Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008569.1 Hibiscus syriacus cultivar Beakdansim tig00111493_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: 1513883
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1371415 original size:22 final size:22
Alignment explanation
Indices: 1371369--1371414 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1371359 CAACTACAAT
*
1371369 AATAAATCAATCTATATTTTAA
1 AATAAATCAATCTATATTATAA
*
1371391 AATAAATCAATCTATGTTAATAA
1 AATAAATCAATCTATATT-ATAA
1371414 A
1 A
1371415 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (22 bp):
AATAAATCAATCTATATTATAA
Found at i:1371440 original size:134 final size:134
Alignment explanation
Indices: 1371276--1371589 Score: 490
Period size: 134 Copynumber: 2.4 Consensus size: 134
1371266 ACAACTACAA
* *
1371276 TAATAAATTA-TT-AAGTAAATTAATTTATATTTTAAAATAAATCAATCAATATTAATAAATTAT
1 TAATAAATTATTTAAAATAAATTAATTTATATTTTAAAATAAATCAATCAATACTAATAAATTAT
* * *
1371339 TTAAAATAAATCAATTTATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAA-TC
66 TTAAAATAAATCAATCTATACAACTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
**
1371403 TATGT
131 -ATAC
* * * *
1371408 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATTAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATTAATTTATATTTTAAAATAAATCAATCAATACTAATAAATTAT
*
1371473 TTAAAATAAATCAATCTATACAATTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
66 TTAAAATAAATCAATCTATACAACTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
1371538 ATAC
131 ATAC
1371542 TAATAAATTATTTAAAATAAATTAATTTATATTTTAAAATAAATCAAT
1 TAATAAATTATTTAAAATAAATTAATTTATATTTTAAAATAAATCAAT
1371590 TCATATTTTA
Statistics
Matches: 164, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
132 10 0.06
133 2 0.01
134 150 0.91
135 2 0.01
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.39
Consensus pattern (134 bp):
TAATAAATTATTTAAAATAAATTAATTTATATTTTAAAATAAATCAATCAATACTAATAAATTAT
TTAAAATAAATCAATCTATACAACTAAAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
ATAC
Found at i:1371444 original size:22 final size:22
Alignment explanation
Indices: 1371418--1371460 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1371408 TAATAAATTA
*
1371418 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
*
1371440 TTTAAAATAAATTAATCCATA
1 TTTAAAATAAATCAATCCATA
1371461 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1371507 original size:80 final size:76
Alignment explanation
Indices: 1371421--1371646 Score: 337
Period size: 76 Copynumber: 2.9 Consensus size: 76
1371411 TAAATTATTT
*
1371421 AAAATAAATCAATTCATATTTTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCA
1 AAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-A
1371486 ATCTATACAATTAA
65 ATCT-TA-AATTAA
* *
1371500 AATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATT
1 AA-AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA-T
* **
1371565 AAT-TTATATTTT
64 AATCTTAAATTAA
*
1371577 AAAATAAATCAATTCATATTTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATAA
1 AAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAA
1371642 TCTTA
66 TCTTA
1371647 TTAAATTATT
Statistics
Matches: 135, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
75 4 0.03
76 60 0.44
77 5 0.04
78 2 0.01
79 3 0.02
80 60 0.44
81 1 0.01
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (76 bp):
AAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAA
TCTTAAATTAA
Found at i:1371560 original size:14 final size:15
Alignment explanation
Indices: 1371520--1371570 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1371510 CAATCCATAT
*
1371520 TTTAAAATAAATCAA
1 TTTAAAATAAATTAA
*
1371535 TTCATACTAATAAATT-A
1 TT--TA-AAATAAATTAA
1371552 TTTAAAATAAATTAA
1 TTTAAAATAAATTAA
1371567 TTTA
1 TTTA
1371571 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
17 5 0.17
18 7 0.24
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTAAAATAAATTAA
Found at i:1371567 original size:22 final size:22
Alignment explanation
Indices: 1371552--1371616 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
1371542 TAATAAATTA
*
1371552 TTTAAAATAAATTAATTTATAT
1 TTTAAAATAAATTAATTAATAT
* *
1371574 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATTAATTAATAT
* *
1371596 TTTAAAATAAATCAATCAATA
1 TTTAAAATAAATTAATTAATA
1371617 CTAATAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATAAATTAATTAATAT
Found at i:1371611 original size:76 final size:77
Alignment explanation
Indices: 1371418--1371647 Score: 340
Period size: 80 Copynumber: 3.0 Consensus size: 77
1371408 TAATAAATTA
* *
1371418 TTTAAAATAAATCAATTCATATTTTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA
* *
1371483 TCAATCTATACAAT
66 TTAATCT-TA-TAT
** *
1371497 TAAAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAA
1 TTTAA-AATAAATCAATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAA
1371562 ATTAAT-TTATAT
65 ATTAATCTTATAT
1371574 TTTAAAATAAATCAATTCATATTTTAAAATAAATCAA-TCAATACTAATAAATTATTTAAAATAA
1 TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAA
1371638 A-TAATCTTAT
65 ATTAATCTTAT
1371648 TAAATTATTT
Statistics
Matches: 138, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
75 6 0.04
76 60 0.43
77 5 0.04
78 2 0.01
79 4 0.03
80 61 0.44
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.39
Consensus pattern (77 bp):
TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA
TTAATCTTATAT
Found at i:1371632 original size:54 final size:54
Alignment explanation
Indices: 1371369--1371639 Score: 242
Period size: 54 Copynumber: 5.1 Consensus size: 54
1371359 CAACTACAAT
* * **
1371369 AATAAATCAA-TCTATATTTTAAAATAAATCAATCTATGTTAATAAATTATTTAA
1 AATAAATCAATTC-ATATTTTAAAATAAATAAATCAATACTAATAAATTATTTAA
* *
1371423 AATAAATCAATTCATATTTTAAAATAAATTAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATAAATCAATACTAATAAATTATTTAA
** *
1371477 AATAAATCAA-TCTATACAATTAAAAT-AATAAATCAAT-C-CAT--A-T-TTTAA
1 AATAAATCAATTC-ATA-TTTTAAAATAAATAAATCAATACTAATAAATTATTTAA
** * ** * **
1371525 AATAAATCAATTCATACTAATAAATTATTTAAAAT-AA-ATTAATTTA-TATTTTAA
1 AATAAATCAATTCATA-TTTTAAAATAAAT-AAATCAATACTAATAAATTA-TTTAA
*
1371579 AATAAATCAATTCATATTTTAAAATAAATCAATCAATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATAAATCAATACTAATAAATTATTTAA
1371633 AATAAAT
1 AATAAAT
1371640 AATCTTATTA
Statistics
Matches: 177, Mismatches: 25, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
48 25 0.14
49 6 0.03
50 7 0.04
52 7 0.04
53 13 0.07
54 108 0.61
55 11 0.06
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.38
Consensus pattern (54 bp):
AATAAATCAATTCATATTTTAAAATAAATAAATCAATACTAATAAATTATTTAA
Found at i:1372302 original size:2 final size:2
Alignment explanation
Indices: 1372295--1372352 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1372285 AGATTTCAGT
1372295 TA TA TA TA TA 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 TA TA TA TA TA
1372337 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1372353 CAGAAAGCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1373391 original size:65 final size:64
Alignment explanation
Indices: 1373303--1373447 Score: 170
Period size: 64 Copynumber: 2.3 Consensus size: 64
1373293 ATTGAATAAA
* *
1373303 TTGA-ACATCGATGCACATACCATGCATCGATGCACTCGAG-TTTTTATGAAAACATCGAATGCA
1 TTGATACATCGATGCACATACCATGCATCGATACACTCGAGCTTGTT-TG-AAACATCGAATGCA
*
1373366 T
64 C
* *
1373367 TTGATACATCGATGCACA-AGCCATGCATGGATACACTCGGGCTTGTTTGAAACATCGAATGCAC
1 TTGATACATCGATGCACATA-CCATGCATCGATACACTCGAGCTTGTTTGAAACATCGAATGCAC
* * *
1373431 TTCATGCATCAATGCAC
1 TTGATACATCGATGCAC
1373448 TAAGGGTCCA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 33 0.47
