Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008292.1 Hibiscus syriacus cultivar Beakdansim tig00110956_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: 1591938
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 8
Found at i:554211 original size:41 final size:42
Alignment explanation
Indices: 554162--554241 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 42
554152 GCAATGCGAT
* *
554162 TTTGAAAAATATGTTGCGATAGTTAAA-ATGTGTTGCGAGAG
1 TTTGAAAAACATGTTGCGATAGTTAAATAAGTGTTGCGAGAG
*
554203 TTTGAAAAACGTGTTGCGATAGTTAAATAAGTGTTGCGA
1 TTTGAAAAACATGTTGCGATAGTTAAATAAGTGTTGCGA
554242 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 25 0.71
42 10 0.29
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (42 bp):
TTTGAAAAACATGTTGCGATAGTTAAATAAGTGTTGCGAGAG
Found at i:554216 original size:22 final size:20
Alignment explanation
Indices: 554166--554252 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
554156 TGCGATTTTG
*
554166 AAAAATATGTTGCGATAGTT
1 AAAAATGTGTTGCGATAGTT
*
554186 -AAAATGTGTTGCGAGAGTTT
1 AAAAATGTGTTGCGATAG-TT
*
554206 GAAAAACGTGTTGCGATAGTT
1 -AAAAATGTGTTGCGATAGTT
*
554227 AAATAA-GTGTTGCGATAGTG
1 AAA-AATGTGTTGCGATAGTT
554247 AAAAAT
1 AAAAAT
554253 CCAAAATAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
19 17 0.30
20 21 0.37
21 4 0.07
22 15 0.26
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (20 bp):
AAAAATGTGTTGCGATAGTT
Found at i:554699 original size:21 final size:21
Alignment explanation
Indices: 554669--554791 Score: 130
Period size: 21 Copynumber: 6.0 Consensus size: 21
554659 ACCAGTCGTT
*
554669 GCGATTTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
554690 GCGGATTTGGAAAAT----AC
1 GCGAATTTGGAAAATCGCAAC
554707 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
554728 GTGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
* *
554749 GCGAACTT-GAACTATCGCAAC
1 GCGAATTTGGAA-AATCGCAAC
* **
554770 GCGAACTTGGACTATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
554791 G
1 G
554792 AATTTGAACT
Statistics
Matches: 88, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
17 16 0.18
20 3 0.03
21 67 0.76
22 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:554714 original size:17 final size:17
Alignment explanation
Indices: 554688--554721 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
554678 GAAAATCGCA
*
554688 ACGCGGATTTGGAAAAT
1 ACGCGAATTTGGAAAAT
554705 ACGCGAATTTGGAAAAT
1 ACGCGAATTTGGAAAAT
554722 CGCAACGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (17 bp):
ACGCGAATTTGGAAAAT
Found at i:554725 original size:38 final size:38
Alignment explanation
Indices: 554669--554742 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
554659 ACCAGTCGTT
* *
554669 GCGATTTTGGAAAATCGCAACGCGGATTTGGAAAATAC
1 GCGAATTTGGAAAATCGCAACGCGAATTTGGAAAATAC
*
554707 GCGAATTTGGAAAATCGCAACGTGAATTTGGAAAAT
1 GCGAATTTGGAAAATCGCAACGCGAATTTGGAAAAT
554743 CGCAACGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (38 bp):
GCGAATTTGGAAAATCGCAACGCGAATTTGGAAAATAC
Found at i:554867 original size:20 final size:20
Alignment explanation
Indices: 554842--554886 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
554832 TTGTATTATT
554842 GCGTTGCGATAGTCAAAATC
1 GCGTTGCGATAGTCAAAATC
*
554862 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAAAATC
554882 GCGTT
1 GCGTT
554887 ACGAATCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAAATC
Found at i:557107 original size:25 final size:25
Alignment explanation
Indices: 557073--557129 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
557063 CAGGAAACAA
557073 AAACTTCAGATAGATATAAGTCTTG
1 AAACTTCAGATAGATATAAGTCTTG
557098 AAACTTCAGATAGATATAAGTCTTG
1 AAACTTCAGATAGATATAAGTCTTG
557123 AAACTTC
1 AAACTTC
557130 GTAGTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (25 bp):
AAACTTCAGATAGATATAAGTCTTG
Found at i:561693 original size:4 final size:4
Alignment explanation
Indices: 561678--561709 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
561668 AGCCTCAATT
*
561678 ACAA AAAA ACAA ACAA ACAA ACAA ACAA ACAA
1 ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA
561710 GAAGATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:563681 original size:34 final size:34
Alignment explanation
Indices: 563643--563710 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
563633 CGATAGGTAA
*
563643 AAATTTTAAATCCACCCCGCCCATATGTGTATAT
1 AAATTTTAAATCCACCCCACCCATATGTGTATAT
*
563677 AAATTTTAAATTCACCCCACCCATATGTGTATAT
1 AAATTTTAAATCCACCCCACCCATATGTGTATAT
563711 TCTCAAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (34 bp):
AAATTTTAAATCCACCCCACCCATATGTGTATAT
Found at i:564437 original size:2 final size:2
Alignment explanation
Indices: 564432--564460 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
564422 TTTTTTGGAA
564432 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
564461 GTAATTAAAG
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:565053 original size:33 final size:36
Alignment explanation
Indices: 565016--565088 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
565006 ACCGTCACGT
*
565016 TTTAACCATGC-AA-ATAC-GTGACTGATTCAGTAC
1 TTTAACCATGCAAACATACAGTGACTGATTCAGAAC
565049 TTTAACCATGCAAACATACATGTGACTGATTCAGAAC
1 TTTAACCATGCAAACATACA-GTGACTGATTCAGAAC
565086 TTT
1 TTT
565089 TTAAGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
33 11 0.31
34 2 0.06
35 4 0.11
37 18 0.51
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (36 bp):
TTTAACCATGCAAACATACAGTGACTGATTCAGAAC
Found at i:565481 original size:17 final size:17
Alignment explanation
Indices: 565459--565503 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
565449 ACGATCATAT
565459 AAAGTTTAAAATATTAA
1 AAAGTTTAAAATATTAA
565476 AAAGTTTAAAATATTAA
1 AAAGTTTAAAATATTAA
*
565493 AAAGTTGAAAA
1 AAAGTTTAAAA
565504 AACCCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (17 bp):
AAAGTTTAAAATATTAA
Found at i:568071 original size:2 final size:2
Alignment explanation
Indices: 568064--568088 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
568054 AAAGAAAATA
568064 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
568089 CTTATCTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:568691 original size:12 final size:12
Alignment explanation
Indices: 568674--568717 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
568664 CCATATTTCA
568674 TTTTGGTCATTC
1 TTTTGGTCATTC
568686 TTTTGGTCATTC
1 TTTTGGTCATTC
568698 TTTTGGTCATTC
1 TTTTGGTCATTC
568710 TTTTGGTC
1 TTTTGGTC
568718 GAATACTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.07, C:0.16, G:0.18, T:0.59
Consensus pattern (12 bp):
TTTTGGTCATTC
Found at i:570096 original size:20 final size:20
Alignment explanation
Indices: 570071--570127 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
570061 TTTTCCGACT
570071 ATCACAATGCGAATATGTAA
1 ATCACAATGCGAATATGTAA
570091 ATCACAATGCGAATATGTAA
1 ATCACAATGCGAATATGTAA
* *
570111 ATCGCAATGCGATTATG
1 ATCACAATGCGAATATG
570128 ACTATCGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCACAATGCGAATATGTAA
Found at i:570134 original size:20 final size:20
Alignment explanation
Indices: 570067--570157 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
570057 GCGATTTTCC
*
570067 GACTATCACAATGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
570087 GTA-AATCACAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
* *
570107 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGAATAT
* * *
570127 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGAATAT
*
570147 GACTGTCGCAA
1 GACTATCGCAA
570158 CACTGAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.02
20 60 0.97
21 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:571032 original size:24 final size:24
Alignment explanation
Indices: 570974--571020 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
570964 AGTCGGTATT
*
570974 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
570998 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
571021 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:573294 original size:12 final size:12
Alignment explanation
Indices: 573279--573321 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
573269 CAAGAAAAAG
573279 GCAATCAAAATC
1 GCAATCAAAATC
573291 GCAATCAAAATC
1 GCAATCAAAATC
**
573303 AAAATCAAAATC
1 GCAATCAAAATC
573315 GCAATCA
1 GCAATCA
573322 CAACCGGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.53, C:0.23, G:0.07, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:573302 original size:6 final size:6
Alignment explanation
Indices: 573281--573314 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
573271 AGAAAAAGGC
**
573281 AATCAA AATCGC AATCAA AATCAA AATCAA AATC
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATC
573315 GCAATCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (6 bp):
AATCAA
Found at i:573633 original size:140 final size:140
Alignment explanation
