Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 4 of 198
Found at i:1251106 original size:22 final size:23
Alignment explanation
Indices: 1251076--1251244 Score: 78
Period size: 24 Copynumber: 7.4 Consensus size: 23
1251066 AAAATTTGGA
* *
1251076 CAGCTTATATACAACAAA-TGGG
1 CAGCATATATACAACAAATTGAG
* * * *
1251098 CAGCATATACATACCAAATTTAG
1 CAGCATATATACAACAAATTGAG
* * * * *
1251121 CAGCATTTTTACACCAAAATTTAA
1 CAGCATATATACAAC-AAATTGAG
*
1251145 CAGCATATATACAACAAA-TGGG
1 CAGCATATATACAACAAATTGAG
*
1251167 CAGCATATACGTAC--CGAATTGAG
1 CAGCATATA--TACAACAAATTGAG
* * * * * *
1251190 CAACATTTTTACACCAAAATTTAA
1 CAGCATATATACAAC-AAATTGAG
* *
1251214 CCGCATATATACAACAAA-TGGG
1 CAGCATATATACAACAAATTGAG
1251236 CAGCATATA
1 CAGCATATA
1251245 CATAATACGT
Statistics
Matches: 105, Mismatches: 34, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
21 3 0.03
22 36 0.34
23 29 0.28
24 37 0.35
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (23 bp):
CAGCATATATACAACAAATTGAG
Found at i:1251157 original size:24 final size:24
Alignment explanation
Indices: 1251044--1251162 Score: 73
Period size: 24 Copynumber: 5.0 Consensus size: 24
1251034 TTATATACCG
* * *
1251044 AATTAAACAACATTTATACACCAA
1 AATTTAACAGCATATATACACCAA
* * *
1251068 AATTTGGACAGCTTATATACAAC-A
1 AATTT-AACAGCATATATACACCAA
*** * *
1251092 AA-TGGGCAGCATATACATACC-A
1 AATTTAACAGCATATATACACCAA
* * *
1251114 AATTTAGCAGCATTTTTACACCAA
1 AATTTAACAGCATATATACACCAA
*
1251138 AATTTAACAGCATATATACAACAA
1 AATTTAACAGCATATATACACCAA
1251162 A
1 A
1251163 TGGGCAGCAT
Statistics
Matches: 70, Mismatches: 22, Indels: 6
0.71 0.22 0.06
Matches are distributed among these distances:
22 15 0.21
23 14 0.20
24 29 0.41
25 12 0.17
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.26
Consensus pattern (24 bp):
AATTTAACAGCATATATACACCAA
Found at i:1251167 original size:69 final size:69
Alignment explanation
Indices: 1251051--1251248 Score: 315
Period size: 69 Copynumber: 2.9 Consensus size: 69
1251041 CCGAATTAAA
* * *
1251051 CAACATTTATACACCAAAATTTGGACAGCTTATATACAACAAATGGGCAGCATATACATACCAAA
1 CAACATTTTTACACCAAAATTT-AACAGCATATATACAACAAATGGGCAGCATATACATACCAAA
*
1251116 TTTAG
65 TTGAG
* * *
1251121 CAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACGTACCGAAT
1 CAACATTTTTACACCAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACATACCAAAT
1251186 TGAG
66 TGAG
*
1251190 CAACATTTTTACACCAAAATTTAACCGCATATATACAACAAATGGGCAGCATATACATA
1 CAACATTTTTACACCAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACATA
1251249 ATACGTCATA
Statistics
Matches: 118, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
69 98 0.83
70 20 0.17
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (69 bp):
CAACATTTTTACACCAAAATTTAACAGCATATATACAACAAATGGGCAGCATATACATACCAAAT
TGAG
Found at i:1252763 original size:15 final size:15
Alignment explanation
Indices: 1252745--1252777 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1252735 TGTTGGACAT
1252745 AAGCCTATCTCACAA
1 AAGCCTATCTCACAA
1252760 AAGCCTATCTCACAA
1 AAGCCTATCTCACAA
1252775 AAG
1 AAG
1252778 GATTCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.18
Consensus pattern (15 bp):
AAGCCTATCTCACAA
Found at i:1254034 original size:25 final size:25
Alignment explanation
Indices: 1254000--1254056 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
1253990 GTGAAAATCT
1254000 AATGCATATGATGCAATGCGATGCA
1 AATGCATATGATGCAATGCGATGCA
1254025 AATGCATATGATGCAATGCGATGCA
1 AATGCATATGATGCAATGCGATGCA
1254050 AATGCAT
1 AATGCAT
1254057 GGAATGAATG
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:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (25 bp):
AATGCATATGATGCAATGCGATGCA
Found at i:1256637 original size:3 final size:3
Alignment explanation