65 33 0.47
66 4 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
TTGATACATCGATGCACATACCATGCATCGATACACTCGAGCTTGTTTGAAACATCGAATGCAC
Found at i:1386128 original size:21 final size:21
Alignment explanation
Indices: 1386102--1386145 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1386092 GTGTGTACTG
1386102 ACTGCTTTCTCCAATGACACC
1 ACTGCTTTCTCCAATGACACC
1386123 ACTGCTTTCTCCAATGACACC
1 ACTGCTTTCTCCAATGACACC
1386144 AC
1 AC
1386146 AGTTTTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.39, G:0.09, T:0.27
Consensus pattern (21 bp):
ACTGCTTTCTCCAATGACACC
Found at i:1386152 original size:21 final size:21
Alignment explanation
Indices: 1386105--1386153 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1386095 TGTACTGACT
*
1386105 GCTTTCTCCAATGACACCACT
1 GCTTTCTCCAATGACACCACA
1386126 GCTTTCTCCAATGACACCACA
1 GCTTTCTCCAATGACACCACA
*
1386147 GTTTTCT
1 GCTTTCT
1386154 GATACTCGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.35, G:0.10, T:0.33
Consensus pattern (21 bp):
GCTTTCTCCAATGACACCACA
Found at i:1393305 original size:5 final size:5
Alignment explanation
Indices: 1393295--1393323 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1393285 GCTATGGTAC
1393295 TAAAA TAAAA TAAAA T-AAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1393324 CATTAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:1393316 original size:14 final size:14
Alignment explanation
Indices: 1393297--1393323 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1393287 TATGGTACTA
1393297 AAATAAAATAAAAT
1 AAATAAAATAAAAT
1393311 AAATAAAATAAAA
1 AAATAAAATAAAA
1393324 CATTAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:1397672 original size:27 final size:28
Alignment explanation
Indices: 1397642--1397700 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
1397632 TTTAAAATAA
* *
1397642 AAATCAACAAACAATTATT-TAATAATT
1 AAATCAAAAAACAATTATTATAAAAATT
* **
1397669 AAATTAAAAAATTATTATTATAAAAATT
1 AAATCAAAAAACAATTATTATAAAAATT
1397697 AAAT
1 AAAT
1397701 AGCACAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATCAAAAAACAATTATTATAAAAATT
Found at i:1398270 original size:18 final size:19
Alignment explanation
Indices: 1398239--1398277 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1398229 CAAAAATCAC
*
1398239 AATAAAAAAGTATTGTTAA
1 AATAAAAAAGTATTATTAA
1398258 AATAAAAAA-TATTATTAA
1 AATAAAAAAGTATTATTAA
1398276 AA
1 AA
1398278 GAATTTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AATAAAAAAGTATTATTAA
Found at i:1398577 original size:41 final size:40
Alignment explanation
Indices: 1398531--1398610 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
1398521 TATAGGATAC
* * *
1398531 TATTTTATTGAGTCTCTCGATTATTAAAAGTTATAAAATGT
1 TATTTTATTGAGTCCCTCGACTATTAAAA-TTACAAAATGT
*
1398572 TATTTTGTTGAGTCCCTCGACTATTAAAATTACAAAATG
1 TATTTTATTGAGTCCCTCGACTATTAAAATTACAAAATG
1398611 ATCAACTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 9 0.26
41 26 0.74
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (40 bp):
TATTTTATTGAGTCCCTCGACTATTAAAATTACAAAATGT
Found at i:1403174 original size:27 final size:25
Alignment explanation
Indices: 1403110--1403176 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 25
1403100 TGGAATCCCT
1403110 GATGGAATTCAATTCCATCAAATGA
1 GATGGAATTCAATTCCATCAAATGA
* * *
1403135 GA-GAAAGTGAATTCCATCCAAAAATG-
1 GATGGAATTCAATTCCAT-C--AAATGA
1403161 GATGGAATTCAATTCC
1 GATGGAATTCAATTCC
1403177 CTTGTTGGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
24 12 0.38
25 3 0.09
26 2 0.06
27 15 0.47
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (25 bp):
GATGGAATTCAATTCCATCAAATGA
Found at i:1404091 original size:21 final size:21
Alignment explanation
Indices: 1404054--1404098 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1404044 GAGTTCTGGG
*
1404054 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
1404075 CAAGGGGAA-CTGATACCCCTT
1 CAAGGGGAATC-GATACCCATT
1404096 CAA
1 CAA
1404099 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:1404900 original size:2 final size:2
Alignment explanation
Indices: 1404893--1404919 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1404883 CATGAGTTAG
1404893 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
1404920 GGAATTGTAT
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:1405630 original size:30 final size:30
Alignment explanation
Indices: 1405586--1405739 Score: 247
Period size: 30 Copynumber: 5.1 Consensus size: 30
1405576 TCGAGACATA
1405586 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
1405617 TGGACAGTTACCGAGGATTTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1405647 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1405677 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
1405707 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1405736 TGGA
1 TGGA
1405740 TAGGTCCTTC
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
29 18 0.16
30 91 0.78
31 7 0.06
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1408849 original size:21 final size:21
Alignment explanation
Indices: 1408812--1408856 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1408802 GAGTTCTGGG
*
1408812 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
1408833 CAAGGGGAA-CTGATACCCCTT
1 CAAGGGGAATC-GATACCCATT
1408854 CAA
1 CAA
1408857 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:1409281 original size:16 final size:17
Alignment explanation
Indices: 1409247--1409286 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1409237 TTATATGAAA
*
1409247 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
1409264 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
1409280 TGATATG
1 TGATATG
1409287 CCATATGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:1409663 original size:2 final size:2
Alignment explanation
Indices: 1409656--1409728 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
1409646 CATGAGTTAG
1409656 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1409697 AT AT -T 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 A
1409729 GGAATTGTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 67 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1410449 original size:30 final size:30
Alignment explanation
Indices: 1410413--1410561 Score: 255
Period size: 30 Copynumber: 5.0 Consensus size: 30
1410403 TATGGACAGT
*
1410413 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
1410443 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
*
1410473 TTACCGAGGATCTTTATGATCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
1410503 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
* *
1410533 TTACCG-GGGTCTTTGTGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
1410562 GTCCTTCGGG
Statistics
Matches: 114, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 21 0.18
30 93 0.82
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:1412028 original size:18 final size:16
Alignment explanation
Indices: 1411992--1412037 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
1411982 TATGGAATTG
1411992 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
*
1412008 GATTCTAATTCCTTCACA
1 GATTCCAATTCC-T-ACA
*
1412026 GATTACAATTCC
1 GATTCCAATTCC
1412038 CATATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:1412584 original size:27 final size:26
Alignment explanation
Indices: 1412524--1412590 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
1412514 ACATGAACAA
*
1412524 ATATAAAATTTTATATTGAATATAAAC
1 ATATAAAA-ATTATATTGAATATAAAC
* * *
1412551 ATTTAAAAATTATATTGAAATATATAG
1 ATATAAAAATTATATTG-AATATAAAC
1412578 ATAT-AAAATTATA
1 ATATAAAAATTATA
