAGGGTT
558600 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:559171 original size:34 final size:34
Alignment explanation
Indices: 559121--559218 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
559111 AAATGTTTTT
*
559121 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
559155 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
559189 AAAATATAAATTATAGTATTTGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
559219 CATTAAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:559948 original size:127 final size:128
Alignment explanation
Indices: 559618--560871 Score: 1902
Period size: 127 Copynumber: 9.9 Consensus size: 128
559608 TTACCTGATT
* *
559618 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* ****
559683 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGT--CCCCTGAGAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGA-AATAATAGG
* * *
559745 TACTGATATGA-ATAATGT-CCCGAGGGAAATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* * * *** *
559808 ATGACAAAATAATGGAAGGCGCG-CCCCGGGAGCGCGCCTTCAAGTCCCCT-GAGAAATAATAGG
65 CTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
559871 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* * *** *
559935 ATGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCAAGTCCCCT-GAGAAATAATAGG
65 CTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
559998 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* * * *
560062 ATGACAAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTAATGTGAATAGTGAAATAATATG
65 CTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
560126 TACTGATATATCTAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
560191 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGCGAATAGTGAAA-AATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
560253 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
560318 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATTGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
560381 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
560446 TGACAAAATAATGGAAGGCGC-CACCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* * *
560508 TACTGATATATCTATTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATAATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
560573 TG---AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
560633 TACTGATATATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATTATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
560698 TG---AAATAATGGAAGGCGCCCCCCCGTGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
560758 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
560823 TG---AAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
560872 ACTCCGATTA
Statistics
Matches: 1070, Mismatches: 47, Indels: 22
0.94 0.04 0.02
Matches are distributed among these distances:
124 16 0.01
125 290 0.27
126 93 0.09
127 436 0.41
128 235 0.22
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:560185 original size:255 final size:255
Alignment explanation
Indices: 559618--560871 Score: 1868
Period size: 255 Copynumber: 5.0 Consensus size: 255
559608 TTACCTGATT
* *
559618 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* ***
559683 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAG-AATAATAGGTA
66 TGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCGAATGAGAAATAATAGGTA
* * *
559747 CTGATATGA-ATAATGT-CCCGAGGGAAATGAGTGACATAATAGGGCAATGATAACATATTCTAT
130 CTGATAT-ATCTAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* * *** *
559810 GACAAAATAATGGAAGGCGCG-CCCCGGGAGCGCGCCTTCAAGTCCCCT-GAGAAATAATAGG
194 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
559871 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* * ***
559935 ATGACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTA
65 CTGACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTCGAATGAGAAATAATAGGTA
* *
560000 CTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTAT
130 CTGATAT-ATCTAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* * *
560064 GACAAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTAATGTGAATAGTGAAATAATATG
194 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
560126 TACTGATATATCTAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
560191 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATG-CGAATAGTGAAA-AATAGGT
66 TGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCGAAT-GAGAAATAATAGGT
* *
560254 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATATTCTCT
129 ACTGATATATCTAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
560319 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATTGG
194 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
560381 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
560446 TGACAAAATAATGGAAGGCGC-CACCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGT
66 TGACAAAATAATGGAAGGCGCGC-CCCGGGAACGCGCCTTCATGTCGAAT-GAGAAATAATAGGT
* * *
560509 ACTGATATATCTATTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCT
129 ACTGATATATCTAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
560574 G---AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
194 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
560633 TACTGATATATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATTATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