Indices: 573381--573650 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
573371 AAACGTTGTA
573381 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
573446 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
573511 TATGTGTATT
131 TATGTGTATT
*
573521 TTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
573586 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
573651 CGTAACGCGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:573646 original size:20 final size:20
Alignment explanation
Indices: 573621--573845 Score: 186
Period size: 20 Copynumber: 11.8 Consensus size: 20
573611 TTACACATTC
*
573621 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
573641 ATTTGACTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
573661 ATTTGATTATCACAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
573680 A----A-AACCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
573695 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
573715 ATATGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
573734 A----A-AATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
573749 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
573769 ATTTGACTATTGTACCGCGA
1 ATTTGACTATCGCAACGCGA
*
573789 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
573809 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
573829 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
573846 AGAAAATTGC
Statistics
Matches: 160, Mismatches: 33, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
14 15 0.09
15 6 0.04
19 5 0.03
20 134 0.84
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:573716 original size:54 final size:54
Alignment explanation
Indices: 573631--573778 Score: 224
Period size: 54 Copynumber: 2.7 Consensus size: 54
573621 ATTTGAATAT
* *
573631 CGCAACGCGAATTTGACTATCGTAACGCGAATTTGATTATCACAACTCAAAAAC
1 CGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACTCAAAAAC
* * * *
573685 CGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACTCAAAAAT
1 CGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACTCAAAAAC
* *
573739 CGCAATGCGAATTTGTCTATCGCAACGCGAATTTGACTAT
1 CGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTAT
573779 TGTACCGCGA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (54 bp):
CGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACTCAAAAAC
Found at i:573913 original size:20 final size:20
Alignment explanation
Indices: 573888--573926 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
573878 TGCAAATTGA
573888 CTTTCGCATTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
573908 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
573927 AGTTTAGCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.49
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:573939 original size:20 final size:20
Alignment explanation
Indices: 573884--573941 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
573874 GCAATGCAAA
*
573884 TTGACTTTCGCATTGCGATT
1 TTGACTTTAGCATTGCGATT
* *
573904 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCATTGCGATT
* *
573924 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCATTGCGA
573942 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGACTTTAGCATTGCGATT
Found at i:575676 original size:18 final size:18
Alignment explanation
Indices: 575653--575737 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 18
575643 GAAACTTAAA
575653 ATCGCAACACGAATGACT
1 ATCGCAACACGAATGACT
* *
575671 ATCGCAACGCGAAAACGACT
1 ATCGCAACACG--AATGACT
**
575691 ATCGCAACGCAAAAATGACT
1 ATCGCAA--CACGAATGACT
*
575711 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAA--TGACT
575731 ATCGCAA
1 ATCGCAA
575738 TGAGAGAATC
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
18 13 0.25
20 38 0.73
22 1 0.02
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (18 bp):
ATCGCAACACGAATGACT
Found at i:575692 original size:20 final size:20
Alignment explanation
Indices: 575664--575737 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
575654 TCGCAACACG
575664 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
* *
575684 AACGACTATCGCAACGCAAA
1 AATGACTATCGCAACGCGAA
575704 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
575724 TTTGACTATCGCAA
1 AATGACTATCGCAA
575738 TGAGAGAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:575807 original size:20 final size:20
Alignment explanation
Indices: 575782--575865 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
575772 GCGGTTCTTT
**
575782 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
575802 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
575822 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
575842 CATTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
575862 CGTT
1 CGTT
575866 ACGAAAGTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:577800 original size:20 final size:20
Alignment explanation
Indices: 577777--577863 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
577767 TTTGAAACTT
577777 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
577797 AAAACCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
577817 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
* *
577836 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
577855 AAAATCGCA
1 AAAATCGCA
577864 TTGCGATTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 26 0.45
20 32 0.55
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:578486 original size:20 final size:20
Alignment explanation
Indices: 578463--578569 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
578453 GAAAATCGTA
*
578463 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
578483 TTGCGACAGTCAGAATCGTG
1 TTGCGATAGTCAGAATCGCG
* *
578503 TTGCGACAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
578523 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* * *
578543 TTGCGATAGTCATACTCGCA
1 TTGCGATAGTCAGAATCGCG
578563 TTGCGAT
1 TTGCGAT
578570 TTACATATTC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:581628 original size:20 final size:22
Alignment explanation
Indices: 581587--581628 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
581577 CAATGAGGAA
581587 AAGGAAAGTTCTGTATGCTTTG
1 AAGGAAAGTTCTGTATGCTTTG
*
581609 AAGGAAA-TTCT-TATGGTTTG
1 AAGGAAAGTTCTGTATGCTTTG
581629 TGGGGAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.38
Consensus pattern (22 bp):
AAGGAAAGTTCTGTATGCTTTG
Found at i:582067 original size:22 final size:22
Alignment explanation
Indices: 582023--582063 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
582013 TGTCCCCAAC
*
582023 TTTGGTTAAGTAAATGAAATCA
1 TTTGGTTAAGTAAATAAAATCA
*
582045 TTTGGTTCAGTAAA-AAAAT
1 TTTGGTTAAGTAAATAAAAT
582064 TCATATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (22 bp):
TTTGGTTAAGTAAATAAAATCA
Found at i:594056 original size:20 final size:22
Alignment explanation
Indices: 594031--594074 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
594021 CACCCTCAGC
594031 ATCCATCCACCCAT-TA-ATAT
1 ATCCATCCACCCATATATATAT
*
594051 ATCCATCCATCCATATATATAT
1 ATCCATCCACCCATATATATAT
594073 AT
1 AT
594075 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (22 bp):
ATCCATCCACCCATATATATAT
Found at i:594068 original size:2 final size:2
Alignment explanation
Indices: 594063--594141 Score: 142
Period size: 2 Copynumber: 40.0 Consensus size: 2
594053 CCATCCATCC
594063 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
*
594105 AT AT AT AT AT AT AT AT AT AC AT AT -T 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
594142 TTAAAAAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:594458 original size:18 final size:17
Alignment explanation
Indices: 594439--594519 Score: 61
Period size: 17 Copynumber: 5.1 Consensus size: 17
594429 TTGTTCATGT
594439 TTTGGTTTCTAAGAATG
1 TTTGGTTTCTAAGAATG
*
594456 TTTGAGTATC----AATG
1 TTTG-GTTTCTAAGAATG
594470 TTTGGTTTCTAAGAATG
1 TTTGGTTTCTAAGAATG
*
594487 TTTGAGTATC----AATG
1 TTTG-GTTTCTAAGAATG
*
594501 TTTGGTTTCTATGAATG
1 TTTGGTTTCTAAGAATG
594518 TT
1 TT
594520 AGAAGAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
13 8 0.16
14 16 0.32
17 18 0.36
18 8 0.16
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.48
Consensus pattern (17 bp):
TTTGGTTTCTAAGAATG
Found at i:594471 original size:14 final size:14
Alignment explanation
Indices: 594452--594504 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
594442 GGTTTCTAAG
594452 AATGTTTGAGTATC
1 AATGTTTGAGTATC
*
594466 AATGTTTG-GTTTC
1 AATGTTTGAGTATC
594479 TAAGAATGTTTGAGTATC
1 ----AATGTTTGAGTATC
594497 AATGTTTG
1 AATGTTTG
594505 GTTTCTATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 4 0.12
14 16 0.50
17 8 0.25
18 4 0.12
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (14 bp):
AATGTTTGAGTATC
Found at i:594475 original size:31 final size:31
Alignment explanation
Indices: 594439--594519 Score: 153
Period size: 31 Copynumber: 2.6 Consensus size: 31
594429 TTGTTCATGT
594439 TTTGGTTTCTAAGAATGTTTGAGTATCAATG