1412591 AAACTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 17 0.50
27 17 0.50
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (26 bp):
ATATAAAAATTATATTGAATATAAAC
Found at i:1414533 original size:20 final size:21
Alignment explanation
Indices: 1414508--1414560 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1414498 CCCTTCAAGG
*
1414508 AGTATCGATACTCG-GGGTCC
1 AGTATCGATACTCGTAGGTCC
*
1414528 AGTATCGATACTCGTAGGTTC
1 AGTATCGATACTCGTAGGTCC
*
1414549 AATATCGATACT
1 AGTATCGATACT
1414561 GAGGCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (21 bp):
AGTATCGATACTCGTAGGTCC
Found at i:1418123 original size:35 final size:35
Alignment explanation
Indices: 1418099--1418225 Score: 148
Period size: 35 Copynumber: 3.6 Consensus size: 35
1418089 AATGTTATTT
*
1418099 TATGATTTTCAATTACTAGATATTTACAGTTATCA
1 TATGATTTTCAATTACCAGATATTTACAGTTATCA
*
1418134 TATGATTTTCAGTTACCAGATATTTACAGTTATCA
1 TATGATTTTCAATTACCAGATATTTACAGTTATCA
* * * * **
1418169 GATGATTTACAATTATCAGATAATTACAAATATCA
1 TATGATTTTCAATTACCAGATATTTACAGTTATCA
* *
1418204 TAT-ATTTTACAGTTATCAGATA
1 TATGATTTT-CAATTACCAGATA
1418226 CAAATTAATA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 4 0.05
35 75 0.95
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (35 bp):
TATGATTTTCAATTACCAGATATTTACAGTTATCA
Found at i:1418146 original size:18 final size:18
Alignment explanation
Indices: 1418099--1418221 Score: 69
Period size: 17 Copynumber: 7.0 Consensus size: 18
1418089 AATGTTATTT
*
1418099 TATGATTTTCAATTA-C-
1 TATGATTTTCAGTTATCA
1418115 TA-GATATTTACAGTTATCA
1 TATGAT-TTT-CAGTTATCA
*
1418134 TATGATTTTCAGTTACCA
1 TATGATTTTCAGTTATCA
* *
1418152 GAT-ATTTACAGTTATCA
1 TATGATTTTCAGTTATCA
* * *
1418169 GATGATTTACAATTATCA
1 TATGATTTTCAGTTATCA
* * * **
1418187 GAT-AATTACAAATATCA
1 TATGATTTTCAGTTATCA
1418204 TAT-ATTTTACAGTTATCA
1 TATGATTTT-CAGTTATCA
1418222 GATACAAATT
Statistics
Matches: 87, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
15 3 0.03
16 5 0.06
17 37 0.43
18 34 0.39
19 5 0.06
20 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (18 bp):
TATGATTTTCAGTTATCA
Found at i:1418166 original size:70 final size:70
Alignment explanation
Indices: 1418070--1418225 Score: 167
Period size: 70 Copynumber: 2.2 Consensus size: 70
1418060 AAGTATGATA
* * *** * * **
1418070 TTTACA-TTATCACATATTTAATGTTATTTTATGATTTTCAATTA-CTAGATATTTACAGTTATC
1 TTTACAGTTACCAGATATTTAATGTTATCAGATGATTTACAATTATC-AGATAATTACAAATATC
1418133 ATATGAT
65 ATAT-AT
1418140 TTT-CAGTTACCAGATATTTACA-GTTATCAGATGATTTACAATTATCAGATAATTACAAATATC
1 TTTACAGTTACCAGATATTTA-ATGTTATCAGATGATTTACAATTATCAGATAATTACAAATATC
1418203 ATATAT
65 ATATAT
*
1418209 TTTACAGTTATCAGATA
1 TTTACAGTTACCAGATA
1418226 CAAATTAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
69 7 0.10
70 63 0.88
71 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (70 bp):
TTTACAGTTACCAGATATTTAATGTTATCAGATGATTTACAATTATCAGATAATTACAAATATCA
TATAT
Found at i:1420045 original size:40 final size:40
Alignment explanation
Indices: 1420001--1420081 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
1419991 GTATATGAAG
*
1420001 AATGACTCCAAGTGATAGAGTAGTAATTTAACTGTTGAGA
1 AATGACTCCAAGTGATAGAGTAGTAATTTAACTATTGAGA
1420041 AATGACTCCAAGTGATAGAGTAGTAATTTAACTATTGAGA
1 AATGACTCCAAGTGATAGAGTAGTAATTTAACTATTGAGA
1420081 A
1 A
1420082 TAGAATTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (40 bp):
AATGACTCCAAGTGATAGAGTAGTAATTTAACTATTGAGA
Found at i:1423982 original size:209 final size:209
Alignment explanation
Indices: 1423639--1424030 Score: 610
Period size: 209 Copynumber: 1.9 Consensus size: 209
1423629 ATTAGTAACT
*
1423639 TTATACAACATACAATATCATTTTCTATCTATAATATTATATAAAGTATCGATATTTATTTTCTA
1 TTATACAACATACAATATCATTTTCTACCTATAATATTATATAAAGTATCGATATTTATTTTCTA
* *
1423704 CCTAGAATATCACTTTATACCTGTAATCAGTCCCAAATCATTCTTTACTTCAAAAACCCCAAACC
66 CATAGAATATCACTTTATACCTGTAATCAGTCCCAAATCATTATTTACTTCAAAAACCCCAAACC
* *
1423769 CATAAACCTAATCCCTAT-TTTC-GAATACTGTAATACT-AAAAAACTAGGGTTTTCTTCGAAGG
131 CATAAACCTAAT-CC-ATGTTTCTAAATACTGTAATACTAAAAAAACTAAGGTTTTCTTCGAAGG
1423831 ACAAGTATCAATACCA
194 ACAAGTATCAATACCA
* *
1423847 TTATACAACTTACAATATCATTTTCTACCTATAATATTATATAAAAGTATCGATTTTTATTTTCT
1 TTATACAACATACAATATCATTTTCTACCTATAATATTATAT-AAAGTATCGATATTTATTTTCT
* * * ** *
1423912 ACATAGAATATCACTTTCTACCTGTAATCGGTCCCAAATCGTTATTTACTTTGAAAACCCCAAGC
65 ACATAGAATATCACTTTATACCTGTAATCAGTCCCAAATCATTATTTACTTCAAAAACCCCAAAC
*
1423977 CCATAAACCTAATCCATGTTTCTAAATACTGTAATATTAAAAAAACTAAGGTTT
130 CCATAAACCTAATCCATGTTTCTAAATACTGTAATACTAAAAAAACTAAGGTTT
1424031 CAACAACATA
Statistics
Matches: 166, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
207 2 0.01
208 46 0.28
209 104 0.63
210 14 0.08
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (209 bp):
TTATACAACATACAATATCATTTTCTACCTATAATATTATATAAAGTATCGATATTTATTTTCTA
CATAGAATATCACTTTATACCTGTAATCAGTCCCAAATCATTATTTACTTCAAAAACCCCAAACC
CATAAACCTAATCCATGTTTCTAAATACTGTAATACTAAAAAAACTAAGGTTTTCTTCGAAGGAC
AAGTATCAATACCA
Found at i:1424775 original size:200 final size:198
Alignment explanation
Indices: 1424236--1424815 Score: 654
Period size: 200 Copynumber: 2.9 Consensus size: 198
1424226 TACCCAAGTC
* * * *
1424236 TCGATACTTTTGTGTAAGGTATCGATACTTTCGATACGTTTTCATTTTTTTTTCATTTCTTTTAA
1 TCGATACATGTGTGTAAGGTATCGATACTTTCAAGAC-TTTTCA---TTTTTTCATTTCTTTTAA
* * *
1424301 ATTCCTAAAGTACCGATACTATGATACATATACTTATAAAAGTATCGAT----ATCGTCAACATA
62 ATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAAT-TTCAACAT-
** * * * * *
1424362 TCCGGTAGCGCTTTACCGGTATTGTCATATTAAAACCAGTTTTGTCAAATTTTAACATGTTATAT
125 TCCGGTAGTTCTTTACCGGTTTTGTCAAATTGAAACCAGTTTTGTCAAATTTCAACCTGTTATAT
1424427 TGTCATGTA
190 TGTCATGTA
* * * * * * *
1424436 TCGATACATGTGTCTAAGGTATCGATA-TTTTATAGGC-TCT-ATTATTACAATTCTTTTAAATT
1 TCGATACATGTGTGTAAGGTATCGATACTTTCA-AGACTTTTCATTTTTTCATTTCTTTTAAATT
* * * * *
1424498 CATATAGTACCGATACTTTGGTGCATATATTTATAAAAGTATCGACACAAATTTCAACCATTCCG
65 CCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAA-CATTCCG
** * * * *
1424563 ACA-TCTCTTTACCGGTTTTGTCAAACTGAAACCGGTTTTGTCCAACTTCAACCTGTTATATTGT
129 GTAGT-TCTTTACCGGTTTTGTCAAATTGAAACCAGTTTTGTCAAATTTCAACCTGTTATATTGT
1424627 CATGTA
193 CATGTA
*
1424633 TCGATACATGTGTGTAAGGTATCGATACTTTCAAGACATTTTCCTTTTTTCATTTCTTTTAAATT
1 TCGATACATGTGTGTAAGGTATCGATACTTTCAAGAC-TTTTCATTTTTTCATTTCTTTTAAATT
* * *
1424698 CCTACAGTACCGATACTTTGGTACATATACTTATACACGTATCGATACAAATTTCAACAATTCCG
65 CCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAAC-ATTCCG
* * *
1424763 GTAGTTCTTTACCGGTTTTCTCAAATTGAAATCTGTTTTGTCAAATTTCAACC
129 GTAGTTCTTTACCGGTTTTGTCAAATTGAAACCAGTTTTGTCAAATTTCAACC
1424816 AGTTTTGTCA
Statistics
Matches: 312, Mismatches: 55, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
194 57 0.18
197 94 0.30
198 11 0.04
199 6 0.02
200 143 0.46
201 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (198 bp):
TCGATACATGTGTGTAAGGTATCGATACTTTCAAGACTTTTCATTTTTTCATTTCTTTTAAATTC
CTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAACATTCCGGT
AGTTCTTTACCGGTTTTGTCAAATTGAAACCAGTTTTGTCAAATTTCAACCTGTTATATTGTCAT
GTA
Found at i:1424806 original size:20 final size:20
Alignment explanation
Indices: 1424777--1424854 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
1424767 TTCTTTACCG
*
1424777 GTTTTCTCAAATTGAAATCT
1 GTTTTGTCAAATTGAAATCT
** * *
1424797 GTTTTGTCAAATTTCAACCA
1 GTTTTGTCAAATTGAAATCT
* *
1424817 GTTTTGTCAAATT-CATTACAT
1 GTTTTGTCAAATTGAAAT-C-T
1424838 GTTTTGTCAAATTGAAA
1 GTTTTGTCAAATTGAAA
1424855 CTGAAATTCT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 13 0.29
22 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.44
Consensus pattern (20 bp):