560698 TG---AAATAATGGAAGGCGCCCCCCCGTGAACGCGCCTTCATGT-GAAT-AGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCG-CGCCCCGGGAACGCGCCTTCATGTCGAATGAG--AAATAATAGG
*
560758 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
128 TACTGATATATCTAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
560823 TG---AAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
193 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
560872 ACTCCGATTA
Statistics
Matches: 941, Mismatches: 44, Indels: 35
0.92 0.04 0.03
Matches are distributed among these distances:
248 1 0.00
249 15 0.02
250 145 0.15
251 1 0.00
252 152 0.16
253 110 0.12
254 101 0.11
255 391 0.42
256 25 0.03
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (255 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTCGAATGAGAAATAATAGGTAC
TGATATATCTAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
CAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:560953 original size:8 final size:8
Alignment explanation
Indices: 560942--560982 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
560932 TCACAAACTT
560942 TCAAATTC
1 TCAAATTC
560950 TCAAATTC
1 TCAAATTC
* *
560958 CCAAACTC
1 TCAAATTC
560966 T-AAATTC
1 TCAAATTC
560973 TCAAATTC
1 TCAAATTC
560981 TC
1 TC
560983 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:563908 original size:23 final size:24
Alignment explanation
Indices: 563882--563928 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
563872 TATTTAAATG
*
563882 AATGTTTTTGT-TTCTA-ATAATTT
1 AATGTTATTGTATT-TATATAATTT
563905 AATGTTATTGTATTTATATAATTT
1 AATGTTATTGTATTTATATAATTT
563929 GTCAATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.60
Consensus pattern (24 bp):
AATGTTATTGTATTTATATAATTT
Found at i:571379 original size:22 final size:22
Alignment explanation
Indices: 571330--571382 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
571320 CATATAATTA
571330 AAAATTAGTTAAAAATTTAATGG
1 AAAATTA-TTAAAAATTTAATGG
* *
571353 TAAATTATTTAAAA-TTAATGGG
1 AAAATTATTAAAAATTTAAT-GG
571375 AAAATTAT
1 AAAATTAT
571383 ACCATTGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 15 0.58
23 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (22 bp):
AAAATTATTAAAAATTTAATGG
Found at i:582638 original size:2 final size:2
Alignment explanation
Indices: 582631--582657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
582621 ATGATAATCT
582631 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
582658 GGAAAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:592267 original size:35 final size:36
Alignment explanation
Indices: 592225--592302 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 36
592215 TAACGTTTTA
* *
592225 ATTTAATTTAAATTATTAGTAATATTTAGTT-ATTT
1 ATTTAATTTAAATTATTAGTAATAATTAGTTGATTC
*
592260 ATTTAATTTAAATTATTATTAATAATTAGTTGATTC
1 ATTTAATTTAAATTATTAGTAATAATTAGTTGATTC
592296 ATTTAAT
1 ATTTAAT
592303 GCATGATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 29 0.74
36 10 0.26
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (36 bp):
ATTTAATTTAAATTATTAGTAATAATTAGTTGATTC
Found at i:592278 original size:17 final size:17
Alignment explanation
Indices: 592225--592279 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
592215 TAACGTTTTA
592225 ATTTAATTTAAATTATT
1 ATTTAATTTAAATTATT
* * *
592242 A-GTAATATTTAGTTATTT
1 ATTTAAT-TTAAATTA-TT
592260 ATTTAATTTAAATTATT
1 ATTTAATTTAAATTATT
592277 ATT
1 ATT
592280 AATAATTAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 4 0.14
17 12 0.41
18 9 0.31
19 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
ATTTAATTTAAATTATT
Found at i:600731 original size:18 final size:18
Alignment explanation
Indices: 600708--600745 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
600698 TTAGAGCACT
600708 AGCATTGGGAATATGCGA
1 AGCATTGGGAATATGCGA
600726 AGCATTGGGAATATGCGA
1 AGCATTGGGAATATGCGA
600744 AG
1 AG
600746 GAATTTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.21
Consensus pattern (18 bp):
AGCATTGGGAATATGCGA
Found at i:624653 original size:96 final size:96
Alignment explanation
Indices: 624505--624691 Score: 275
Period size: 96 Copynumber: 1.9 Consensus size: 96
624495 CAGAACGAAA
* *
624505 TTCCTTCTGTCCCTCAACGAGATGCTTACTATCCACCACCTGACCAACCTCAGGAGACTCCAAGT
1 TTCCTTCTGTCCCTCAACGAGATGCTTACTACCCACCACCTGACCAAACTCAGGAGACTCCAAGT
* * *
624570 CAGCAATTCCCGATGCCTCCTACTCATCAAG
66 CAACAATTCACAATGCCTCCTACTCATCAAG
* * * * *
624601 TTCCTTCTGTCTCTCAGCGAGATGCTTACTACCCACCTCCTGGCCAAACTCAGGAGATTCCAAGT
1 TTCCTTCTGTCCCTCAACGAGATGCTTACTACCCACCACCTGACCAAACTCAGGAGACTCCAAGT
*
624666 CAACAATTCACAATGCCTCCTGCTCA
66 CAACAATTCACAATGCCTCCTACTCA
624692 GCAGCCGCAG
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (96 bp):
TTCCTTCTGTCCCTCAACGAGATGCTTACTACCCACCACCTGACCAAACTCAGGAGACTCCAAGT
CAACAATTCACAATGCCTCCTACTCATCAAG
Found at i:628218 original size:19 final size:18
Alignment explanation
Indices: 628165--628224 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
628155 AGTACCCGAT
*
628165 TAATTTTTTATATATATA
1 TAATTATTTATATATATA
* *
628183 TAATTATATA-AAATATAA
1 TAATTATTTATATATAT-A
628201 TGAATTATTTATAT-TATA
1 T-AATTATTTATATATATA
628219 T-ATTAT
1 TAATTAT
628225 ATATTTGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.15
17 5 0.15
18 12 0.35