1 TTTGGTTTCTAAGAATGTTTGAGTATCAATG
594470 TTTGGTTTCTAAGAATGTTTGAGTATCAATG
1 TTTGGTTTCTAAGAATGTTTGAGTATCAATG
*
594501 TTTGGTTTCTATGAATGTT
1 TTTGGTTTCTAAGAATGTT
594520 AGAAGAATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.48
Consensus pattern (31 bp):
TTTGGTTTCTAAGAATGTTTGAGTATCAATG
Found at i:595566 original size:21 final size:22
Alignment explanation
Indices: 595522--595567 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
595512 ACTAAAAATT
* * *
595522 AAATAATATTTGGTAAATTGAA
1 AAATAAGATTTGGTAAAATAAA
595544 AAATAAGATTT-GTAAAATAAA
1 AAATAAGATTTGGTAAAATAAA
595565 AAA
1 AAA
595568 GAAAAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (22 bp):
AAATAAGATTTGGTAAAATAAA
Found at i:595706 original size:44 final size:44
Alignment explanation
Indices: 595658--595992 Score: 221
Period size: 43 Copynumber: 7.8 Consensus size: 44
595648 ATAAAATTTT
* * *
595658 AAAAAATTAAAGACCTTAATTATAAAGATAGAAATTGAAATTGA
1 AAAAAATTAAAGACCTCAATTATAAAGATAGAAAATGAGATTGA
* * * * *
595702 AAAAAAATAGAGACCTCAATTAAAAAGTTAGAAAGTGAGATT-A
1 AAAAAATTAAAGACCTCAATTATAAAGATAGAAAATGAGATTGA
* *
595745 AAAAAACTT-AAGAATCTCAATTATAAA-ATTAAGAAAATGATATTGA
1 AAAAAA-TTAAAG-ACCTCAATTATAAAGA-T-AGAAAATGAGATTGA
* * * * *
595791 AAAAACTTAAAAACATCCATTATAAA-ATTA-AAAGTGAGATT--
1 AAAAAATTAAAGACCTCAATTATAAAGA-TAGAAAATGAGATTGA
* ** ** *
595832 ACAAAATTAGGGGTCTCAATTATAAAGATAAAAAATG-GATTGA
1 AAAAAATTAAAGACCTCAATTATAAAGATAGAAAATGAGATTGA
* ** *
595875 AAAAAA-TAGAGATTTCAATTATAAAGATA-AAAAGTTAGATTGA
1 AAAAAATTAAAGACCTCAATTATAAAGATAGAAAA-TGAGATTGA
* * * * * *
595918 ATAATATTAAA-ACCTTAATTATAAAGCTAAAAAATAAGATTG-
1 AAAAAATTAAAGACCTCAATTATAAAGATAGAAAATGAGATTGA
* *
595960 AAAAAATTAAGGACCT-AAATATAAAGAT-GAAAA
1 AAAAAATTAAAGACCTCAATTATAAAGATAGAAAA
595993 AATGGGGACC
Statistics
Matches: 226, Mismatches: 50, Indels: 33
0.73 0.16 0.11
Matches are distributed among these distances:
41 31 0.14
42 45 0.20
43 58 0.26
44 57 0.25
45 27 0.12
46 8 0.04
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (44 bp):
AAAAAATTAAAGACCTCAATTATAAAGATAGAAAATGAGATTGA
Found at i:595794 original size:45 final size:44
Alignment explanation
Indices: 595716--595837 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 44
595706 AAATAGAGAC
* *
595716 CTCAATTA-AAAAGTT-AGAAAGTGAGATTAAAAAAACTTAAGAAT
1 CTCAATTATAAAA-TTAAGAAAATGAGATTAAAAAAACTTAA-AAA
* *
595760 CTCAATTATAAAATTAAGAAAATGATATTGAAAAAACTTAAAAA
1 CTCAATTATAAAATTAAGAAAATGAGATTAAAAAAACTTAAAAA
* * *
595804 CATCCATTATAAAATT-A-AAAGTGAGATTACAAAA
1 C-TCAATTATAAAATTAAGAAAATGAGATTAAAAAA
595838 TTAGGGGTCT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
43 13 0.20
44 14 0.21
45 39 0.59
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (44 bp):
CTCAATTATAAAATTAAGAAAATGAGATTAAAAAAACTTAAAAA
Found at i:595864 original size:41 final size:43
Alignment explanation
Indices: 595675--595965 Score: 184
Period size: 42 Copynumber: 6.7 Consensus size: 43
595665 TAAAGACCTT
* * * *
595675 AATTATAAAGATAGAAATTGAAATTGAAAAAAAATAGAGACCTC
1 AATTATAAAGATAAAAAGTGAGATTG-AAAAAAATAGAGATCTC
* * *
595719 AATTAAAAAGTTAGAAAGTGAGATT-AAAAAAACTTA-AGAATCTC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAA--TAGAG-ATCTC
* * * * *
595763 AATTATAAA-ATTAAGAAAATGATATTGAAAAAACTTA-AAAACATC
1 AATTATAAAGA-TAA-AAAGTGAGATTGAAAAAA-ATAGAGATC-TC
* * * * * *
595808 CATTATAAA-ATTAAAAGTGAGATT-ACAAAATTAGGGGTCTC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATCTC
* *
595849 AATTATAAAGATAAAAAATG-GATTGAAAAAAATAGAGATTTC
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATCTC
* * * * * *
595891 AATTATAAAGATAAAAAGTTAGATTGAATAATATTA-AAACCTT
1 AATTATAAAGATAAAAAGTGAGATTGAA-AAAAATAGAGATCTC
* * *
595934 AATTATAAAGCTAAAAAATAAGATTGAAAAAA
1 AATTATAAAGATAAAAAGTGAGATTGAAAAAA
595966 TTAAGGACCT
Statistics
Matches: 192, Mismatches: 42, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
41 17 0.09
42 54 0.28
43 46 0.24
44 46 0.24
45 23 0.12
46 6 0.03
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (43 bp):
AATTATAAAGATAAAAAGTGAGATTGAAAAAAATAGAGATCTC
Found at i:597852 original size:17 final size:15
Alignment explanation
Indices: 597816--597846 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
597806 AAATTCTAAA
597816 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
597831 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
597846 T
1 T
597847 TTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:601688 original size:24 final size:25
Alignment explanation
Indices: 601661--601754 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 25
601651 CACCACAGCT
601661 CGTATA-AATTGCACCGAAGTGCCA
1 CGTATAGAATTGCACCGAAGTGCCA
* *
601685 CGTAGA-AATTGTC-CCGAAG-GAC-
1 CGTATAGAATTG-CACCGAAGTGCCA
* *
601707 CGTGTAGAAATGCACCGAAGTGCCA
1 CGTATAGAATTGCACCGAAGTGCCA
*
601732 C--ATAGAATTGCACCGTAGTGCCA
1 CGTATAGAATTGCACCGAAGTGCCA
601755 TATAAGATTG
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
22 5 0.09
23 31 0.55
24 18 0.32
25 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (25 bp):
CGTATAGAATTGCACCGAAGTGCCA
Found at i:604982 original size:2 final size:2
Alignment explanation
Indices: 604975--605001 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
604965 TTTACATTAT
604975 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
605002 TAATGACCTA
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:605979 original size:125 final size:125
Alignment explanation
Indices: 605743--605993 Score: 457
Period size: 125 Copynumber: 2.0 Consensus size: 125
605733 GTTGTTTTAG
*
605743 GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACGCAATCTCCATC
1 GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACACAATCTCCATC
* * *
605808 ATTTGCAGTTGTAAAATAAGAATTGTGGCGATATGCGTCTTCTTTCGCATTGGTAAACGA
66 ATTTGCAGTTGTAAAATAAGAATTATGGCGAGATGCATCTTCTTTCGCATTGGTAAACGA
605868 GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACACAATCTCCATC
1 GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACACAATCTCCATC
*
605933 ATTTGCAGTTGTAAAATAAGAATTATGGCGAGATGCATCTTTTTTCGCATTGGTAAACGA
66 ATTTGCAGTTGTAAAATAAGAATTATGGCGAGATGCATCTTCTTTCGCATTGGTAAACGA
605993 G
1 G
605994 CCATAACTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 121 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (125 bp):
GTCGATTTTTATATTTTCTAAGAATAACTGAAATAACCATAAGCATATGACACACAATCTCCATC
ATTTGCAGTTGTAAAATAAGAATTATGGCGAGATGCATCTTCTTTCGCATTGGTAAACGA
Found at i:607379 original size:44 final size:43
Alignment explanation
Indices: 607331--607487 Score: 133
Period size: 45 Copynumber: 3.6 Consensus size: 43
607321 AGACCTATCG
607331 AAAAATCTTAGAGACCTCAATTA-AAAAGTTAGAAAGTGAGATTA
1 AAAAATCTTA-AGACCTCAATTATAAAA-TTAGAAAGTGAGATTA
* * *
607375 AAAAAACTTAAGAGCCTCAATTATAAAATTAAGAAAATGATATTGA
1 AAAAATCTTAAGA-CCTCAATTATAAAATT-AGAAAGTGAGATT-A
* * * *
607421 ATAAA-CTTAAAAACATCCATTATAAAATTA-AAAGTGAGATTA
1 AAAAATCTT-AAGACCTCAATTATAAAATTAGAAAGTGAGATTA
* * **
607463 CAAAAT-TAAAGGTCTCAATTATAAA
1 AAAAATCTTAAGACCTCAATTATAAA
607488 GATAAAAAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
41 12 0.13
42 5 0.06
43 12 0.13
44 21 0.23
45 32 0.36
46 8 0.09
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.27
Consensus pattern (43 bp):
AAAAATCTTAAGACCTCAATTATAAAATTAGAAAGTGAGATTA
Found at i:607380 original size:45 final size:43
Alignment explanation
Indices: 607331--607467 Score: 134
Period size: 45 Copynumber: 3.1 Consensus size: 43
607321 AGACCTATCG
*
607331 AAAAATCTTAGAGACCTCAATTA-AAAAGTTAGAAAGTGAGATTA
1 AAAAAACTTA-AGACCTCAATTATAAAA-TTAGAAAGTGAGATTA
* * *
607375 AAAAAACTTAAGAGCCTCAATTATAAAATTAAGAAAATGATATTG
1 AAAAAACTTAAGA-CCTCAATTATAAAATT-AGAAAGTGAGATTA
* * * *
607420 AATAAACTTAAAAACATCCATTATAAAATTA-AAAGTGAGATTA
1 AAAAAACTT-AAGACCTCAATTATAAAATTAGAAAGTGAGATTA
*
607463 CAAAA
1 AAAAA
607468 TTAAAGGTCT
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
43 15 0.20
44 21 0.28
45 37 0.49
46 3 0.04
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (43 bp):
AAAAAACTTAAGACCTCAATTATAAAATTAGAAAGTGAGATTA
Found at i:607547 original size:43 final size:41
Alignment explanation
Indices: 607476--607623 Score: 154
Period size: 42 Copynumber: 3.5 Consensus size: 41
607466 AATTAAAGGT
* * *
607476 CTCAATTATAAAGATAAAAAATGGATTGAAAAAAATAGATAT
1 CTCAATTATAAAGATAAAAATTAGATTGAAAAAAATAGA-AC
* * *
607518 TTCAATTATAAAGATAAAAAGTTAGATTGAATAATATTAGAAC
1 CTCAATTATAAAGATAAAAA-TTAGATTGAA-AAAAATAGAAC
* * *
607561 CTCAATTATAAAGATAAAAAATAAGATTGAAAAAATTAAGGAC
1 CTCAATTATAAAGAT-AAAAATTAGATTGAAAAAAAT-AGAAC
607604 CT-AATTATAAAGATGAAAAA
1 CTCAATTATAAAGAT-AAAAA
607624 ATGGGGACCC
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
42 41 0.45
43 38 0.42
44 12 0.13
ACGTcount: A:0.56, C:0.05, G:0.11, T:0.27
Consensus pattern (41 bp):
CTCAATTATAAAGATAAAAATTAGATTGAAAAAAATAGAAC
Found at i:607622 original size:29 final size:29
Alignment explanation
Indices: 607583--607653 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
607573 GATAAAAAAT
*