GTTTTGTCAAATTGAAATCT
Found at i:1424843 original size:21 final size:20
Alignment explanation
Indices: 1424796--1424850 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
1424786 AATTGAAATC
1424796 TGTTTTGTCAAATTTCAACCA
1 TGTTTTGTCAAA-TTCAACCA
1424817 -GTTTTGTCAAATTCATTA-CA
1 TGTTTTGTCAAATTCA--ACCA
1424837 TGTTTTGTCAAATT
1 TGTTTTGTCAAATT
1424851 GAAACTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.13
20 13 0.42
21 14 0.45
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (20 bp):
TGTTTTGTCAAATTCAACCA
Found at i:1428384 original size:228 final size:229
Alignment explanation
Indices: 1428093--1428554 Score: 707
Period size: 228 Copynumber: 2.0 Consensus size: 229
1428083 TAGTAATCGA
* * *
1428093 GTTTCCTTCAAAGGAATGGGTATACACTCTACTACAAGTATTGGTAACTTTATACAACATACAAT
1 GTTTCCTTCAAAGGAATGAGAATACACTCTACTACAAGTATAGGTAACTTTATACAACATACAAT
* *
1428158 ATCATTTTCTATC-TATAATATTATATAAAAGTATCGATATTTATTTTCTACATAGAATATCATT
66 ATCATTTTCTA-CATATAATATTATATAAAAGTATCAATATTTATTTTCTACATAGAATATCACT
* *
1428222 TTCTACCTGTAATCAGTTCCAAATCATTCTTTAC-TTCAAAAACCCTAAACCCATAAACCTAATC
130 TTCTACCTGTAATCAGTCCCAAATCATTATTTACTTTCAAAAA-CCTAAACCCATAAACCTAATC
* *
1428286 CCTATTT-TCGAATACTGTAATACT-AAAACACTAGG
194 CATATTTCT-GAATACTGTAATACTAAAAAAACTAGG
* * *
1428321 GTTTTCTTCAAAGGAATGAGAATACTCTCTACTACAAGTATAGGTACCTTTATACAACATACAAT
1 GTTTCCTTCAAAGGAATGAGAATACACTCTACTACAAGTATAGGTAACTTTATACAACATACAAT
*
1428386 ATCATTTTCTACATATAATATTATATAAAAGTATCAATATTTATTTTCTACCTAGAATATCACTT
66 ATCATTTTCTACATATAATATTATATAAAAGTATCAATATTTATTTTCTACATAGAATATCACTT
* * * *
1428451 TCTACCTGTAATCGGTCCCAAATCCTTATTTACTTTGAAAAACCTAAGCCCATAAACCTAATCCA
131 TCTACCTGTAATCAGTCCCAAATCATTATTTACTTTCAAAAACCTAAACCCATAAACCTAATCCA
*
1428516 TATTTCTGAATACTGTAATATTAAAAAAACTAGG
196 TATTTCTGAATACTGTAATACTAAAAAAACTAGG
1428550 GTTTC
1 GTTTC
1428555 GACAACATAC
Statistics
Matches: 211, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
227 1 0.00
228 188 0.89
229 22 0.10
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (229 bp):
GTTTCCTTCAAAGGAATGAGAATACACTCTACTACAAGTATAGGTAACTTTATACAACATACAAT
ATCATTTTCTACATATAATATTATATAAAAGTATCAATATTTATTTTCTACATAGAATATCACTT
TCTACCTGTAATCAGTCCCAAATCATTATTTACTTTCAAAAACCTAAACCCATAAACCTAATCCA
TATTTCTGAATACTGTAATACTAAAAAAACTAGG
Found at i:1429148 original size:196 final size:197
Alignment explanation
Indices: 1428811--1429324 Score: 567
Period size: 199 Copynumber: 2.6 Consensus size: 197
1428801 ATTTCTTTGC
* * **
1428811 AATTCCTAAAGTACCGATACTATGATACATATACTTATAAAAGTATCGATAC---CGTCAACATA
1 AATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAACAT-
* * * * * * *
1428873 TCCGGTAGCGCTTTACCAGTTTTGTCATATTGAAACCAGTTTTGTCAAATTTTAACATGTTCTAT
65 TCCGGTAGCTCTTTACCGGTTTTGTCAAATTGAAACCAGTTTTGTCAAATTTCAACCTCTTATAT
* *
1428938 TGTCATGTATCGATACAT-TGT-CTAAGATATCGATATTTTAC-AGGC-TCTAC-TATTGCAATT
130 TGTCATGTATCGATACATGTGTGC-AAGATAT-GATACTTT-CGAGACATCTACTTATTGCAATT
1428998 CTCTTA
192 CTCTTA
* * *
1429004 AATTCATAAAGTACCGATACTTTGGTGCATATATTTATAAAAGTATCGATACAAATTTCAACCAT
1 AATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAA-CAT
* * * * * *
1429069 TCCGGTATCTCTTTTCCGGTTTTGTGAAATTGAAACCGGTTTTGTCGAACTTCAACCTCTTATAT
65 TCCGGTAGCTCTTTACCGGTTTTGTCAAATTGAAACCAGTTTTGTCAAATTTCAACCTCTTATAT
* * * * * *
1429134 TGTCATGTATCGATACATGTGTGCAAGGTATGATACTTTCGAGACATTTTCCTTTTTTCATTTCT
130 TGTCATGTATCGATACATGTGTGCAAGATATGATACTTTCGAGACA-TCTACTTATTGCAATTCT
*
1429199 TTTA
194 CTTA
* * * * *
1429203 AATTCCTACAGTACCGATACTTTGGTACATACACTTATACACGTATCGATACAAATTTCAATAAT
1 AATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAA-CAT
* * * *
1429268 TCTGGTAGCTCTTTACCGATTTTCTCAAATTGAAACCAATTTTGTCAAATTTCAACC
65 TCCGGTAGCTCTTTACCGGTTTTGTCAAATTGAAACCAGTTTTGTCAAATTTCAACC
1429325 AGTTTTGTCA
Statistics
Matches: 263, Mismatches: 48, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
193 47 0.18
195 1 0.00
196 84 0.32
197 12 0.05
198 4 0.02
199 115 0.44
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (197 bp):
AATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCAACATT
CCGGTAGCTCTTTACCGGTTTTGTCAAATTGAAACCAGTTTTGTCAAATTTCAACCTCTTATATT
GTCATGTATCGATACATGTGTGCAAGATATGATACTTTCGAGACATCTACTTATTGCAATTCTCT
TA
Found at i:1429315 original size:20 final size:20
Alignment explanation
Indices: 1429286--1429359 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
1429276 CTCTTTACCG
* **
1429286 ATTTTCTCAAATTGAAACCA
1 ATTTTGTCAAATTCCAACCA
*
1429306 ATTTTGTCAAATTTCAACCA
1 ATTTTGTCAAATTCCAACCA
* * * *
1429326 GTTTTGTCAATTTCCAATCG
1 ATTTTGTCAAATTCCAACCA
1429346 ATTTTGTCAAATTC
1 ATTTTGTCAAATTC
1429360 ATTACCTGTT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (20 bp):
ATTTTGTCAAATTCCAACCA
Found at i:1431786 original size:29 final size:29
Alignment explanation
Indices: 1431744--1431802 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1431734 TTTTTCACCT
*
1431744 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAACCAATGACATCAA
1431773 AACTAAATTGATGTAACCAATGACATCAA
1 AACTAAATTGATGTAACCAATGACATCAA
1431802 A
1 A
1431803 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAACCAATGACATCAA
Found at i:1435361 original size:29 final size:29
Alignment explanation
Indices: 1435319--1435377 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1435309 TTTTTCACCT
1435319 AACTAAATTGATGTAAGCAATAACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
*
1435348 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
1435377 A
1 A
1435378 TTAATTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATAACATCAA
Found at i:1436451 original size:16 final size:16
Alignment explanation
Indices: 1436430--1436462 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1436420 CTTCAGTCCT
1436430 TTAGCTTGTTCATGGC
1 TTAGCTTGTTCATGGC
1436446 TTAGCTTGTTCATGGC
1 TTAGCTTGTTCATGGC
1436462 T
1 T
1436463 GTGCTCAATC
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:0.12, C:0.18, G:0.24, T:0.45
Consensus pattern (16 bp):
TTAGCTTGTTCATGGC
Found at i:1437525 original size:14 final size:14
Alignment explanation
Indices: 1437502--1437538 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1437492 CAGAATTTGT
*
1437502 CTTTACACATTAAA
1 CTTTATACATTAAA
1437516 CTTTATACATTAAA
1 CTTTATACATTAAA
1437530 CTTTATACA
1 CTTTATACA
1437539 AAATCTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTTATACATTAAA
Found at i:1441954 original size:25 final size:25
Alignment explanation
Indices: 1441903--1441976 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
1441893 TCATGTGTAC
* * * *
1441903 ATAAGTGATGTTGTGTTACATGCAT
1 ATAAGTGATGATGTGATATATACAT
*
1441928 ATAAGTGATGATGTGATATATATATAT
1 ATAAGTGATGATGTG--ATATATACAT
*
1441955 ATATAGTAATGATGTGATATAT
1 ATA-AGTGATGATGTGATATAT
1441977 GTTGTCATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 14 0.35
26 6 0.15
27 9 0.22
28 11 0.28
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (25 bp):
ATAAGTGATGATGTGATATATACAT
Found at i:1448173 original size:20 final size:20
Alignment explanation
Indices: 1448148--1448186 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1448138 TGTTAAAATG
1448148 GTGGGAATGTCATTACCTTA
1 GTGGGAATGTCATTACCTTA
1448168 GTGGGAATGTCATTACCTT
1 GTGGGAATGTCATTACCTT
1448187 CAAATTCTTA
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:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (20 bp):
GTGGGAATGTCATTACCTTA
Found at i:1449516 original size:20 final size:20
Alignment explanation
Indices: 1449491--1449528 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1449481 ATAATGTCCA
*
1449491 GGGGTACATATTCCCCCCAG
1 GGGGTACAGATTCCCCCCAG
*
1449511 GGGGTACCGATTCCCCCC
1 GGGGTACAGATTCCCCCC