19 11 0.32
20 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTTATATATATA
Found at i:636599 original size:31 final size:31
Alignment explanation
Indices: 636564--636644 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
636554 AAACTAACTA
**
636564 TTTGGTCACCTGTCTATTACTAAATTTATGT
1 TTTGGTCACCCATCTATTACTAAATTTATGT
636595 TTTGGTCACCCATCTATTACTAAATTTATGT
1 TTTGGTCACCCATCTATTACTAAATTTATGT
* *
636626 TTTGGTCACTCAACTATTA
1 TTTGGTCACCCATCTATTA
636645 TTTTTTTTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.46
Consensus pattern (31 bp):
TTTGGTCACCCATCTATTACTAAATTTATGT
Found at i:637122 original size:23 final size:24
Alignment explanation
Indices: 637096--637145 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
637086 AAACAAGAGC
* * *
637096 AAACCA-ACATGTTGACAAACGTT
1 AAACCAGACATATTCACAAACATT
637119 AAA-CAGACATATTCACAAACATT
1 AAACCAGACATATTCACAAACATT
637142 AAAC
1 AAAC
637146 GAGTTGCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.50, C:0.22, G:0.08, T:0.20
Consensus pattern (24 bp):
AAACCAGACATATTCACAAACATT
Found at i:637672 original size:2 final size:2
Alignment explanation
Indices: 637665--637692 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
637655 GTTCCCACCA
637665 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
637693 GCTTATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:641410 original size:2 final size:2
Alignment explanation
Indices: 641403--641430 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
641393 TTACCTAACC
641403 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
641431 TCTTTTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:642015 original size:156 final size:156
Alignment explanation
Indices: 641709--642237 Score: 715
Period size: 157 Copynumber: 3.4 Consensus size: 156
641699 TATGGCATAT
* ** * * *
641709 GAGCATGTGGTTCAAATTTGGTAAAAAGGGGACTTAAAATAAAAGATGAATTGAAGAAATAAAGA
1 GAGCATGCGGTTCAAATTTGGTAAAAA-AAGACTTAAAATAAAGGATAAATTGAAGAAATAAGGA
* * *
641774 AGATATGAAAAGTAGAGGGATTAAATTGAAAAATAGAAATTTTATTATCAAAAAGAGGAATTGAA
65 AGATATGAAAAGTTGAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAA
*
641839 AGTACACATGTATTTTATGATAGTTTAG
130 AGTACACATGTATTCTATGAT-GTTTAG
* *
641867 GAGCATACGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAATGATAAATTGAAGAAATAAGGAA
1 GAGCATGCGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAGGATAAATTGAAGAAATAAGGAA
* * *
641932 TATATGAAAAGTTGAGGGACTGAAA-T-AAAAATAGAAAATTTATTATGAAAACGAGGAATTGAA
66 GATATGAAAAGTTGAGGGACT-AAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAA
641995 AGTACACATGTATTCTATGATGATTTAG
130 AGTACACATGTATTCTATGATG-TTTAG
* * * * *
642023 GAGCATGTGGTTCAAATTTGGTAAAACACAGATTTAAGATAAAGGATGAATTGAA-AATATAAGG
1 GAGCATGCGGTTCAAATTTGGTAAAA-AAAGACTTAAAATAAAGGATAAATTGAAGAA-ATAAGG
* * *
642087 AAGATATGAAAAGTTGAGGGACTAAATTGAAAAATATAAAA-TTATTATCAAAATGATGAATTGA
64 AAGATATGAAAAGTTGAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGA
642151 AAGTACACATGTATTCTATGATTGTTTAG
129 AAGTACACATGTATTCTATGA-TGTTTAG
* ** * *
642180 GAGCATGCGGTTAAAATTTGGTAAAAATGGACTTAAAATGAAGGAGAAATTGAAGAAA
1 GAGCATGCGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAGGATAAATTGAAGAAA
642238 AAATGAAATC
Statistics
Matches: 328, Mismatches: 35, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
155 1 0.00
156 110 0.34
157 176 0.54
158 41 0.12
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.28
Consensus pattern (156 bp):
GAGCATGCGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAGGATAAATTGAAGAAATAAGGAA
GATATGAAAAGTTGAGGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAGAGGAATTGAAA
GTACACATGTATTCTATGATGTTTAG
Found at i:663612 original size:150 final size:149
Alignment explanation
Indices: 663222--663598 Score: 418
Period size: 150 Copynumber: 2.5 Consensus size: 149
663212 CCGAATTGGT
* ** * * * **
663222 GGGGAAGATTTTGGCAGCAGCAAACGAATCTTCCTTCAAACGTCCCGTTGATGATTGTAAGAGTT
1 GGGGAAGATTTTGACAGTGGCAAACAAATCTTCCTTCAAACATCCCATTGATGA-TCCAAGAGTT
* * * *
663287 CCGATTCCATTGCTTCATCGGAATATAGAGCAACTCTGCAGTGTGTACATTATTATGATTCAAGA
65 CCAATTCCATTGCTTCATCGGAATATAGAACAACTCTGCAGTGTGCACATTATTATCATTCAAGA
* *
663352 AAGGGGATATCCAAATCAGC
130 AAGGGGAAATCCAAAGCAGC
* * * * * * * *
663372 AGGAAAGATTTTGACAATGACAAGCAAAGCTTCCTCCAAGCATCCCATTGATGATCCTAAGAGTT
1 GGGGAAGATTTTGACAGTGGCAAACAAATCTTCCTTCAAACATCCCATTGATGATCC-AAGAGTT
* * * *
663437 CTAGTTCCATTGCTTCACCGGAATAT-GAAACAACTGTGCA-TGGTGCACATTATTATCATTCGA
65 CCAATTCCATTGCTTCATCGGAATATAG-AACAACTCTGCAGT-GTGCACATTATTATCATTC-A
*
663500 A-TAAGGGGAAATCCAAAGCAGC
127 AGAAAGGGGAAATCCAAAGCAGC
* *
663522 GGGGAAGATTTTGACAGTGGGAAACAAATCTTCATTCAAACATCCCATTGATGATCACAAGAGTT
1 GGGGAAGATTTTGACAGTGGCAAACAAATCTTCCTTCAAACATCCCATTGATGATC-CAAGAGTT
663587 CCAATTCCATTG
65 CCAATTCCATTG
663599 ATTCGTTGCA
Statistics
Matches: 183, Mismatches: 39, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
149 3 0.02
150 177 0.97
151 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (149 bp):
GGGGAAGATTTTGACAGTGGCAAACAAATCTTCCTTCAAACATCCCATTGATGATCCAAGAGTTC
CAATTCCATTGCTTCATCGGAATATAGAACAACTCTGCAGTGTGCACATTATTATCATTCAAGAA
AGGGGAAATCCAAAGCAGC
Found at i:663661 original size:150 final size:150
Alignment explanation
Indices: 663258--663662 Score: 352
Period size: 150 Copynumber: 2.7 Consensus size: 150
663248 AATCTTCCTT