607583 AAGATTGAAAAAATTAAGGA-CCTAATTATA
1 AAGA-TGAAAAAA-TAAGGACCCTAATTACA
**
607613 AAGATGAAAAAATGGGGACCCTAATTACA
1 AAGATGAAAAAATAAGGACCCTAATTACA
*
607642 AGGATGAAAAAA
1 AAGATGAAAAAA
607654 ATGGGGGCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 4 0.11
29 28 0.78
30 4 0.11
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.20
Consensus pattern (29 bp):
AAGATGAAAAAATAAGGACCCTAATTACA
Found at i:607624 original size:43 final size:41
Alignment explanation
Indices: 607338--607625 Score: 181
Period size: 43 Copynumber: 6.7 Consensus size: 41
607328 TCGAAAAATC
* * * * *
607338 TTAGAGACCTCAATTAAAAAGTTAGAAAGTGAGATTAAAAAAA
1 TTAGA-ACCTCAATTATAAAGATAAAAAAT-AGATTGAAAAAA
* * *
607381 CTTAAGAGCCTCAATTATAAA-ATTAAGAAAATGATATTGAATAAAC
1 -TT-AGAACCTCAATTATAAAGA-TAA-AAAAT-AGATTGAA-AAAA
* * * * * *
607427 TTAAAAACATCCATTATAAA-ATTAAAAGTGAGATT-ACAAAA
1 TT-AGAACCTCAATTATAAAGATAAAAAAT-AGATTGAAAAAA
* *
607468 TTA-AAGGTCTCAATTATAAAGATAAAAAATGGATTGAAAAAA
1 TTAGAA--CCTCAATTATAAAGATAAAAAATAGATTGAAAAAA
* ** * *
607510 ATAGATATTTCAATTATAAAGATAAAAAGTTAGATTGAATAATA
1 TTAGA-ACCTCAATTATAAAGATAAAAA-ATAGATTGAA-AAAA
607554 TTAGAACCTCAATTATAAAGATAAAAAATAAGATTGAAAAAA
1 TTAGAACCTCAATTATAAAGATAAAAAAT-AGATTGAAAAAA
*
607596 TTAAGGACCT-AATTATAAAGATGAAAAAAT
1 TT-AGAACCTCAATTATAAAGAT-AAAAAAT
607626 GGGGACCCTA
Statistics
Matches: 194, Mismatches: 35, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 19 0.10
42 53 0.27
43 59 0.30
44 26 0.13
45 31 0.16
46 3 0.02
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (41 bp):
TTAGAACCTCAATTATAAAGATAAAAAATAGATTGAAAAAA
Found at i:607631 original size:28 final size:30
Alignment explanation
Indices: 607603--607659 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
607593 AAATTAAGGA
*
607603 CCTAATTATAAAGATG-AAAAAATGGGGAC
1 CCTAATTACAAAGATGAAAAAAATGGGGAC
*
607632 CCTAATTACAAGGATGAAAAAAATGGGG
1 CCTAATTACAAAGATGAAAAAAATGGGG
607660 GCCATGAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (30 bp):
CCTAATTACAAAGATGAAAAAAATGGGGAC
Found at i:610312 original size:22 final size:22
Alignment explanation
Indices: 610265--610312 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
610255 TCATATATAA
* **
610265 ATTTTAAAATTTTTATCTTCAG
1 ATTTTAAAATTTATATAATCAG
610287 ATTTTAAAA-TTATATAATCAG
1 ATTTTAAAATTTATATAATCAG
610308 CATTT
1 -ATTT
610313 AATTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTTAAAATTTATATAATCAG
Found at i:615272 original size:20 final size:21
Alignment explanation
Indices: 615234--615282 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
615224 TTCGTTTTTT
*
615234 TTTTGTTTTTTGTTCTCTGTC
1 TTTTGTTTTTTCTTCTCTGTC
* *
615255 TTTT-TTTTTTCTTTTCTGTT
1 TTTTGTTTTTTCTTCTCTGTC
615275 TTGTTGTT
1 TT-TTGTT
615283 GGTTGTGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.65
21 6 0.26
22 2 0.09
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (21 bp):
TTTTGTTTTTTCTTCTCTGTC
Found at i:615830 original size:3 final size:3
Alignment explanation
Indices: 615822--615871 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
615812 ATATATATAT
** *
615822 TAA TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TTAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
615868 TAA T
1 TAA T
615872 TTTAATGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:616275 original size:76 final size:75
Alignment explanation
Indices: 616030--616708 Score: 997
Period size: 76 Copynumber: 9.4 Consensus size: 75
616020 AGGTCTTATG
*
616030 AACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGAA
616095 GGCTTTTTGGA
65 GGCTTTTTGGA
616106 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG-AAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGAA
616170 GGCTTTTTGGA
65 GGCTTTTTGGA
*
616181 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGAA
616246 GGCTTTTTGGA
65 GGCTTTTTGGA
* *
616257 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGAA
616322 GGCTTTTTGGA
65 GGCTTTTTGGA
* *
616333 AACATCATGCACTGAAGGGCTTACAGATG----T--GG---G-AAACATCAAAAAGATCCCGAAG
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTGAAAACATCAAAAAGCTCCCGAAG
616388 GCTTTTTGGA
66 GCTTTTTGGA
616398 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGAA
616463 GGCTTTTTGGA
65 GGCTTTTTGGA
* *
616474 AACATCATGCACTGAAGGGCTTACAGATG----T--GG---G-AAACATCAAAAAGATCCCGAAG
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTGAAAACATCAAAAAGCTCCCGAAG
616529 GCTTTTTGGA
66 GCTTTTTGGA
616539 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAA
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGAA
616604 GGCTTTTTGGA
65 GGCTTTTTGGA
* *
616615 AACATCATGCACTGAAGGGCTTACAGATG----T--GG---G-AAACATCAAAAAGATCCCGAAG
1 AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTGAAAACATCAAAAAGCTCCCGAAG
616670 GCTTTTTGGA
66 GCTTTTTGGA
616680 AACATCATGCACTGAAGGACTTACAGATG
1 AACATCATGCACTGAAGGACTTACAGATG
616709 TGGGAAATAG
Statistics
Matches: 561, Mismatches: 19, Indels: 57
0.88 0.03 0.09
Matches are distributed among these distances:
65 176 0.31
66 3 0.01
69 2 0.00
70 6 0.01
71 4 0.01
72 2 0.00
75 77 0.14
76 291 0.52
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (75 bp):
AACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTGAAAACATCAAAAAGCTCCCGAAG
GCTTTTTGGA
Found at i:616409 original size:65 final size:65
Alignment explanation
Indices: 616305--616715 Score: 570
Period size: 65 Copynumber: 6.0 Consensus size: 65
616295 CTTTGAAAAT
* *
616305 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGGAAAC
1 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAAC
616370 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG----T--G
616435 GTTTTGAAAAC
60 G----G-AAAC
* *
616446 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGGAAAC
1 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAAC
616511 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG----T--G
616576 GTTTTGAAAAC
60 G----G-AAAC
* *
616587 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGTGGGAAAC
1 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAAC
616652 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAA
1 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAA
616716 TAGTTTACTA
Statistics
Matches: 314, Mismatches: 10, Indels: 44
0.85 0.03 0.12
Matches are distributed among these distances:
65 180 0.57
66 2 0.01
69 2 0.01
70 4 0.01
71 4 0.01
72 2 0.01
75 2 0.01
76 118 0.38
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (65 bp):
ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAAC
Found at i:616593 original size:282 final size:285
Alignment explanation
Indices: 616074--616708 Score: 1116
Period size: 282 Copynumber: 2.2 Consensus size: 285
616064 AAGGTTTTGA
*
616074 AAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
616139 TAAGGCTTTGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
66 TAAGGCTTTGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
616204 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCAC
131 CAGATG---CT-AGG---TGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCAC
*
616269 TGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGGAA
189 TGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAA
616334 ACATCATGCACTGAAGGGCTTACAGATGTGGG
254 ACATCATGCACTGAAGGGCTTACAGATGTGGG
616366 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
* *
616431 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
66 TAAGGCTTTG-AAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
616496 ACAGATG-T-GG-G-AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
130 ACAGATGCTAGGTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
* *
616557 ACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
195 ACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
616622 TGCACTGAAGGGCTTACAGATGTGGG
260 TGCACTGAAGGGCTTACAGATGTGGG
616648 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
616709 TGGGAAATAG
Statistics
Matches: 336, Mismatches: 6, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
282 199 0.59
283 1 0.00
287 2 0.01
289 1 0.00
292 73 0.22
293 60 0.18
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (285 bp):
AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
TAAGGCTTTGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTA
CAGATGCTAGGTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
CTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
GCACTGAAGGGCTTACAGATGTGGG
Found at i:616752 original size:141 final size:141
Alignment explanation
Indices: 616225--616708 Score: 941
Period size: 141 Copynumber: 3.4 Consensus size: 141
616215 AAGGCTTTGA
616225 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
* * *
616290 GAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
66 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
616355 ACAGATGTGGG
131 ACAGATGTGGG
616366 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
616431 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