1449529 TGTTTAACGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.39, G:0.26, T:0.18
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCCAG
Found at i:1449914 original size:34 final size:32
Alignment explanation
Indices: 1449875--1449944 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1449865 TTTTGTAAAG
* *
1449875 GGGAAAGGTTCTAGCTTGGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1449909 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1449941 GGGA
1 GGGA
1449945 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.30, C:0.16, G:0.33, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1451206 original size:28 final size:28
Alignment explanation
Indices: 1451166--1451222 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1451156 ATGTAAAAGA
* *
1451166 AGCCTTGTGTCCCATGAGATGGATAGTC
1 AGCCCTGTGTCCCATGAAATGGATAGTC
1451194 AGCCCTGTGTCCCATGAAATGGATAGTC
1 AGCCCTGTGTCCCATGAAATGGATAGTC
1451222 A
1 A
1451223 CATATGAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (28 bp):
AGCCCTGTGTCCCATGAAATGGATAGTC
Found at i:1452396 original size:25 final size:25
Alignment explanation
Indices: 1452362--1452424 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
1452352 TTCACTTAAC
1452362 AAAAATTATTTAATTTGATTTGATGT
1 AAAAA-TATTTAATTTGATTTGATGT
* * * *
1452388 AAAAATATTCAATTTTATTTTATTT
1 AAAAATATTTAATTTGATTTGATGT
*
1452413 AAAAAAATTTAA
1 AAAAATATTTAA
1452425 ATTCGAACCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
25 26 0.84
26 5 0.16
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
AAAAATATTTAATTTGATTTGATGT
Found at i:1452531 original size:2 final size:2
Alignment explanation
Indices: 1452524--1452561 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1452514 ATATGAAGAA
*
1452524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1452562 GATTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1455424 original size:29 final size:29
Alignment explanation
Indices: 1455392--1455457 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
1455382 AATAATATTT
* *
1455392 ATAAATAAACAAACAAAGAAT-ATCGATAA
1 ATAAATAAACAAA-AAACAATGATAGATAA
* *
1455421 ATAAACAAACAAAAAACATTGATAGATAA
1 ATAAATAAACAAAAAACAATGATAGATAA
1455450 ATAAATAA
1 ATAAATAA
1455458 GTACAATCGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.67, C:0.09, G:0.06, T:0.18
Consensus pattern (29 bp):
ATAAATAAACAAAAAACAATGATAGATAA
Found at i:1455444 original size:25 final size:25
Alignment explanation
Indices: 1455377--1455450 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 25
1455367 AAATAAAGAA
* *
1455377 AAACAAATAATATTTATAAATAAAC
1 AAACAAAAAATATTGATAAATAAAC
* *
1455402 AAACAAAGAATATCGATAAATAAAC
1 AAACAAAAAATATTGATAAATAAAC
* *
1455427 AAACAAAAAACATTGATAGATAAA
1 AAACAAAAAATATTGATAAATAAA
1455451 TAAATAAGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.20
Consensus pattern (25 bp):
AAACAAAAAATATTGATAAATAAAC
Found at i:1455603 original size:25 final size:26
Alignment explanation
Indices: 1455549--1455604 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1455539 ATATGATTAA
* *
1455549 AAATAAAGAAAAATAAAAATATCGAT
1 AAATAAACAAAAATAAAAATATCGAC
* *
1455575 AAATAAACAAACA-AAAAATATTGAC
1 AAATAAACAAAAATAAAAATATCGAC
1455600 AAATA
1 AAATA
1455605 GATAAATACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (26 bp):
AAATAAACAAAAATAAAAATATCGAC
Found at i:1462668 original size:17 final size:18
Alignment explanation
Indices: 1462629--1462670 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
1462619 AGTCGAGTCC
1462629 TTGACCATTGATCGTCTTCG
1 TTGACCATTGATCG--TTCG
1462649 TTGACCATTGATCG-TCG
1 TTGACCATTGATCGTTCG
1462666 TTGAC
1 TTGAC
1462671 TTTTTCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
20 14 0.64
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (18 bp):
TTGACCATTGATCGTTCG
Found at i:1470770 original size:17 final size:17
Alignment explanation
Indices: 1470745--1470794 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1470735 TAAGAGCAAA
*
1470745 GAAACTAAAAATATAAT
1 GAAAATAAAAATATAAT
1470762 GAAAATAAATAA-ATAAT
1 GAAAATAAA-AATATAAT
1470779 -ATAAATAAAATATATA
1 GA-AAATAAAA-ATATA
1470795 TATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 2 0.07
17 21 0.75
18 5 0.18
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (17 bp):
GAAAATAAAAATATAAT
Found at i:1470773 original size:4 final size:4
Alignment explanation
Indices: 1470764--1470912 Score: 53
Period size: 4 Copynumber: 37.2 Consensus size: 4
1470754 AATATAATGA
* * * *
1470764 AAAT AAAT AAAT AATAT AAAT AAAAT ATAT ATAT ATAT ATAT AAAT ATAA-
1 AAAT AAAT AAAT AA-AT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT A-AAT
* ** *
1470814 AAAT ATAT GTAT -AAT ATAAT AAA- ATACT AAAT AGTAAT -AAT -AAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT A-AAT AAAT A--AAT AAAT AAAT
* * * *
1470858 -AAT AAAT AAAT GAA- AAAT AAAT AAAT ATAT ATAT ATAAT -ATT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
*
1470904 AAAA AAAT A
1 AAAT AAAT A
1470913 GTAATCATAG
Statistics
Matches: 116, Mismatches: 15, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
3 18 0.16
4 78 0.67
5 17 0.15
6 3 0.03
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (4 bp):
AAAT
Found at i:1471627 original size:37 final size:37
Alignment explanation
Indices: 1471586--1471678 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
1471576 ATGCTTGTGG
* * *
1471586 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
1471623 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
1471660 ATCATATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
1471679 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:1472620 original size:106 final size:106
Alignment explanation
Indices: 1472439--1473617 Score: 1776
Period size: 106 Copynumber: 11.2 Consensus size: 106
1472429 GCATTGTTCT
* * *
1472439 GAGTCCAATATCC-TC-CATCGTGAAGTTGAAATTGGCTCT-AGAATCGGGAAATTATTTGTTGA
1 GAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTTGTTGA
* * * *
1472501 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTTTC
63 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
* * *
1472545 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1472610 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGCCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
1472651 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1472716 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
* * *
1472757 GAGTCCAATATCCTTCGTTGTGAAGTTTAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1472822 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
* * * *
1472863 GAGTCCAATATCATTCGCTGTGAAATTGAAATTGGCTCAGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1472928 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
* * * * * *
1472969 GAGTCCAATATCTTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1473034 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
1473075 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1473140 CCAGCGGTCGCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
* ** *
1473181 GAGTCTAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1473246 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTC-G
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
* *
1473286 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1473351 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTT-TCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
* * * *
1473391 GTGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-TGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1473455 CCAGTGGTCACTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