* * ** * * * * * ** *
663258 CAAACGTCCCGTTGATGATTGTAAGAGTTCCGATTCCATTGCTTCATCGGAATATAGAGCAACTC
1 CAAACATCCCATTGATGATCCTAAGAGTTCCAATTCCATTGATTCACCGCAATATAAAAAAACTG
* * * * *
663323 TGCA-GTGTGTACATTATTATGATTCAAGAAAGGGGATATCCAAATCAGCAGGAAAGATTTTGAC
66 TGCATG-GTGAACAATATTATGATTCGAGAAAGGGGAAATCCAAAGCAGCAGGAAAGATTTTGAC
* *
663387 AATGACAAGCAAAGCTTCCTC
130 AATGACAAACAAAGCTTCATC
* * * * * * *
663408 CAAGCATCCCATTGATGATCCTAAGAGTTCTAGTTCCATTGCTTCACCGGAATATGAAACAACTG
1 CAAACATCCCATTGATGATCCTAAGAGTTCCAATTCCATTGATTCACCGCAATATAAAAAAACTG
* * * * *
663473 TGCATGGTGCACATTATTATCATTCGA-ATAAGGGGAAATCCAAAGCAGCGGGGAAGATTTTGAC
66 TGCATGGTGAACAATATTATGATTCGAGA-AAGGGGAAATCCAAAGCAGCAGGAAAGATTTTGAC
* ** * *
663537 AGTGGGAAACAAATCTTCATT
130 AATGACAAACAAAGCTTCATC
***
663558 CAAACATCCCATTGATGATCAC-AAGAGTTCCAATTCCATTGATTCGTTGCAATATAAAAAAAAC
1 CAAACATCCCATTGATGATC-CTAAGAGTTCCAATTCCATTGATTCACCGCAATAT-AAAAAAAC
* * *
663622 -GTGGC-TGGTGAACAATATTATGATTTGAGCAAGGTGAAATC
64 TGT-GCATGGTGAACAATATTATGATTCGAGAAAGGGGAAATC
663663 AGAACCACTG
Statistics
Matches: 206, Mismatches: 43, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
149 1 0.00
150 195 0.95
151 10 0.05
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (150 bp):
CAAACATCCCATTGATGATCCTAAGAGTTCCAATTCCATTGATTCACCGCAATATAAAAAAACTG
TGCATGGTGAACAATATTATGATTCGAGAAAGGGGAAATCCAAAGCAGCAGGAAAGATTTTGACA
ATGACAAACAAAGCTTCATC
Found at i:667632 original size:2 final size:2
Alignment explanation
Indices: 667625--667661 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
667615 GCCGCAATTT
667625 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
667662 ACATTTAAAA
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:671033 original size:26 final size:27
Alignment explanation
Indices: 671004--671064 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
670994 ATTAAATCTT
* *
671004 TTTATATTTTTAATTTTGTAAA-AAAA
1 TTTATAATTTAAATTTTGTAAAGAAAA
*
671030 TTTATAAATTTAAATTTTTTAAAGAAAA
1 TTTAT-AATTTAAATTTTGTAAAGAAAA
*
671058 TATATAA
1 TTTATAA
671065 ATATCTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 5 0.17
27 16 0.55
28 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (27 bp):
TTTATAATTTAAATTTTGTAAAGAAAA
Found at i:671282 original size:80 final size:80
Alignment explanation
Indices: 671143--671307 Score: 226
Period size: 80 Copynumber: 2.1 Consensus size: 80
671133 GATCAAATAT
* * *
671143 ACATT-TCAATAATATTTTATTCTTTTAACCAAACACGTTAATCTTACCTTACTGCTAAACCAAC
1 ACATTCTCAATAATATTTTATTCTTTTAACCAAACACGGTAATCTTACATTACTACTAAACCAAC
671207 CAAACACAAAATACA
66 CAAACACAAAATACA
* * *
671222 ACATTCTCAATAATCTTTTATTCTTTTAACCAAATACGGTAATCTTACATT-CATATTAAACCAA
1 ACATTCTCAATAATATTTTATTCTTTTAACCAAACACGGTAATCTTACATTAC-TACTAAACCAA
* *
671286 CCAAATATAAAATACA
65 CCAAACACAAAATACA
*
671302 ATATTC
1 ACATTC
671308 CTAGTAATTT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
79 6 0.08
80 69 0.92
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.34
Consensus pattern (80 bp):
ACATTCTCAATAATATTTTATTCTTTTAACCAAACACGGTAATCTTACATTACTACTAAACCAAC
CAAACACAAAATACA
Found at i:675083 original size:29 final size:29
Alignment explanation
Indices: 675051--675110 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
675041 TACATGATAA
* *
675051 AAGGAGATCGCCATATAATCCGGGCAACC
1 AAGGAGATCCCCATACAATCCGGGCAACC
*
675080 AAGGAGATCCCCATACAATCCGGGCGACC
1 AAGGAGATCCCCATACAATCCGGGCAACC
675109 AA
1 AA
675111 TGAGTGATGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.30, G:0.23, T:0.12
Consensus pattern (29 bp):
AAGGAGATCCCCATACAATCCGGGCAACC
Found at i:675156 original size:40 final size:40
Alignment explanation
Indices: 675101--675183 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
675091 CATACAATCC
* *
675101 GGGCGACCAATGAGTGATGCATGTGAGAGCTGTGAGTTGT
1 GGGCGACCAAGGAGTGATGCATGTGAGAGCTGTGAGCTGT
675141 GGGCGACCAAGGAGTGATGCATGTGAGAGCTGTGAGCTGT
1 GGGCGACCAAGGAGTGATGCATGTGAGAGCTGTGAGCTGT
675181 GGG
1 GGG
675184 ATGCATGTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.22, C:0.13, G:0.43, T:0.22
Consensus pattern (40 bp):
GGGCGACCAAGGAGTGATGCATGTGAGAGCTGTGAGCTGT
Found at i:676322 original size:21 final size:21
Alignment explanation
Indices: 676289--676333 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
676279 GATTTACATA
676289 TTCGCATTACGATAGTCCAAG
1 TTCGCATTACGATAGTCCAAG
* * *
676310 TTCGCGTTGCGATAGTCGAAG
1 TTCGCATTACGATAGTCCAAG
676331 TTC
1 TTC
676334 TTCACTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTACGATAGTCCAAG
Found at i:678362 original size:382 final size:383
Alignment explanation
Indices: 677656--678428 Score: 1485
Period size: 382 Copynumber: 2.0 Consensus size: 383
677646 GAGATTACGT
677656 ATTGCCACTGTTACATCTTAAAGGAACTAAAATTGAAATTTAGATATTTTCTCATTTAATATACA
1 ATTGCCACTGTTACATCTTAAAGGAACTAAAATTGAAATTTAGATATTTTCTCATTTAATATACA
677721 TTAATTTATTGAGATTGAAAATTATTAAGATCGTACATATACATTGGGTGTTAGATGAATATTAA
66 TTAATTTATTGAGATTGAAAATTATTAAGATCGTACATATACATTGGGTGTTAGATGAATATTAA
677786 CGTTTAAAACTTTCATATTATAGATAAAGATCAATTTGAGGCAATCTGATATATACAGTTTTAAG
131 CGTTTAAAACTTTCATATTATAGATAAAGATCAATTTGAGGCAATCTGATATATACAGTTTTAAG
*
677851 TGTTGCGTTAATTTTTAAAAATATTTATTTATTTTTTGGGATAGAGATTAACCAAAACCCGTAAG
196 TGTTGCGTTAATTTTTAAAAATATTTATTTATTTTTTGGGATAAAGATTAACCAAAACCCGTAAG
*
677916 GATCCGTAAGGGATAGACATAGAGACAAAAAAATCCCCGAAACATATAATGAAAATTCCCCAAAA