66 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
616496 ACAGATGTGGG
131 ACAGATGTGGG
616507 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
616572 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
66 TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
616637 ACAGATGTGGG
131 ACAGATGTGGG
616648 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
616709 TGGGAAATAG
Statistics
Matches: 340, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 340 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (141 bp):
AAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
TAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTT
ACAGATGTGGG
Found at i:617413 original size:22 final size:22
Alignment explanation
Indices: 617388--617442 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
617378 CATAAAGTTT
*
617388 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
617410 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
617432 TCATCTTTGAA
1 TCATCTTTGAA
617443 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:618329 original size:24 final size:24
Alignment explanation
Indices: 618302--618374 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
618292 CGTTCATTTA
618302 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
618326 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
618350 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
618374 C
1 C
618375 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:618331 original size:14 final size:14
Alignment explanation
Indices: 618312--618367 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
618302 CGTTCGTGAA
618312 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
618326 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
618340 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
618350 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
618364 CGTT
1 CGTT
618368 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:618384 original size:24 final size:23
Alignment explanation
Indices: 618313--618387 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
618303 GTTCGTGAAC
* *
618313 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
618337 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
618361 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
618385 GTT
1 GTT
618388 TAACCTAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:619130 original size:10 final size:10
Alignment explanation
Indices: 619115--619189 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
619105 AGGTCTCCAA
619115 CGTTTATGTT
1 CGTTTATGTT
619125 CGTTTATGTT
1 CGTTTATGTT
619135 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
619146 ATGTTCGTGTT
1 -CGTTTATGTT
619157 CGTTTATGTT
1 CGTTTATGTT
619167 CG----TGTT
1 CGTTTATGTT
619173 CGTTTATGTT
1 CGTTTATGTT
619183 CGTTTAT
1 CGTTTAT
619190 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:619146 original size:16 final size:16
Alignment explanation
Indices: 619121--619185 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
619111 CCAACGTTTA
619121 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
619137 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
619153 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
619169 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
619185 T
1 T
619186 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:619276 original size:16 final size:16
Alignment explanation
Indices: 619255--619287 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
619245 AAAAAAATTT
619255 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
619271 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
619287 T
1 T
619288 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:623521 original size:12 final size:12
Alignment explanation
Indices: 623504--623533 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
623494 TTCAGTTTTT
623504 TTCTTTTTCTTC
1 TTCTTTTTCTTC
*
623516 TTCTTTTTTTTC
1 TTCTTTTTCTTC
623528 TTCTTT
1 TTCTTT
623534 CTTTGCTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:623527 original size:15 final size:16
Alignment explanation
Indices: 623507--623537 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
623497 AGTTTTTTTC
623507 TTTTTCTTC-TTCTTT
1 TTTTTCTTCTTTCTTT
623522 TTTTTCTTCTTTCTTT
1 TTTTTCTTCTTTCTTT
623538 GCTGGATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTCTTTCTTT
Found at i:630510 original size:2 final size:2
Alignment explanation
Indices: 630503--630529 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
630493 TGGGCTTGTA
630503 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 A
630530 ATAATAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:631854 original size:369 final size:369
Alignment explanation
Indices: 631175--631911 Score: 1465
Period size: 369 Copynumber: 2.0 Consensus size: 369
631165 TTACTCTTGG
631175 ATTCAGTGGCTTATCTGCTAGCTCAAAACATGATCAATCTTTAAATATGTTTATGTTTGTTCTAA
1 ATTCAGTGGCTTATCTGCTAGCTCAAAACATGATCAATCTTTAAATATGTTTATGTTTGTTCTAA
631240 TCTTCTCATATCAGTTTACGGAATGGTATATTATTGTCAAGGTTGTGAGATGTTGGATGTAGCAG
66 TCTTCTCATATCAGTTTACGGAATGGTATATTATTGTCAAGGTTGTGAGATGTTGGATGTAGCAG
631305 TTACTAGAAAGCTTAAAATGTTATATGATGGAGCTTCTCACGTGATGTTCTTGTTTGTTGTTTTC
131 TTACTAGAAAGCTTAAAATGTTATATGATGGAGCTTCTCACGTGATGTTCTTGTTTGTTGTTTTC
631370 AGGATTGATTTCTCAAGTTTCTGCTGAAACGGATCCAGTTTCTCTTCTGCCGAAAGTTGTTTCCC
196 AGGATTGATTTCTCAAGTTTCTGCTGAAACGGATCCAGTTTCTCTTCTGCCGAAAGTTGTTTCCC
631435 TACTTTACATACAAGTCGGTAGATAGAACACCCAATTATGGATTACCTATATCTGAATGTCTAAT
261 TACTTTACATACAAGTCGGTAGATAGAACACCCAATTATGGATTACCTATATCTGAATGTCTAAT
631500 CATCATTTTAACATTCTTTTGCTAAATTCAAATATGGATGCTAA
326 CATCATTTTAACATTCTTTTGCTAAATTCAAATATGGATGCTAA
631544 ATTCAGTGGCTTATCTGCTAGCTCAAAACATGATCAATCTTTAAATATGTTTATGTTTGTTCTAA
1 ATTCAGTGGCTTATCTGCTAGCTCAAAACATGATCAATCTTTAAATATGTTTATGTTTGTTCTAA
631609 TCTTCTCATATCAGTTTACGGAATGGTATATTATTGTCAAGGTTGTGAGATGTTGGATGTAGCAG
66 TCTTCTCATATCAGTTTACGGAATGGTATATTATTGTCAAGGTTGTGAGATGTTGGATGTAGCAG
631674 TTACTAGAAAGCTTAAAATGTTATATGATGGAGCTTCTCACGTGATGTTCTTGTTTGTTGTTTTC
131 TTACTAGAAAGCTTAAAATGTTATATGATGGAGCTTCTCACGTGATGTTCTTGTTTGTTGTTTTC
631739 AGGATTGATTTCTCAAGTTTCTGCTGAAACGGATCCAGTTTCTCTTCTGCCGAAAGTTGTTTCCC
196 AGGATTGATTTCTCAAGTTTCTGCTGAAACGGATCCAGTTTCTCTTCTGCCGAAAGTTGTTTCCC
*
631804 TACTTTACATACAAGTCGGTAGATAGAGCACCCAATTATGGATTACCTATATCTGAATGTCTAAT
261 TACTTTACATACAAGTCGGTAGATAGAACACCCAATTATGGATTACCTATATCTGAATGTCTAAT
631869 CATCATTTTAACATTCTTTTGCTAAATTCAAATATGGATGCTA
326 CATCATTTTAACATTCTTTTGCTAAATTCAAATATGGATGCTA
631912 TTCATAGGTT
Statistics
Matches: 367, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
369 367 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (369 bp):
ATTCAGTGGCTTATCTGCTAGCTCAAAACATGATCAATCTTTAAATATGTTTATGTTTGTTCTAA
TCTTCTCATATCAGTTTACGGAATGGTATATTATTGTCAAGGTTGTGAGATGTTGGATGTAGCAG
TTACTAGAAAGCTTAAAATGTTATATGATGGAGCTTCTCACGTGATGTTCTTGTTTGTTGTTTTC
AGGATTGATTTCTCAAGTTTCTGCTGAAACGGATCCAGTTTCTCTTCTGCCGAAAGTTGTTTCCC
TACTTTACATACAAGTCGGTAGATAGAACACCCAATTATGGATTACCTATATCTGAATGTCTAAT
CATCATTTTAACATTCTTTTGCTAAATTCAAATATGGATGCTAA
Found at i:633252 original size:2 final size:2
Alignment explanation
Indices: 633245--633270 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
633235 TTTTACGCAC
633245 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
633271 TATTCAAACT
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:633479 original size:17 final size:17
Alignment explanation
Indices: 633457--633497 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
633447 TTTTATTATA
633457 TTATTTTTTATCTTGTT
1 TTATTTTTTATCTTGTT
*
633474 TTATTTTTTATTTTGTT
1 TTATTTTTTATCTTGTT
*
633491 TTGTTTT
1 TTATTTT
633498 GTTTTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.80
Consensus pattern (17 bp):
TTATTTTTTATCTTGTT
Found at i:633503 original size:16 final size:17
Alignment explanation
Indices: 633457--633508 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
633447 TTTTATTATA
* *
633457 TTATTTTTTATCTTGTT
1 TTATTTTGTATTTTGTT
*
633474 TTATTTTTTATTTTGTT
1 TTATTTTGTATTTTGTT
*
633491 TTGTTTTGT-TTTTGTT
1 TTATTTTGTATTTTGTT
633507 TT
1 TT
633509 TGATATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 9 0.28
17 23 0.72
ACGTcount: A:0.08, C:0.02, G:0.10, T:0.81
Consensus pattern (17 bp):
TTATTTTGTATTTTGTT
Found at i:634421 original size:16 final size:16
Alignment explanation
Indices: 634400--634453 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 16
634390 AATGAATATT
634400 AAAAATAAAAAAAATA
1 AAAAATAAAAAAAATA
634416 AAAAATAAAAAAAATTA
1 AAAAATAAAAAAAA-TA
*
634433 CAAAAAGAAATAAAGAATA
1 -AAAAATAAA-AAA-AATA
634452 AA
1 AA
634454 CCCATGGCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 14 0.42
17 2 0.06
18 10 0.30
19 5 0.15
20 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (16 bp):
AAAAATAAAAAAAATA
Found at i:635154 original size:2 final size:2
Alignment explanation