* * *
1473496 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1473561 CCAGTGGTCCTTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
1473602 GAGTCCAATATCCTTC
1 GAGTCCAATATCCTTC
1473618 ATTTTTTGTT
Statistics
Matches: 987, Mismatches: 80, Indels: 12
0.91 0.07 0.01
Matches are distributed among these distances:
104 51 0.05
105 183 0.19
106 750 0.76
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
Found at i:1475290 original size:24 final size:23
Alignment explanation
Indices: 1475249--1475313 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1475239 TTTTTTGTCC
* **
1475249 CTTTTCCTTTTTGATTTTTG-TT
1 CTTTTCTTTTTTCTTTTTTGCTT
*
1475271 CTTTTTTTTTCTTCTTTTTTGCTT
1 CTTTTCTTTT-TTCTTTTTTGCTT
*
1475295 CTTTTCTTTTTTGTTTTTT
1 CTTTTCTTTTTTCTTTTTT
1475314 CCCTTTTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
22 8 0.23
23 16 0.46
24 11 0.31
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (23 bp):
CTTTTCTTTTTTCTTTTTTGCTT
Found at i:1479680 original size:22 final size:21
Alignment explanation
Indices: 1479655--1479712 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 21
1479645 AATAATAAGA
1479655 GAAAATAAACTAAAAATATAAT
1 GAAAATAAA-TAAAAATATAAT
*
1479677 GAAAATAAAT--AAATATTAT
1 GAAAATAAATAAAAATATAAT
1479696 -AAAA-AAATAAAAATATA
1 GAAAATAAATAAAAATATA
1479713 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 14 0.44
21 1 0.03
22 9 0.28
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (21 bp):
GAAAATAAATAAAAATATAAT
Found at i:1479709 original size:19 final size:20
Alignment explanation
Indices: 1479656--1479731 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 20
1479646 ATAATAAGAG
*
1479656 AAAATAAACTAAAAATATAAT
1 AAAATAAA-TAAAAATATTAT
1479677 GAAAATAAAT--AAATATTAT
1 -AAAATAAATAAAAATATTAT
1479696 AAAA-AAATAAAAATATATAT
1 AAAATAAATAAAAATAT-TAT
*
1479716 ATATATAAATATAAAA
1 A-AAATAAATA-AAAA
1479732 ATGTATGTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.09
18 4 0.09
19 14 0.30
20 4 0.09
21 3 0.07
22 13 0.28
23 4 0.09
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (20 bp):
AAAATAAATAAAAATATTAT
Found at i:1479718 original size:22 final size:23
Alignment explanation
Indices: 1479670--1479852 Score: 110
Period size: 24 Copynumber: 7.9 Consensus size: 23
1479660 TAAACTAAAA
*
1479670 ATATAATGAAAATAAATAA-ATAT
1 ATATAATAAAAATAAA-AATATAT
1479693 -TATAA-AAAAATAAAAATATAT
1 ATATAATAAAAATAAAAATATAT
* *
1479714 ATATATATAAATATAAAAATGTAT
1 ATATA-ATAAAAATAAAAATATAT
* * *
1479738 GTATAAT-ATAAT-AAAATACTAA
1 ATATAATAAAAATAAAAATA-TAT
* *
1479760 ATAGTAATAATAATAATAATA-AT
1 ATA-TAATAAAAATAAAAATATAT
* *
1479783 AAATAAATGAAAAATAAATATATAT
1 ATAT-AAT-AAAAATAAAAATATAT
* *
1479808 ATATAATATTAAATAAAAAAATAGT
1 ATATAATA-AAAATAAAAATATA-T
* *
1479833 A-ATCATAGAAATATAAAATA
1 ATATAATAAAAATA-AAAATA
1479853 AAATGAAGTA
Statistics
Matches: 124, Mismatches: 22, Indels: 27
0.72 0.13 0.16
Matches are distributed among these distances:
20 2 0.02
21 17 0.14
22 17 0.14
23 19 0.15
24 57 0.46
25 12 0.10
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (23 bp):
ATATAATAAAAATAAAAATATAT
Found at i:1479873 original size:2 final size:2
Alignment explanation
Indices: 1479866--1479902 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1479856 TGAAGTAAGA
1479866 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 A
1479903 ACGTTAGGAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1480577 original size:37 final size:37
Alignment explanation
Indices: 1480531--1480620 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
1480521 CTTGTGGATT
* * *
1480531 CTATCTTTAGGAGTTTAAATAATAGTAGAACTCTATC
1 CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTATC
* ** *
1480568 CTATTTTTAGGAGTTTGAATCCTAGCAAAATTCTATC
1 CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTATC
1480605 CTATTTTTAGGAGTTT
1 CTATTTTTAGGAGTTT
1480621 GAATCCTAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTATC
Found at i:1482021 original size:24 final size:22
Alignment explanation
Indices: 1481952--1482031 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 22
1481942 AAATTATAAG
*
1481952 AGATAATTCCTAATAAATTCTA
1 AGATAATTCCTAATAAATTCAA
* * *
1481974 AGATAAATCC-ACAAAAATCACAA
1 AGATAATTCCTA-ATAAAT-TCAA
1481997 ATGATAATTCCTAATAAATTGCAAA
1 A-GATAATTCCTAATAAATT-C-AA
*
1482022 AGAGAATTCC
1 AGATAATTCC
1482032 CTTAATTGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
21 1 0.02
22 14 0.32
23 3 0.07
24 22 0.50
25 4 0.09
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.26
Consensus pattern (22 bp):
AGATAATTCCTAATAAATTCAA
Found at i:1484892 original size:13 final size:13
Alignment explanation
Indices: 1484876--1484900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1484866 TTGTTTGTGT
1484876 TGTTCGTTTATTG
1 TGTTCGTTTATTG
1484889 TGTTCGTTTATT
1 TGTTCGTTTATT
1484901 ATTTAAATGA
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:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:1486130 original size:20 final size:20
Alignment explanation
Indices: 1486105--1486178 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1486095 TTTTCCCAAT
*
1486105 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
1486125 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
1486146 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
1486166 TCGCAACGCGAAT
1 TCGCAACGCGAAT
1486179 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:1486148 original size:21 final size:21
Alignment explanation
Indices: 1486122--1486192 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
1486112 GCGAATAAGT
1486122 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1486143 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1486163 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
1486184 AAATCGCAA
1 AAATCGCAA
1486193 TGTGATACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1486150 original size:41 final size:41
Alignment explanation
Indices: 1486105--1486194 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
1486095 TTTTCCCAAT
1486105 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1486146 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1486187 TCGCAATG
1 TCGCAATG
1486195 TGATACTGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1486210 original size:41 final size:41
Alignment explanation
Indices: 1486124--1486258 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1486114 GAATAAGTAA
* * *
1486124 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAG-ATACTG-ACT
*
1486165 ATCGCAACGCGAATTGGGAAAATCGCAATGTGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
* * ** * *
1486206 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGAGATACTGACT
*
1486247 TTCGCAACGCGA
1 ATCGCAACGCGA
1486259 TACTGTCTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
Found at i:1486253 original size:20 final size:20
Alignment explanation
Indices: 1486228--1486280 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1486218 TAATAAAAAA
*
1486228 TCGCAACGAGATACT-TACTT
1 TCGCAACGCGATACTGT-CTT
1486248 TCGCAACGCGATACTGTCTT
1 TCGCAACGCGATACTGTCTT
1486268 TCGCAACGCGATA
1 TCGCAACGCGATA
1486281 ATACATAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGTCTT
Found at i:1486497 original size:22 final size:22
Alignment explanation
Indices: 1486469--1486511 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1486459 ACTCTCTCAT
1486469 CCATCTCCGAAGAAATCCGTCC
1 CCATCTCCGAAGAAATCCGTCC
**
1486491 CCATCTCCGGTGAAATCCGTC
1 CCATCTCCGAAGAAATCCGTC
1486512 TATCTAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.21
Consensus pattern (22 bp):
CCATCTCCGAAGAAATCCGTCC