261 GATCCGTAAAGGATAGACATAGAGACAAAAAAATCCCCGAAACATATAATGAAAATTCCCCAAAA
*
677981 CCCTACCTGCAAGTATTGGGGATTGAATGAGTAATGCAAAACCGTCCCAACCCA-CCC
326 CCCTACCCGCAAGTATTGGGGATTGAATGAGTAATGCAAAACCGTCCCAACCCACCCC
*
678038 ATTGCCACTGTTACATCTTAAAGGAACTAAAATTGAAGTTTAGATATTTTCTCATTTAATATACA
1 ATTGCCACTGTTACATCTTAAAGGAACTAAAATTGAAATTTAGATATTTTCTCATTTAATATACA
678103 TTAATTTATTGAGATTGAAAATTATTAAGATCGTACATATACATTGGGTGTTAGATGAATATTAA
66 TTAATTTATTGAGATTGAAAATTATTAAGATCGTACATATACATTGGGTGTTAGATGAATATTAA
678168 CGTTTAAAACTTTCATATTATAGATAAAGATCAATTTGAGGCAATCTGATATATACAGTTTTAAG
131 CGTTTAAAACTTTCATATTATAGATAAAGATCAATTTGAGGCAATCTGATATATACAGTTTTAAG
*
678233 TGTTGCGTTAATTTTTAAAAATATTTATTTATTTTTTGGGATAAAGATTAACCAAAACCCGTAGG
196 TGTTGCGTTAATTTTTAAAAATATTTATTTATTTTTTGGGATAAAGATTAACCAAAACCCGTAAG
678298 GATCCGTAAAGGATAGACATAGAGACAAAAAAATCCCCGAAACATATAATGAAAATTCCCCAAAA
261 GATCCGTAAAGGATAGACATAGAGACAAAAAAATCCCCGAAACATATAATGAAAATTCCCCAAAA
678363 CCCTACCCGCAAGTATTGGGGATTGAATGAGTAATGCAAAACCGTCCCAACCCACCCC
326 CCCTACCCGCAAGTATTGGGGATTGAATGAGTAATGCAAAACCGTCCCAACCCACCCC
*
678421 GTTGCCAC
1 ATTGCCAC
678429 CCCTAGACGT
Statistics
Matches: 384, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
382 374 0.97
383 10 0.03
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (383 bp):
ATTGCCACTGTTACATCTTAAAGGAACTAAAATTGAAATTTAGATATTTTCTCATTTAATATACA
TTAATTTATTGAGATTGAAAATTATTAAGATCGTACATATACATTGGGTGTTAGATGAATATTAA
CGTTTAAAACTTTCATATTATAGATAAAGATCAATTTGAGGCAATCTGATATATACAGTTTTAAG
TGTTGCGTTAATTTTTAAAAATATTTATTTATTTTTTGGGATAAAGATTAACCAAAACCCGTAAG
GATCCGTAAAGGATAGACATAGAGACAAAAAAATCCCCGAAACATATAATGAAAATTCCCCAAAA
CCCTACCCGCAAGTATTGGGGATTGAATGAGTAATGCAAAACCGTCCCAACCCACCCC
Found at i:685370 original size:60 final size:60
Alignment explanation
Indices: 685246--685370 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
685236 AACGAGTGAC
* *** * * * *
685246 CATTTTGTAACTTTTAATAGTTGAGGGACTCAATAAAGCAAGTTCCTATAGTCGAGGGAT
1 CATTTTATAACTTTTAATAGCCAAGGGACTCAATAAAGCAAGTTCCTATAATCAAAGGAA
*
685306 CATTTTATAACTTTTAATAGCCAAGGGACTTAATAAAGCAA-TATCCTATAATCAAAGGAA
1 CATTTTATAACTTTTAATAGCCAAGGGACTCAATAAAGCAAGT-TCCTATAATCAAAGGAA
685366 CATTT
1 CATTT
685371 ATGTATTTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 54 0.98
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGCCAAGGGACTCAATAAAGCAAGTTCCTATAATCAAAGGAA
Found at i:691461 original size:22 final size:22
Alignment explanation
Indices: 691414--691461 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
691404 TCATGTCACG
*
691414 TTTATGACACGTTTTCATCTGCC
1 TTTATGACACCTTTT-ATCTGCC
*
691437 TTTATGACACACTTTT-TCTGTC
1 TTTATGACAC-CTTTTATCTGCC
691459 TTT
1 TTT
691462 TGGCATGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 10 0.45
24 4 0.18
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.50
Consensus pattern (22 bp):
TTTATGACACCTTTTATCTGCC
Found at i:693482 original size:45 final size:47
Alignment explanation
Indices: 693394--693485 Score: 161
Period size: 45 Copynumber: 2.0 Consensus size: 47
693384 ACGAACATAT
693394 TTTTCAAACTTTGCATCCATAATGATTTCTAAATTAAATAAAACTTCC
1 TTTTCAAACTTTGCATCCATAA-GATTTCTAAATTAAATAAAACTTCC
693442 TTTTCAAACTTTGCATCCAT-A-ATTTCTAAATTAAATAAAACTTC
1 TTTTCAAACTTTGCATCCATAAGATTTCTAAATTAAATAAAACTTC
693486 AAACTCCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
45 23 0.52
47 1 0.02
48 20 0.45
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.40
Consensus pattern (47 bp):
TTTTCAAACTTTGCATCCATAAGATTTCTAAATTAAATAAAACTTCC
Found at i:693869 original size:30 final size:30
Alignment explanation
Indices: 693835--693909 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
693825 TCTATCACTC
693835 GTCTTCCTAAAGATGTCATATATTTTGCGT
1 GTCTTCCTAAAGATGTCATATATTTTGCGT
693865 GTCTTCCTAAAGATGTCATATATTTTGCGT
1 GTCTTCCTAAAGATGTCATATATTTTGCGT
693895 GTCTTCCTAAAGATG
1 GTCTTCCTAAAGATG
693910 ATATGTCTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (30 bp):
GTCTTCCTAAAGATGTCATATATTTTGCGT
Found at i:695411 original size:28 final size:28
Alignment explanation
Indices: 695329--695416 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
695319 TTGATTTATT
695329 ATTTTTGATTCAATAGTATTTTTCATCA
1 ATTTTTGATTCAATAGTATTTTTCATCA
* * * * **
695357 A-TTTAG-TTCAGGTTGCTCA-ATGACATCA
1 ATTTTTGATTCA-ATAG-T-ATTTTTCATCA
695385 ATTTTTGATTCAATAGTATTTTTCATCA
1 ATTTTTGATTCAATAGTATTTTTCATCA
695413 ATTT
1 ATTT
695417 AGTTCAGGCT
Statistics
Matches: 42, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
26 4 0.10
27 7 0.17
28 20 0.48
29 7 0.17
30 4 0.10
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.49
Consensus pattern (28 bp):
ATTTTTGATTCAATAGTATTTTTCATCA
Found at i:695415 original size:56 final size:56
Alignment explanation
Indices: 695329--695442 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
695319 TTGATTTATT
*
695329 ATTTTTGATTCAATAGTATTTTTCATCAATTTAGTTCAGGTTGCTCAATGACATCA
1 ATTTTTGATTCAATAGTATTTTTCATCAATTTAGTTCAGGCTGCTCAATGACATCA
695385 ATTTTTGATTCAATAGTATTTTTCATCAATTTAGTTCAGGCTGCTCAATGACATCA
1 ATTTTTGATTCAATAGTATTTTTCATCAATTTAGTTCAGGCTGCTCAATGACATCA
695441 AT
1 AT
695443 GTTTAATATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (56 bp):
ATTTTTGATTCAATAGTATTTTTCATCAATTTAGTTCAGGCTGCTCAATGACATCA
Found at i:707731 original size:20 final size:18