Indices: 635147--635181 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
635137 ATAATAATAA
635147 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
635182 AAATGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:636146 original size:19 final size:20
Alignment explanation
Indices: 636113--636160 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
636103 ATTCTCCACC
*
636113 CAAAAACCTTAAATTGAATT
1 CAAAAACCCTAAATTGAATT
636133 CAAAAACCCT-AATTGAATT
1 CAAAAACCCTAAATTGAATT
*
636152 CAAGAACCC
1 CAAAAACCC
636161 ACTGTTCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (20 bp):
CAAAAACCCTAAATTGAATT
Found at i:637683 original size:57 final size:58
Alignment explanation
Indices: 637603--637715 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 58
637593 TTATATTGTG
637603 TTTTATTTGTTTTTTATGCTGTTTTGTATTTCAGGTTTT-GAGAATTTCTTTTATTTAC
1 TTTTATTTGTTTTTTATGCTGTTTTGTATTTCAGGTTTTGGA-AATTTCTTTTATTTAC
*
637661 TTTTATTTG-TTTTTATGCTGTTTTTTATTTCAGGTTTTGGAAATTTCTTTTATTT
1 TTTTATTTGTTTTTTATGCTGTTTTGTATTTCAGGTTTTGGAAATTTCTTTTATTT
637716 CCATGTTTCT
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
57 42 0.79
58 11 0.21
ACGTcount: A:0.15, C:0.06, G:0.13, T:0.65
Consensus pattern (58 bp):
TTTTATTTGTTTTTTATGCTGTTTTGTATTTCAGGTTTTGGAAATTTCTTTTATTTAC
Found at i:648462 original size:10 final size:10
Alignment explanation
Indices: 648447--648474 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
648437 AAAGAGGATG
648447 ACTCGACTGT
1 ACTCGACTGT
648457 ACTCGACTGT
1 ACTCGACTGT
648467 ACTCGACT
1 ACTCGACT
648475 CAGTGAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (10 bp):
ACTCGACTGT
Found at i:648864 original size:21 final size:21
Alignment explanation
Indices: 648840--648897 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
648830 TTGGTGTGGT
*
648840 AGTTCACGGTGCTGAAGTGAC
1 AGTTCACGGTGCTGAAGTAAC
* * * *
648861 AGTTTACGATGTTGACGTAAC
1 AGTTCACGGTGCTGAAGTAAC
**
648882 AGCCCACGGTGCTGAA
1 AGTTCACGGTGCTGAA
648898 ATGGCAATCC
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (21 bp):
AGTTCACGGTGCTGAAGTAAC
Found at i:649851 original size:18 final size:18
Alignment explanation
Indices: 649828--649865 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
649818 ATTGAAAGTT
649828 AGGGTTTATGGATTTTGA
1 AGGGTTTATGGATTTTGA
649846 AGGGTTTATGGATTTTGA
1 AGGGTTTATGGATTTTGA
649864 AG
1 AG
649866 AGTTAATGAA
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:0.24, C:0.00, G:0.34, T:0.42
Consensus pattern (18 bp):
AGGGTTTATGGATTTTGA
Found at i:654556 original size:22 final size:21
Alignment explanation
Indices: 654505--654557 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
654495 GATCGAAATT
*
654505 ACTGTAGCAAGGGTATCGGTAC
1 ACTGTAGC-AGGGTATCGATAC
*
654527 ACTATAGCAGGGTATCGATACC
1 ACTGTAGCAGGGTATCGATA-C
*
654549 CCTGTAGCA
1 ACTGTAGCA
654558 TTCTGTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGGGTATCGATAC
Found at i:657744 original size:78 final size:77
Alignment explanation
Indices: 657616--657770 Score: 181
Period size: 78 Copynumber: 2.0 Consensus size: 77
657606 AAAAAATAAC
* *
657616 ATTTTAGGTAGCGTCCAATATTAACATTTCTATAAAAAAAATAATGTTTTATA-TAACGCTTTAC
1 ATTTTAGGTAGCGCCCAATATTAACATTTCTATAAAAAAAATAA-GTTTTA-AGTAACACTTTAC
657680 CAGAAATACTAAAT
64 CAGAAATACTAAAT
* * *
657694 ATTTTAGGTAGTGCCCAATATTAATATTTTCGGTATAAAAAAAAT-A-TTTTAAGTAACATTTTA
1 ATTTTAGGTAGCGCCCAATATTAACA-TTTC--TATAAAAAAAATAAGTTTTAAGTAACACTTTA
* *
657757 CCTGAAATATTAAA
63 CCAGAAATACTAAA
657771 AAATATTAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
77 1 0.02
78 48 0.73
79 4 0.06
80 1 0.02
81 12 0.18
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (77 bp):
ATTTTAGGTAGCGCCCAATATTAACATTTCTATAAAAAAAATAAGTTTTAAGTAACACTTTACCA
GAAATACTAAAT
Found at i:661298 original size:29 final size:30
Alignment explanation
Indices: 661261--661319 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
661251 GCTATTAAAT
661261 GCCTAATTTTTTAAATACTTGTTATTAGGG
1 GCCTAATTTTTTAAATACTTGTTATTAGGG
* * *
661291 GCCT-ATTTTTTTAATATTTGTTGTTAGGG
1 GCCTAATTTTTTAAATACTTGTTATTAGGG
661320 ATTTACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (30 bp):
GCCTAATTTTTTAAATACTTGTTATTAGGG
Found at i:663286 original size:26 final size:26
Alignment explanation
Indices: 663256--663333 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 26
663246 AATTTTAAAA
663256 TATATTATAATTATAATATTATTAAT
1 TATATTATAATTATAATATTATTAAT
*
663282 TATATT-TAATAAGTAATATTATTAA-
1 TATATTATAATTA-TAATATTATTAAT
* * *
663307 -CTATTATTATTATATTTATTATTAAT
1 TATATTATAATTATA-ATATTATTAAT
663333 T
1 T
663334 TCAATTTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
24 6 0.14
25 18 0.43
26 18 0.43
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (26 bp):
TATATTATAATTATAATATTATTAAT
Found at i:665816 original size:6 final size:6
Alignment explanation
Indices: 665805--665867 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
665795 GACACGTATT
* *
665805 ACCACG ACCACG ACCACG ACCATG ACCATG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
665853 ACCACG ACCACG ACC
1 ACCACG ACCACG ACC
665868 CGAGCCGAGC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.33, C:0.48, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:676178 original size:22 final size:20
Alignment explanation
Indices: 676137--676189 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
676127 CAGTTCCCAG
676137 AATCGCAACGCGAATATAAA
1 AATCGCAACGCGAATATAAA
* * *
676157 AATCGCAATGCGAACATATA
1 AATCGCAACGCGAATATAAA
*
676177 AATCACAACGCGA
1 AATCGCAACGCGA
676190 TTCTGACTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.23, G:0.15, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAATATAAA
Found at i:676242 original size:20 final size:20
Alignment explanation
Indices: 676198--676280 Score: 112
Period size: 20 Copynumber: 4.1 Consensus size: 20
676188 GATTCTGACT
676198 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
676219 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
676239 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* *
676259 ATCGCAATGTGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
676279 AT
1 AT
676281 GTGCTCCGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
20 37 0.69
21 17 0.31
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:677344 original size:24 final size:24
Alignment explanation
Indices: 677310--677363 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
677300 CTGAAAAAGC
677310 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
677334 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
677358 ATCAAA
1 ATCAAA
677364 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:677377 original size:24 final size:24
Alignment explanation
Indices: 677310--677377 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
677300 CTGAAAAAGC
* * *
677310 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
677334 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
677358 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
677378 TAATACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:678241 original size:20 final size:20
Alignment explanation
Indices: 678218--678270 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
678208 CGATAGTCAG
*
678218 AATCTCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
678238 AATCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
* *
678258 ATTCGCATTGCGA
1 AATCGCGTTGCGA
678271 ATTAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
AATCGCGTTGCGATTTACGT
Found at i:678291 original size:21 final size:21
Alignment explanation
Indices: 678267--678307 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
678257 TATTCGCATT
678267 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
678288 GCGAATTTGGAAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
678308 TACGATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:687544 original size:577 final size:578
Alignment explanation
Indices: 686549--687703 Score: 2172
Period size: 577 Copynumber: 2.0 Consensus size: 578
686539 TGACCAAATT
*
686549 GTCTCTATTATATATTTGTATAATCTTACAAATTGTAAAATATTTATATATTTTCTTTAAAAAAT
1 GTCTCTATTATATATTTGTATAATATTACAAATTGTAAAATATTTATATATTTTCTTTAAAAAAT
*
686614 TAAATTCATAATATTTATATAATTTTTTTTACAAAATTAAAAATATAAAAAATGTTTAATAAAAG
66 TAAATTCATAATATTTATATAACTTTTTTTACAAAATTAAAAATATAAAAAATGTTTAATAAAAG
*
686679 GGTAATTTTTTTTAACCTCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAATAT
131 GGTAATTTTTTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAATAT
686744 AAAATAATTTAAGGATAAATTTATAATTTAACCTTCGTAGAATTTTTATTATTCAATGACAGAAG
196 AAAATAATTTAAGGATAAATTTATAATTTAACCTTCGTAGAATTTTTATTATTCAATGACAGAAG
686809 AATGATATTTTTGAAAAAAAAATAAAAATGTAAGGGCATTTTAGTCCAAAATGCCGGTAATGTTA
261 AATGATATTTTTGAAAAAAAAATAAAAATGTAAGGGCATTTTAGTCCAAAATGCCGGTAATGTTA
686874 CAATACATAAAGGAATGGAGGTAATGACATTCCCAGCAATATACCCCAAAAAATCTACTATTGAT
326 CAATACATAAAGGAATGGAGGTAATGACATTCCCAGCAATATACCCCAAAAAATCTACTATTGAT