Found at i:1488151 original size:18 final size:18
Alignment explanation
Indices: 1488130--1488174 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1488120 TCCACTTCGG
*
1488130 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1488148 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1488166 GAGCCATCA
1 GAGCCATCA
1488175 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1488695 original size:19 final size:20
Alignment explanation
Indices: 1488641--1488707 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1488631 TAGTTTACTT
* *
1488641 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1488661 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1488681 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1488700 TCGCAACG
1 TCGCAACG
1488708 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1488715 original size:14 final size:14
Alignment explanation
Indices: 1488696--1488753 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1488686 ATGCGAAATG
1488696 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1488710 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1488726 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1488742 AAAATCGCAACG
1 AAAATCGCAACG
1488754 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1488738 original size:32 final size:33
Alignment explanation
Indices: 1488680--1488770 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1488670 GGAAATGGCT
*
1488680 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1488713 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1488745 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1488771 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1488764 original size:19 final size:19
Alignment explanation
Indices: 1488641--1488775 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
1488631 TAGTTTACTT
* **
1488641 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1488661 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1488681 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1488700 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1488714 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1488732 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1488746 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1488765 TCGCAATGCGA
1 TCGCAACGCGA
1488776 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1488806 original size:14 final size:14
Alignment explanation
Indices: 1488787--1488844 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1488777 TTGTGTTTCG
1488787 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1488801 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1488817 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
1488833 CGTTGTGATTTT
1 CGTTGCGATTTT
1488845 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1488821 original size:32 final size:33
Alignment explanation
Indices: 1488782--1488860 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1488772 GCGATTTGTG
1488782 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1488814 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1488847 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1488861 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1488879 original size:20 final size:19
Alignment explanation
Indices: 1488845--1488899 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1488835 TTGTGATTTT
*
1488845 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1488864 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1488884 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1488900 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1491489 original size:24 final size:24
Alignment explanation
Indices: 1491462--1491515 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1491452 GTATTCAAAA
* *
1491462 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1491486 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1491510 TTTGAT
1 TTTGAT
1491516 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1494031 original size:33 final size:33
Alignment explanation
Indices: 1493984--1494109 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
1493974 GGAAATTACT
1493984 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
1494017 ATCGTAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1494049 TTTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1494082 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1494110 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
32 26 0.32
33 55 0.68
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1494068 original size:65 final size:65
Alignment explanation
Indices: 1493987--1494116 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 65
1493977 AATTACTATC
* *
1493987 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
*
1494052 GCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1494117 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (65 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
Found at i:1494131 original size:19 final size:20
Alignment explanation
Indices: 1494109--1494151 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1494099 AAATCGCAAC
1494109 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1494128 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1494148 GCGA
1 GCGA
1494152 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1494136 original size:14 final size:14
Alignment explanation
Indices: 1494137--1494170 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1494127 TGCGATTTTC
1494137 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1494151 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1494165 ATTTTC
1 ATTTTC
1494171 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1494311 original size:14 final size:14
Alignment explanation
Indices: 1494292--1494342 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
1494282 CATCAATTAA
1494292 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1494306 ACAAATCACCTTTT
1 ACAAATCAACTTTT
*
1494320 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1494334 ACAAATCAA
1 ACAAATCAA
1494343 TTAAACAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1495756 original size:21 final size:21
Alignment explanation
Indices: 1495690--1495756 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1495680 GTGAATCGGG
*
1495690 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1495710 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1495732 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1495753 CTCT
1 CTCT
1495757 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1495775 original size:42 final size:41
Alignment explanation
Indices: 1495690--1495812 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1495680 GTGAATCGGG
* * * * *
1495690 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1495732 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1495774 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1495813 CGAGTCGGCT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1497823 original size:20 final size:19
Alignment explanation
Indices: 1497792--1497932 Score: 77
Period size: 19 Copynumber: 7.8 Consensus size: 19
1497782 TCTTTTGGTT
1497792 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1497811 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1497832 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1497851 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
1497865 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