Alignment explanation
Indices: 707702--707756 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
707692 TATTGGACCT
*
707702 AAAGTATCGAAACTTTAATG
1 AAAGTATCGAAACTTT--GG
*
707722 AAAGTTTCGAAACTATTGG
1 AAAGTATCGAAACT-TTGG
707741 AAAGTATCGAAACTTT
1 AAAGTATCGAAACTTT
707757 TCGGGAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 13 0.42
21 2 0.06
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (18 bp):
AAAGTATCGAAACTTTGG
Found at i:709260 original size:15 final size:17
Alignment explanation
Indices: 709224--709258 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
709214 TATGAGGTGC
*
709224 AAATATTATTATTGTAA
1 AAATATAATTATTGTAA
709241 AAATATAATTATT-TAA
1 AAATATAATTATTGTAA
709257 AA
1 AA
709259 TAATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATAATTATTGTAA
Found at i:710115 original size:2 final size:2
Alignment explanation
Indices: 710108--710137 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
710098 CTATTTTATC
710108 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
710138 CCTACTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:710128 original size:13 final size:13
Alignment explanation
Indices: 710110--710135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
710100 ATTTTATCAT
710110 ATATATATATATA
1 ATATATATATATA
710123 ATATATATATATA
1 ATATATATATATA
710136 TACCTACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:710128 original size:15 final size:15
Alignment explanation
Indices: 710108--710137 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
710098 CTATTTTATC
710108 ATATATATATATATA
1 ATATATATATATATA
710123 ATATATATATATATA
1 ATATATATATATATA
710138 CCTACTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:717040 original size:29 final size:28
Alignment explanation
Indices: 716982--717042 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
716972 GAAACATTTC
* *
716982 AAAGAAAAATAACCCCTTTTTTTTATAG
1 AAAGAAAAATAACCCCTTTTATCTATAG
717010 AAAGAAAAATAACCCCTTAATTATCT-TAG
1 AAAGAAAAATAACCCCTT--TTATCTATAG
717039 AAAG
1 AAAG
717043 CACAAGAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 18 0.62
29 7 0.24
30 4 0.14
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.30
Consensus pattern (28 bp):
AAAGAAAAATAACCCCTTTTATCTATAG
Found at i:730259 original size:4 final size:4
Alignment explanation
Indices: 730238--730287 Score: 75
Period size: 4 Copynumber: 12.2 Consensus size: 4
730228 TGTAGAATTT
730238 TTAG TTAG TATA- TATAG TTAG TTAG TTAG TTAG TTAG TTAG TTAG TTAG
1 TTAG TTAG T-TAG T-TAG TTAG TTAG TTAG TTAG TTAG TTAG TTAG TTAG
730287 T
1 T
730288 GTGTTTCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
4 41 0.93
5 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TTAG
Found at i:731397 original size:29 final size:30
Alignment explanation
Indices: 731351--731421 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
731341 TTTTCTAGTG
**
731351 ACTAAAATGTAAGTTTTGAAA-GTTT-GGT
1 ACTAAAATGTAAACTTTGAAACGTTTAGGT
*
731379 ACCTAAAGTGTAAACTTTGAAACGTTTAGGT
1 A-CTAAAATGTAAACTTTGAAACGTTTAGGT
731410 ACTAAAATGTAA
1 ACTAAAATGTAA
731422 TTTTGATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 17 0.47
30 14 0.39
31 4 0.11
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (30 bp):
ACTAAAATGTAAACTTTGAAACGTTTAGGT
Found at i:733641 original size:7 final size:7
Alignment explanation
Indices: 733629--733653 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
733619 TGAGTACTTT
733629 TCAGTTA
1 TCAGTTA
733636 TCAGTTA
1 TCAGTTA
733643 TCAGTTA
1 TCAGTTA
733650 TCAG
1 TCAG
733654 ATCAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (7 bp):
TCAGTTA
Found at i:742392 original size:21 final size:20
Alignment explanation
Indices: 742362--742425 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
742352 TAGGGGATAT
*
742362 TATCTATTTAGTACCTAAAC
1 TATCAATTTAGTACCTAAAC
* * * *
742382 TATCAGCTTTAATACATAAAT
1 TATCA-ATTTAGTACCTAAAC
* *
742403 TTTCAATTTTGTACCTAAAC
1 TATCAATTTAGTACCTAAAC
742423 TAT
1 TAT
742426 AACATTTAGA
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (20 bp):
TATCAATTTAGTACCTAAAC
Found at i:742629 original size:37 final size:37
Alignment explanation
Indices: 742584--742659 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 37
742574 AATTTAATGT
* * *
742584 TAAATTTTTAACG-GGATATTAAAATGAAACAAAAAC
1 TAAATTTTTAACGAAGACACTAAAATGAAACAAAAAC
742620 TAAAGTTTTTAACGACAGACACTAAAATGAAACAAAAAC
1 TAAA-TTTTTAACGA-AGACACTAAAATGAAACAAAAAC
742659 T
1 T
742660 GAACTTTAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 4 0.12
37 9 0.26
39 21 0.62
ACGTcount: A:0.53, C:0.12, G:0.11, T:0.25
Consensus pattern (37 bp):
TAAATTTTTAACGAAGACACTAAAATGAAACAAAAAC
Found at i:749519 original size:10 final size:10
Alignment explanation
Indices: 749504--749586 Score: 67
Period size: 10 Copynumber: 7.7 Consensus size: 10
749494 AATATATTTT
749504 TTCATTTATG
1 TTCATTTATG
*
749514 TTCATTTACG
1 TTCATTTATG
*
749524 TTCGTTTATG
1 TTCATTTATG
749534 TTCATTTATTGTG
1 TTCATTTA---TG
* *
749547 TTCGTTTATA
1 TTCATTTATG
749557 TTCATTTATTGTG
1 TTCATTTA---TG
*
749570 TTCGTTTATG
1 TTCATTTATG
749580 TTCATTT
1 TTCATTT
749587 GTATTCGTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
10 40 0.70
13 17 0.30
ACGTcount: A:0.16, C:0.11, G:0.13, T:0.60
Consensus pattern (10 bp):
TTCATTTATG