686939 AATAAAATATTACCGGGAATGAGATTCCCGGCCAACCAAACATGAGAATATGGGATT-TCCATCC
391 AATAAAATATTACCGGGAATGAGATTCCCGGCCAACCAAACATGAGAATATGGGATTCT-CATCC
687003 CACACCCCCTTAATGGATCTTATGTTGTTGTAAGACTTTTGGGGTTCTCGTGTATTTTGATGCAG
455 CACACCCCCTTAATGGATCTTATGTTGTTGTAAGACTTTTGGGGTTCTCGTGTATTTTGATGCAG
687068 GACAAAACTATACAAATGGTTTTTGGATTATAAGGTATTGTTTTGCTGACTCACTCAAG
520 GACAAAACTATACAAATGGTTTTTGGATTATAAGGTATTGTTTTGCTGACTCACTCAAG
*
687127 GTCTTTATTATATATTTGTATAATATTACAAATTGTAAAATATTTATATATTTTCTTTAAAAAAT
1 GTCTCTATTATATATTTGTATAATATTACAAATTGTAAAATATTTATATATTTTCTTTAAAAAAT
*
687192 TAAATTCATAATATTTATAT-ACTTTTTTTACAAAATTAAAAATATAAAAAATGTTTAATGAAAG
66 TAAATTCATAATATTTATATAACTTTTTTTACAAAATTAAAAATATAAAAAATGTTTAATAAAAG
687256 GGTAATTTTTTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGA-TTTTTTTTGTAAATAT
131 GGTAATTTTTTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAATAT
687320 AAAATAATTTAAGGATAAATTTATAATTTAACCTTCGTAGAATTTTTATTATTCAATGACAGAAG
196 AAAATAATTTAAGGATAAATTTATAATTTAACCTTCGTAGAATTTTTATTATTCAATGACAGAAG
* *
687385 AATGATATTTTTGAAAAAATAAATAAAAATTTAAGGGCATTTTAGTCCAAAATGTCGGTAATGTT
261 AATGATATTTTTGAAAAAA-AAATAAAAATGTAAGGGCATTTTAGTCCAAAATGCCGGTAATGTT
* *
687450 ACAATACCTAAAGGAATGGAGGTAATGACATTCCCAGCAATATACCCCAAAAAATCTACTATTGG
325 ACAATACATAAAGGAATGGAGGTAATGACATTCCCAGCAATATACCCCAAAAAATCTACTATTGA
*
687515 TAATAAAATATTACCGGGAATGAGATTCCCGGCCAACCAAACATGAGAATGTGGGATTCTCATCC
390 TAATAAAATATTACCGGGAATGAGATTCCCGGCCAACCAAACATGAGAATATGGGATTCTCATCC
687580 CACACCCCCTTAATGGATCTTATGTTGTTGTAAGACTTTTGGGGTTCTCGTGTATTTTGATGCAG
455 CACACCCCCTTAATGGATCTTATGTTGTTGTAAGACTTTTGGGGTTCTCGTGTATTTTGATGCAG
*
687645 GACAAAACTATACAAATGGTTTTTGGATTATAAGGTATTGTTTTGTTGACTCACTCAAG
520 GACAAAACTATACAAATGGTTTTTGGATTATAAGGTATTGTTTTGCTGACTCACTCAAG
687704 TATTAAAATT
Statistics
Matches: 564, Mismatches: 11, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
576 100 0.18
577 380 0.67
578 84 0.15
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (578 bp):
GTCTCTATTATATATTTGTATAATATTACAAATTGTAAAATATTTATATATTTTCTTTAAAAAAT
TAAATTCATAATATTTATATAACTTTTTTTACAAAATTAAAAATATAAAAAATGTTTAATAAAAG
GGTAATTTTTTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTAAATAT
AAAATAATTTAAGGATAAATTTATAATTTAACCTTCGTAGAATTTTTATTATTCAATGACAGAAG
AATGATATTTTTGAAAAAAAAATAAAAATGTAAGGGCATTTTAGTCCAAAATGCCGGTAATGTTA
CAATACATAAAGGAATGGAGGTAATGACATTCCCAGCAATATACCCCAAAAAATCTACTATTGAT
AATAAAATATTACCGGGAATGAGATTCCCGGCCAACCAAACATGAGAATATGGGATTCTCATCCC
ACACCCCCTTAATGGATCTTATGTTGTTGTAAGACTTTTGGGGTTCTCGTGTATTTTGATGCAGG
ACAAAACTATACAAATGGTTTTTGGATTATAAGGTATTGTTTTGCTGACTCACTCAAG
Found at i:694006 original size:48 final size:49
Alignment explanation
Indices: 693920--694014 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 49
693910 GTGAAGTGAC
* * *
693920 TATTTTATAAATTTTAATAGTCGAGTGACTCGACAAAGTAAT-TCCTTA
1 TATTTTATAAATTTTAATAGTCAAATGACTCAACAAAGTAATATCCTTA
* * * *
693968 TATTTTGTAACTTTTAATAGTCAAATGACTTAATAAAGTAATATCCT
1 TATTTTATAAATTTTAATAGTCAAATGACTCAACAAAGTAATATCCT
694015 ATAATAAGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 35 0.90
49 4 0.10
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (49 bp):
TATTTTATAAATTTTAATAGTCAAATGACTCAACAAAGTAATATCCTTA
Found at i:698843 original size:6 final size:6
Alignment explanation
Indices: 698832--698866 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
698822 TAAGATTATG
698832 TTCTGA TTCTGA TTCTGA TTCTGA TTCTGA TTCTG
1 TTCTGA TTCTGA TTCTGA TTCTGA TTCTGA TTCTG
698867 CCGCACATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.51
Consensus pattern (6 bp):
TTCTGA
Found at i:701143 original size:23 final size:24
Alignment explanation
Indices: 701097--701144 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
701087 AGCTTTATAC
* *
701097 TTTATTTTATTTAATTTTAGTATT
1 TTTATTTTATATAATTGTAGTATT
*
701121 TTTATTTT-TATAATTGTATTATT
1 TTTATTTTATATAATTGTAGTATT
701144 T
1 T
701145 GTCCCAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (24 bp):
TTTATTTTATATAATTGTAGTATT
Found at i:704392 original size:20 final size:20
Alignment explanation
Indices: 704367--704408 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
704357 GAATGGTGTA
704367 TGTCCTGCGTACTTTCCCAG
1 TGTCCTGCGTACTTTCCCAG
704387 TGTCCTGCGTACTTTCCCAG
1 TGTCCTGCGTACTTTCCCAG
704407 TG
1 TG
704409 AGGTAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.33, G:0.21, T:0.36
Consensus pattern (20 bp):
TGTCCTGCGTACTTTCCCAG
Found at i:704981 original size:5 final size:5
Alignment explanation
Indices: 704973--705000 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
704963 TTAGTATCAC
704973 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
705001 CTGTCACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:707587 original size:24 final size:24
Alignment explanation
Indices: 707555--707680 Score: 206
Period size: 24 Copynumber: 5.4 Consensus size: 24
707545 TGATTGGTGT
707555 ATCGATGCACATGTTAAAGAATGC
1 ATCGATGCACATGTTAAAGAATGC
*
707579 ATCGATGCACATGTTAAATAATGC
1 ATCGATGCACATGTTAAAGAATGC
707603 ATCGATGCACATGTTAAAGAATGC
1 ATCGATGCACATGTTAAAGAATGC
707627 ATCGATGCACATGTTAAAGAATGC
1 ATCGATGCACATGTTAAAGAATGC
*
707651 ATCGATGCAC-TG-T--AGAATGT
1 ATCGATGCACATGTTAAAGAATGC
707671 ATCGATGCAC
1 ATCGATGCAC
707681 TTCAAAGGGG
Statistics
Matches: 99, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
20 16 0.16
22 1 0.01
23 2 0.02
24 80 0.81
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (24 bp):
ATCGATGCACATGTTAAAGAATGC
Found at i:708464 original size:32 final size:31
Alignment explanation
Indices: 708423--708545 Score: 126
Period size: 31 Copynumber: 3.9 Consensus size: 31
708413 AGTCGAGGGT
708423 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACA-AA
*
708455 TTACCTATG-TCTTTC-GAGACATATGGAC-AA
1 TTACCTATGTTC-TACGGA-ACATATGGACAAA
* *
708485 TATACCTATGTTCTAAGGAACATATGGACAAT
1 T-TACCTATGTTCTACGGAACATATGGACAAA
* * * *
708517 TTACCTAGGTTCTTCGGGACCTATGGACA
1 TTACCTATGTTCTACGGAACATATGGACA
708546 GTTGCCGAGG
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
30 3 0.04
31 46 0.61
32 27 0.36
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAAA
Found at i:719519 original size:29 final size:29
Alignment explanation
Indices: 719462--719519 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
719452 GTGTTGGCCG
* *
719462 TAGGTCGCCATGCTTTCCGGGTGACCTAC
1 TAGGTCGCCATGCTTTCCCGGCGACCTAC
*
719491 TAGGTCGCCATG-TCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCT-TTCCCGGCGACCTAC
719520 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.14, C:0.33, G:0.28, T:0.26
Consensus pattern (29 bp):
TAGGTCGCCATGCTTTCCCGGCGACCTAC
Found at i:719572 original size:10 final size:10
Alignment explanation
Indices: 719559--719611 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 10
719549 ACACGCTGGG
719559 CATCCGAGGC
1 CATCCGAGGC
719569 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
719583 CATCCGAGGC
1 CATCCGAGGC
719593 CATCCGAGAG-
1 CATCCGAG-GC
719603 CATCCGAGG
1 CATCCGAGG
719612 GCAACCGAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 1 0.03
10 24 0.63
11 3 0.08
13 2 0.05
14 8 0.21
ACGTcount: A:0.23, C:0.38, G:0.30, T:0.09
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:719581 original size:14 final size:14
Alignment explanation
Indices: 719562--719589 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
719552 CGCTGGGCAT
719562 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
719576 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
719590 GGCCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:719619 original size:20 final size:20
Alignment explanation
Indices: 719558--719620 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 20
719548 AACACGCTGG
*
719558 GCATCCGAGGCCATCCGACCGA
1 GCATCCGAGGCCAACCGA--GA
*
719580 GGCCATCCGAGGCCATCCGAGA
1 -G-CATCCGAGGCCAACCGAGA
*
719602 GCATCCGAGGGCAACCGAG
1 GCATCCGAGGCCAACCGAG
719621 CGAGCTATGC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.43
21 1 0.03
22 2 0.05
23 1 0.03
24 17 0.46
ACGTcount: A:0.24, C:0.37, G:0.32, T:0.08
Consensus pattern (20 bp):
GCATCCGAGGCCAACCGAGA
Found at i:719620 original size:10 final size:10
Alignment explanation
Indices: 719576--719611 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
719566 GGCCATCCGA
719576 CCGAGGCCAT
1 CCGAGGCCAT
719586 CCGAGGCCAT
1 CCGAGGCCAT
719596 CCGAGAG-CAT
1 CCGAG-GCCAT
719606 CCGAGG
1 CCGAGG
719612 GCAACCGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 1 0.04
10 23 0.92
11 1 0.04
ACGTcount: A:0.22, C:0.36, G:0.33, T:0.08
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:719693 original size:29 final size:29
Alignment explanation
Indices: 719661--719716 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
719651 GAGCGAGGGT
*
719661 AGGTCGCCCGAAGTGCATGGCGACCTACA
1 AGGTCGCCCGAAGGGCATGGCGACCTACA
* *
719690 AGGTCGCTCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGAAGGGCATGGCGACCTA
719717 TGTGTTGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.36, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGAAGGGCATGGCGACCTACA
Found at i:725198 original size:3 final size:3
Alignment explanation
Indices: 725190--725216 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
725180 TTTCCAGATA
725190 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
725217 GTTTAGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:726530 original size:21 final size:21
Alignment explanation
Indices: 726504--726548 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
726494 GATTTCTGGG
* *
726504 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
726525 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
726546 CAA
1 CAA
726549 ACGAACAACA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:727155 original size:18 final size:18
Alignment explanation
Indices: 727132--727166 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
727122 CTAGGAGATT
727132 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
727150 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
727167 CTAGATGGGA
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:727418 original size:2 final size:2
Alignment explanation
Indices: 727411--727451 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
727401 AATCTTGAGA
727411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
727452 AAATGAAATG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:728358 original size:149 final size:149
Alignment explanation
Indices: 728106--728402 Score: 506
Period size: 149 Copynumber: 2.0 Consensus size: 149
728096 CGGGATATAT
* ** *
728106 ATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATATATGATCCCTAGCATAT
1 ATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATATATGATCCCTAACATAT
728171 GTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAA
66 GTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAA
*
728236 TTCTACGCGGTTCTTCGGG
131 TTCTACGCGGTACTTCGGG
*
728255 ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACT-TGATCCCTAACATA
1 ATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATA-TATGATCCCTAACATA
* *
728319 TGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGTACTACGGTGCA
65 TGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCA
728384 ATTCTACGCGGTACTTCGG
130 ATTCTACGCGGTACTTCGG
728403 TGCAATTATA
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
149 138 0.99
150 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (149 bp):
ATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATATATGATCCCTAACATAT
GTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAA
TTCTACGCGGTACTTCGGG
Found at i:728403 original size:23 final size:23
Alignment explanation
Indices: 728370--728414 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
728360 ATTATTATAT
*
728370 GGTACTACGGTGCAATTCTACGC
1 GGTACTACGGTGCAATTATACGC
*
728393 GGTACTTCGGTGCAATTATACG
1 GGTACTACGGTGCAATTATACG
728415 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
GGTACTACGGTGCAATTATACGC
Found at i:731707 original size:21 final size:21
Alignment explanation
Indices: 731681--731725 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
731671 GATTTTTGGG
* *
731681 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
731702 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
731723 CAA
1 CAA
731726 ACGAACAACA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:732332 original size:18 final size:18
Alignment explanation
Indices: 732309--732343 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
732299 CTAGGAGATT
732309 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
732327 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
732344 CTAGATGGGA
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:733416 original size:147 final size:148
Alignment explanation
Indices: 733245--733557 Score: 515
Period size: 149 Copynumber: 2.1 Consensus size: 148
733235 GAGTCGAGGG
* **
733245 TCTACGCGGTCCTTCGGG-ATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATA
733309 -TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 CT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
733373 TATGGCACTATGGTGCAAT
130 TATGGCACTACGGTGCAAT
* *
733392 TCTACGCGGTTCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
733457 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
733522 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
733541 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
733558 TGCAATTATA
Statistics
Matches: 154, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
147 17 0.11
149 136 0.88
150 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATA
CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
ATGGCACTACGGTGCAAT
Found at i:733558 original size:23 final size:23
Alignment explanation
Indices: 733525--733569 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
733515 ATTATTATAT
*
733525 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
733548 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
733570 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:734959 original size:21 final size:22
Alignment explanation
Indices: 734935--734994 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
734925 TGATTTATTA
*
734935 TTATGGATTTCAATTTTCTTG-
1 TTATGGATTTCAAGTTTCTTGT
* *
734956 TTATGGATTTTAAGTTTGTTGT
1 TTATGGATTTCAAGTTTCTTGT
*
734978 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
734995 ATTGGAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (22 bp):
TTATGGATTTCAAGTTTCTTGT
Found at i:735244 original size:43 final size:43
Alignment explanation
Indices: 735189--735370 Score: 220
Period size: 43 Copynumber: 4.2 Consensus size: 43
735179 ACCAGATCTT
** *
735189 TTGCGGCGTTTGTGGGAAAAACATCGCTAAATCTCAAGACATA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAGACCTA
* ** * ** *
735232 TTGCGACGTTTGTGTCAAAAACGCCGCTAAATATTTACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAGACCTA
* *
735275 TTGCGGCGTTTGTTGGACAAACGCCGCTAAATCTCAAGACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAGACCTA
* * * *
735318 TTGCGGTGTTTGTGGGAAAAACGCCTCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAGACCTA
735361 TTGCGGCGTT
1 TTGCGGCGTT
735371 AAACGCCGCT
Statistics
Matches: 113, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 113 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (43 bp):
TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAGACCTA
Found at i:735307 original size:86 final size:86
Alignment explanation
Indices: 735189--735370 Score: 256
Period size: 86 Copynumber: 2.1 Consensus size: 86
735179 ACCAGATCTT
* *
735189 TTGCGGCGTTTGTGGGAAAAACATCGCTAAATCTCAAGACATATTGCGACGTTTGTGTCAAAAAC
1 TTGCGGCGTTTGTGGGAAAAACACCGCTAAATCTCAAGACATATTGCGACGTTTGTGGCAAAAAC
**
735254 GCCGCTAAATATTTACACCTA
66 GCCGCTAAATATCAACACCTA
* * * * ** *
735275 TTGCGGCGTTTGTTGGACAAACGCCGCTAAATCTCAAGACCTATTGCGGTGTTTGTGGGAAAAAC
1 TTGCGGCGTTTGTGGGAAAAACACCGCTAAATCTCAAGACATATTGCGACGTTTGTGGCAAAAAC
*
735340 GCCTCTAAATATCAACACCTA
66 GCCGCTAAATATCAACACCTA
735361 TTGCGGCGTT
1 TTGCGGCGTT
735371 AAACGCCGCT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (86 bp):
TTGCGGCGTTTGTGGGAAAAACACCGCTAAATCTCAAGACATATTGCGACGTTTGTGGCAAAAAC
GCCGCTAAATATCAACACCTA
Found at i:735404 original size:35 final size:35
Alignment explanation
Indices: 735336--735405 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
735326 TTTGTGGGAA
* *
735336 AAACGCCTCTAAATATCAACACCTATTGCGGCGTT
1 AAACGCCGCTAAATATCAACACCTATTACGGCGTT
* * *
735371 AAACGCCGCTATATATCAACACTTATTATGGCGTT
1 AAACGCCGCTAAATATCAACACCTATTACGGCGTT
735406 TGTTGGACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (35 bp):
AAACGCCGCTAAATATCAACACCTATTACGGCGTT
Found at i:735592 original size:2 final size:2
Alignment explanation
Indices: 735585--735609 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
735575 TGTTGTAGTG
735585 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 A
735610 ATTGAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:736069 original size:23 final size:23
Alignment explanation
Indices: 736032--736088 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
736022 AAAAACTACC
* *
736032 AAAAGACAGAGATAAAAGTGCCA
1 AAAAGACATAAATAAAAGTGCCA
* *
736055 CAAAA-ACATAAATAAACGTGTCA
1 -AAAAGACATAAATAAAAGTGCCA
736078 AAAAGACATAA
1 AAAAGACATAA
736089 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 4 0.14
23 20 0.71
24 4 0.14
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (23 bp):
AAAAGACATAAATAAAAGTGCCA
Found at i:736255 original size:16 final size:16
Alignment explanation
Indices: 736234--736272 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
736224 CAACTTGTAA
736234 AGAGAGAAAAAAAGAG
1 AGAGAGAAAAAAAGAG
* *
736250 AGAGAGAAAGAGAGAG
1 AGAGAGAAAAAAAGAG
736266 AGAGAGA
1 AGAGAGA
736273 GTAAGAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AGAGAGAAAAAAAGAG
Done.