1497881 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* *
1497898 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
1497917 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1497933 TGCGATTTTT
Statistics
Matches: 92, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 17 0.18
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 34 0.37
20 29 0.32
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1497874 original size:33 final size:33
Alignment explanation
Indices: 1497817--1497902 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
1497807 ACGAGATAAT
*
1497817 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1497851 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
1497884 GACAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
1497903 AAAAATCGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1497909 original size:19 final size:19
Alignment explanation
Indices: 1497887--1497937 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
1497877 GCGACCAGAC
1497887 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
1497906 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
*
1497925 AATCGCAATGCGA
1 AATCGCAACGCGA
1497938 TTTTTATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:1497949 original size:19 final size:19
Alignment explanation
Indices: 1497927--1497968 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1497917 GAAATGAAAA
1497927 TCGCAATGCGATTTTTATT
1 TCGCAATGCGATTTTTATT
**
1497946 TCGCGTTGCGATTTTTATT
1 TCGCAATGCGATTTTTATT
1497965 TCGC
1 TCGC
1497969 GTTGCGATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (19 bp):
TCGCAATGCGATTTTTATT
Found at i:1497969 original size:19 final size:19
Alignment explanation
Indices: 1497933--1497999 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
1497923 AAAATCGCAA
1497933 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
1497952 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1497971 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1497991 TGCGATTTT
1 TGCGATTTT
1498000 CATTCTCGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 31 0.72
20 12 0.28
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1498517 original size:20 final size:20
Alignment explanation
Indices: 1498492--1498543 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1498482 CGCTATGTAA
*
1498492 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
1498512 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
1498532 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1498544 TTTTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:1498563 original size:41 final size:41
Alignment explanation
Indices: 1498511--1498588 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1498501 CGAAAGTCAG
* * *
1498511 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTTT
* *
1498552 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
1498589 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.41
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTTT
Found at i:1498577 original size:20 final size:20
Alignment explanation
Indices: 1498492--1498585 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1498482 CGCTATGTAA
*
1498492 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
1498512 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** ***
1498532 ATCTCGTTGCGATTTTTTTTT
1 ATCGCGTTGCGA-TAGTCAGT
*
1498553 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1498573 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1498586 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 46 0.79
21 12 0.21
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1498603 original size:21 final size:21
Alignment explanation
Indices: 1498574--1498670 Score: 142
Period size: 21 Copynumber: 4.7 Consensus size: 21
1498564 ATAGTCAGTA
*
1498574 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
1498595 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
1498615 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
1498636 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
1498657 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1498671 ACTTATTCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
20 16 0.24
21 50 0.76
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:1498679 original size:41 final size:41
Alignment explanation
Indices: 1498574--1498687 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
1498564 ATAGTCAGTA
* **
1498574 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTACCAATTCGCGTTGCGATTTACCAAT
* *
1498615 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAATTCGCGTTGCGA-TTTACCAAT
* ** *
1498657 TCGCGTTGCGA-TTTACTTATTCGCATTGCGA
1 TCGCATTGCGATTTTACCAATTCGCGTTGCGA
1498688 ATTGGGAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 48 0.75
42 16 0.25
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGATTTTACCAATTCGCGTTGCGATTTACCAAT
Found at i:1499208 original size:31 final size:31
Alignment explanation
Indices: 1499139--1499210 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1499129 AACTTAATTC
** * *
1499139 GTAATCACTTTCGTTTTGTTTTAATCAATAT
1 GTAATCACTTTCAATTCGTTTTAATCAAGAT
* * *
1499170 ATGATCACTTTCAATTCGTTTTAATTAAGAT
1 GTAATCACTTTCAATTCGTTTTAATCAAGAT
1499201 GTAATCACTT
1 GTAATCACTT
1499211 ACCTAAACAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (31 bp):
GTAATCACTTTCAATTCGTTTTAATCAAGAT
Found at i:1499754 original size:86 final size:87
Alignment explanation
Indices: 1499659--1499854 Score: 340
Period size: 86 Copynumber: 2.3 Consensus size: 87
1499649 GTCGGATGGT
* *
1499659 AGAAAATATCCACTTTCGTTTGTATTATTGAAAATAAAATTTTCTGATCTTAAAATAAGGCATAC
1 AGAAAATATCCACTTTCGTTTGTATTATTGAAAAGAAAATTTTCTGATCTTAAAATAAGACATAC
1499724 T-AAAAAATCATGAAATTTATC
66 TAAAAAAATCATGAAATTTATC
* *
1499745 AGAAAATATCCACTTTCGTTTGTATTATTTAAAAGAAAATTTTCTGATCTTAAAATAATACATAC
1 AGAAAATATCCACTTTCGTTTGTATTATTGAAAAGAAAATTTTCTGATCTTAAAATAAGACATAC
*
1499810 TAAAAAAATCATGAAATTTATT
66 TAAAAAAATCATGAAATTTATC
1499832 AGAAAATATCCACTTTCGTTTGT
1 AGAAAATATCCACTTTCGTTTGT
1499855 TTGTGAGGTG
Statistics
Matches: 104, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
86 62 0.60
87 42 0.40
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (87 bp):
AGAAAATATCCACTTTCGTTTGTATTATTGAAAAGAAAATTTTCTGATCTTAAAATAAGACATAC
TAAAAAAATCATGAAATTTATC
Found at i:1502619 original size:21 final size:21
Alignment explanation
Indices: 1502595--1502635 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1502585 TATGATATTG
1502595 ACTCGA-TCAAAAAACTGATTA
1 ACTCGATTCAAAAAA-TGATTA
1502616 ACTCGATTCAAAAAATGATT
1 ACTCGATTCAAAAAATGATT
1502636 GATCTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (21 bp):
ACTCGATTCAAAAAATGATTA
Found at i:1511981 original size:31 final size:31
Alignment explanation
Indices: 1511946--1512010 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1511936 CTTAATAAAA
*
1511946 AATCAAATATAAACAATTTAGAGTAAGTTTT
1 AATCAAATATAAACAATTTAGAATAAGTTTT
*
1511977 AATCAAATATAAATAATTTAGAATAAGTTTT
1 AATCAAATATAAACAATTTAGAATAAGTTTT
1512008 AAT
1 AAT
1512011 TCTTCTCTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.37
Consensus pattern (31 bp):
AATCAAATATAAACAATTTAGAATAAGTTTT
Found at i:1513659 original size:23 final size:23
Alignment explanation
Indices: 1513628--1513696 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1513618 TACCACAGCT
*
1513628 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1513651 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1513674 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1513697 TATAATGTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Done.