Found at i:749553 original size:23 final size:23
Alignment explanation
Indices: 749508--749664 Score: 161
Period size: 23 Copynumber: 7.2 Consensus size: 23
749498 TATTTTTTCA
*
749508 TTTATGTTCATTTA---CGTTCG
1 TTTATGTTCATTTATTGTGTTCG
749528 TTTATGTTCATTTATTGTGTTCG
1 TTTATGTTCATTTATTGTGTTCG
*
749551 TTTATATTCATTTATTGTGTTCG
1 TTTATGTTCATTTATTGTGTTCG
*
749574 TTTATGTTCA--T-TTGTATTCG
1 TTTATGTTCATTTATTGTGTTCG
* * *
749594 TTTACGTTCGTTTATTGTGTTCT
1 TTTATGTTCATTTATTGTGTTCG
* *
749617 TTTATGTT--TAT-TTGTATTCG
1 TTTATGTTCATTTATTGTGTTCG
* *
749637 TTTACGTTCGTTTATTGTGTTCG
1 TTTATGTTCATTTATTGTGTTCG
749660 TTTAT
1 TTTAT
749665 CATTTACATG
Statistics
Matches: 112, Mismatches: 16, Indels: 15
0.78 0.11 0.10
Matches are distributed among these distances:
20 44 0.39
21 3 0.03
22 3 0.03
23 62 0.55
ACGTcount: A:0.13, C:0.10, G:0.16, T:0.61
Consensus pattern (23 bp):
TTTATGTTCATTTATTGTGTTCG
Found at i:749594 original size:43 final size:43
Alignment explanation
Indices: 749523--749664 Score: 203
Period size: 43 Copynumber: 3.2 Consensus size: 43
749513 GTTCATTTAC
* ** *
749523 GTTCGTTTATGTTCATTTATTGTGTTCGTTTATATTCATTTATTGT
1 GTTCGTTTATGTTCA--T-TTGTATTCGTTTACGTTCGTTTATTGT
749569 GTTCGTTTATGTTCATTTGTATTCGTTTACGTTCGTTTATTGT
1 GTTCGTTTATGTTCATTTGTATTCGTTTACGTTCGTTTATTGT
* *
749612 GTTCTTTTATGTTTATTTGTATTCGTTTACGTTCGTTTATTGT
1 GTTCGTTTATGTTCATTTGTATTCGTTTACGTTCGTTTATTGT
749655 GTTCGTTTAT
1 GTTCGTTTAT
749665 CATTTACATG
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
43 73 0.82
44 1 0.01
46 15 0.17
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.61
Consensus pattern (43 bp):
GTTCGTTTATGTTCATTTGTATTCGTTTACGTTCGTTTATTGT
Found at i:752846 original size:21 final size:21
Alignment explanation
Indices: 752799--752847 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
752789 AAGCGTTAAT
* *
752799 TAAAATGTTATTTTTTCTATC
1 TAAAATGTTAATTTTACTATC
752820 -AGAAATGTTAATTTTACTATC
1 TA-AAATGTTAATTTTACTATC
752841 TAAAATG
1 TAAAATG
752848 AATATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (21 bp):
TAAAATGTTAATTTTACTATC
Found at i:753476 original size:2 final size:2
Alignment explanation
Indices: 753471--753511 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
753461 ACTACTACTT
753471 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
753512 TCATTGATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:754056 original size:44 final size:44
Alignment explanation
Indices: 754006--754096 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
753996 TATACAAACT
*
754006 ATTAATATTAAAATCAAGTTTAAGATAATGATGATTATTTATAA
1 ATTAATATTAAAACCAAGTTTAAGATAATGATGATTATTTATAA
* *
754050 ATTAATATTAAAACCAAGTTTAAGGTGATGATGATTATTTATAA
1 ATTAATATTAAAACCAAGTTTAAGATAATGATGATTATTTATAA
754094 ATT
1 ATT
754097 GACAAAATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (44 bp):
ATTAATATTAAAACCAAGTTTAAGATAATGATGATTATTTATAA
Found at i:760485 original size:39 final size:37
Alignment explanation
Indices: 760430--760511 Score: 128
Period size: 39 Copynumber: 2.2 Consensus size: 37
760420 AAAGAACTAA
760430 CACTCATAAAAGAAAATGCAAATACAACCATAGAATG
1 CACTCATAAAAGAAAATGCAAATACAACCATAGAATG
* *
760467 CACTCATATATAAGAAAATGCAAATGCAACCGTAGAATG
1 CACTCATA-A-AAGAAAATGCAAATACAACCATAGAATG
760506 CACTCA
1 CACTCA
760512 CTTGGAAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 8 0.20
38 1 0.02
39 32 0.78
ACGTcount: A:0.49, C:0.21, G:0.12, T:0.18
Consensus pattern (37 bp):
CACTCATAAAAGAAAATGCAAATACAACCATAGAATG
Found at i:762822 original size:51 final size:51
Alignment explanation
Indices: 762765--762862 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 51
762755 TTTAATATAT
* * * *
762765 TTTTTA-TAAATAAAAATATATATTTAATAAGTTAAGACAAAGAATATTTTA
1 TTTTTATTAAATAAAAA-ATATATTTAAGAAATTAAAACAAAAAATATTTTA
** *
762816 TTTTTATTTTATTAAAAATATATTTAAGAAATTAAAACAAAAAATAT
1 TTTTTATTAAATAAAAAATATATTTAAGAAATTAAAACAAAAAATAT
762863 ATATTTAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
51 32 0.82
52 7 0.18
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (51 bp):
TTTTTATTAAATAAAAAATATATTTAAGAAATTAAAACAAAAAATATTTTA
Found at i:762859 original size:27 final size:28
Alignment explanation
Indices: 762829--762884 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
762819 TTATTTTATT
762829 AAAA-ATATATTTAAGAAATTAAAACAA
1 AAAATATATATTTAAGAAATTAAAACAA
* * *
762856 AAAATATATATTTAATAATTTAAGACAA
1 AAAATATATATTTAAGAAATTAAAACAA
762884 A
1 A
762885 TATAGAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (28 bp):
AAAATATATATTTAAGAAATTAAAACAA
Found at i:763648 original size:17 final size:17
Alignment explanation
Indices: 763614--763650 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
763604 CATTAATTAA
* *
763614 AAAATTATTTAGTTATT
1 AAAATTATTTAATAATT
763631 AAAATTATTTAATAATT
1 AAAATTATTTAATAATT
763648 AAA
1 AAA
763651 TATTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AAAATTATTTAATAATT
Found at i:765748 original size:22 final size:21
Alignment explanation
Indices: 765716--765760 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
765706 TTTTTAATAA
765716 TTTTGCCTTTATAACATGTCTT
1 TTTTGCCTTTATAACATGT-TT
* *
765738 TTTTGCTTTTATGACATGTTT
1 TTTTGCCTTTATAACATGTTT
765759 TT
1 TT
765761 CATCTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.60
Consensus pattern (21 bp):
TTTTGCCTTTATAACATGTTT
Found at i:770178 original size:20 final size:20
Alignment explanation
Indices: 770153--770196 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
770143 CAATCTTCTT
770153 TTTAATTT-AAAATTTTAACA
1 TTTAATTTAAAAATTTTAA-A
770173 TTTAATTTAAAAATTTTAAA
1 TTTAATTTAAAAATTTTAAA
770193 TTTA
1 TTTA
770197 TAATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAATTTAAAAATTTTAAA
Found at i:771561 original size:27 final size:28
Alignment explanation
Indices: 771531--771622 Score: 125
Period size: 28 Copynumber: 3.4 Consensus size: 28
771521 ATTTATGTAT
771531 CTAAAGTATTTTTTGT-AAAATAAGTAC
1 CTAAAGTATTTTTTGTCAAAATAAGTAC
771558 CTAAAGT-TTTTTTGTCAAAATAAGTAC
1 CTAAAGTATTTTTTGTCAAAATAAGTAC
* * * *
771585 ATAAATTATTTTATGTCAAAATAGGTAC
1 CTAAAGTATTTTTTGTCAAAATAAGTAC
*
771613 CTAAACTATT
1 CTAAAGTATT
771623 CAAAATTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.14
27 23 0.40
28 26 0.46
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (28 bp):
CTAAAGTATTTTTTGTCAAAATAAGTAC
Found at i:771605 original size:28 final size:27
Alignment explanation
Indices: 771531--771622 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
771521 ATTTATGTAT
*
771531 CTAAAGTATTTTTTGT-AAAATAAGTAC
1 CTAAATTA-TTTTTGTCAAAATAAGTAC
771558 CTAAAGTT-TTTTTGTCAAAATAAGTAC
1 CTAAA-TTATTTTTGTCAAAATAAGTAC
* *
771585 ATAAATTATTTTATGTCAAAATAGGTAC
1 CTAAATTATTTT-TGTCAAAATAAGTAC
*
771613 CTAAACTATT
1 CTAAATTATT
771623 CAAAATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
26 9 0.16
27 24 0.43
28 23 0.41
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (27 bp):
CTAAATTATTTTTGTCAAAATAAGTAC
Found at i:771745 original size:32 final size:30
Alignment explanation
Indices: 771704--771810 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 30
771694 GAAAAAGTTG
771704 AATACTTTAGGTATCTATATTTTGAACAAAAA
1 AATACTTTAGGTA-CT-TATTTTGAACAAAAA
*
771736 AATACTTTAGGTACTTATTTTGACCAAAAA
1 AATACTTTAGGTACTTATTTTGAACAAAAA
* * ** *
771766 TATAATTT---TAAATATTTTG-A-TAAAA
1 AATACTTTAGGTACTTATTTTGAACAAAAA
771791 AATACTTTAGGTACTTATTT
1 AATACTTTAGGTACTTATTT
771811 GTTATATAGG
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
25 10 0.16
27 9 0.15
28 7 0.11
30 20 0.33
31 2 0.03
32 13 0.21
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (30 bp):
AATACTTTAGGTACTTATTTTGAACAAAAA
Found at i:781676 original size:2 final size:2
Alignment explanation
Indices: 781669--781701 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
781659 GATCCTAGCC
781669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
781702 TTGATTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:782182 original size:2 final size:2
Alignment explanation
Indices: 782175--782201 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
782165 TAGATTTACT
782175 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
782202 GTCCATCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:784259 original size:24 final size:24
Alignment explanation
Indices: 784232--784313 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
784222 CATAATTCAA
*
784232 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
784256 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
* *
784280 GTTAA-TATCAGATCAGAATCTAG
1 GTCAAGTATCAGATCAGAATCCAG
784303 GTCAAGTATCA
1 GTCAAGTATCA
784314 TAACATAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.41
24 29 0.59
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:784292 original size:23 final size:24
Alignment explanation
Indices: 784238--784306 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
784228 TCAAGTCAAG
* *
784238 TATCATATCAGAATCCAGGTCATG
1 TATCAGATCAGAATCCAGGTCATA
* *
784262 TATCAGATCAGAATCCATGTTA-A
1 TATCAGATCAGAATCCAGGTCATA
*
784285 TATCAGATCAGAATCTAGGTCA
1 TATCAGATCAGAATCCAGGTCA
784307 AGTATCATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (24 bp):
TATCAGATCAGAATCCAGGTCATA
Found at i:785791 original size:23 final size:23
Alignment explanation
Indices: 785765--785809 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
785755 CACCACAGCT
*
785765 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
785788 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
785810 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:785957 original size:25 final size:25
Alignment explanation
Indices: 785929--785994 Score: 132
Period size: 25 Copynumber: 2.6 Consensus size: 25
785919 ATATATATCT
785929 CGAAGGACCGCGTAGAATATTGTCC
1 CGAAGGACCGCGTAGAATATTGTCC
785954 CGAAGGACCGCGTAGAATATTGTCC
1 CGAAGGACCGCGTAGAATATTGTCC
785979 CGAAGGACCGCGTAGA
1 CGAAGGACCGCGTAGA
785995 CCCTCTACTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.24, G:0.30, T:0.17
Consensus pattern (25 bp):
CGAAGGACCGCGTAGAATATTGTCC
Found at i:787663 original size:64 final size:63
Alignment explanation
Indices: 787565--787725 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
787555 TAATGAAGGT
* * * *
787565 ATGCATCGATGCACTACACCATGCATCGATGCATATATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAAT--
*
787628 AG
62 AC
*
787630 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATAC
* *
787694 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
787726 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 56 0.67
65 24 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATAC
Done.