Indices: 1256619--1256667 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
1256609 GTATATATAT
*
1256619 ATA AGTA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1256664 ATA A
1 ATA A
1256668 GACAAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1256732 original size:3 final size:3
Alignment explanation
Indices: 1256712--1256762 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
1256702 AAATGGGAAT
* * * *
1256712 ATA ACA ATA ATA ACA ATA AT- ATA GATA ATA ATA CTA ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
1256757 ATA ATA
1 ATA ATA
1256763 TATTAGTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1258496 original size:44 final size:44
Alignment explanation
Indices: 1258417--1258522 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
1258407 CTAATTCGGC
* * *
1258417 CTACTGCAACTTCAGAGG-TATATGATTCATCGTTTTAGTCCGCT
1 CTACTGCAACTTCAG-GGAGATAGGATTCATAGTTTTAGTCCGCT
**
1258461 CTACTGCAACTTCAGGGAGATAGGATT-AGTAGTTTTAGTTTGCT
1 CTACTGCAACTTCAGGGAGATAGGATTCA-TAGTTTTAGTCCGCT
* * *
1258505 CCACTGTAACTTCGGGGA
1 CTACTGCAACTTCAGGGA
1258523 TCTTACTACA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
43 3 0.06
44 49 0.94
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (44 bp):
CTACTGCAACTTCAGGGAGATAGGATTCATAGTTTTAGTCCGCT
Found at i:1258956 original size:44 final size:44
Alignment explanation
Indices: 1258850--1258957 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
1258840 TTTGACCCAT
* *
1258850 TCCACTGCAACTTCAGGGAGATAGGACTCGTATCTTCAACTTGC
1 TCCACTGCAACTTCAGGGGGATAAGACTCGTATCTTCAACTTGC
* *
1258894 TCCACAGCAACTTCAGGGGGATAAGACTTGTAAT-TTCAACTTGC
1 TCCACTGCAACTTCAGGGGGATAAGACTCGT-ATCTTCAACTTGC
* *
1258938 -CCTGCTGCAATTTCAGGGGG
1 TCC-ACTGCAACTTCAGGGGG
1258958 CAAGGTTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 2 0.04
44 51 0.93
45 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGGGATAAGACTCGTATCTTCAACTTGC
Found at i:1259092 original size:228 final size:227
Alignment explanation
Indices: 1258809--1259220 Score: 533
Period size: 228 Copynumber: 1.8 Consensus size: 227
1258799 GATCTGTTCT
* *
1258809 ACTGCAACTTCAGAGAGATAAGATCCATCATTTTGACCCATTCCACTGCAACTTCAGGGAGATAG
1 ACTGCAACTTCAGAGAAATAAGATCCATCATTTTAACCCATTCCACTGCAACTTCAGGGAGATAG
* * * *
1258874 GACTCGTATCTTCAA-CTTGCTCCACAGCAACTTCAGGGGGATAAGACTTGTAAT-TTCAACTTG
66 GACTAGTAACTTCAATC-TGCTCCACAGCAACTTCAGGGAGATAAGACTTGT-ATCTTCAACCTG
** * * * * *
1258937 CCCTGCTGCAATTTCA-GGGGGCAAGGTTTTGGTTTTTTCAACCTACTCTACTGCAACCGCAACT
129 CCCCACTACAACTTCATGGGGACAAGG-TTT-GCTATTTCAACCTACTCTACTGCAACCGCAACT
1259001 TCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCC
192 TCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCC
* * * * * *
1259037 ACTGCAACTTCAGGGAAATAAGATCCATTATTTTAATCCGTTCCACTGTAACTTCAGGGAGGTAG
1 ACTGCAACTTCAGAGAAATAAGATCCATCATTTTAACCCATTCCACTGCAACTTCAGGGAGATAG
* * * * *
1259102 GATTAGTAACTTTAATCTGCTCCACTGTAACTTTAGGGAGATAAGACTTGTATCTTCAACCTGCC
66 GACTAGTAACTTCAATCTGCTCCACAGCAACTTCAGGGAGATAAGACTTGTATCTTCAACCTGCC
* *
1259167 CCACTACAACTTCATGGGGATAAGGTTTGCTATTTCAACCTGCTCTACTGCAAC
131 CCACTACAACTTCATGGGGACAAGGTTTGCTATTTCAACCTACTCTACTGCAAC
1259221 TTCAGAGAGA
Statistics
Matches: 155, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
227 25 0.16
228 121 0.78
229 9 0.06
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (227 bp):
ACTGCAACTTCAGAGAAATAAGATCCATCATTTTAACCCATTCCACTGCAACTTCAGGGAGATAG
GACTAGTAACTTCAATCTGCTCCACAGCAACTTCAGGGAGATAAGACTTGTATCTTCAACCTGCC
CCACTACAACTTCATGGGGACAAGGTTTGCTATTTCAACCTACTCTACTGCAACCGCAACTTCAG
GGAAATAAGATTCACTATCTTCAGTCTGCTCC
Found at i:1259171 original size:44 final size:44
Alignment explanation
Indices: 1259079--1259230 Score: 112
Period size: 44 Copynumber: 3.5 Consensus size: 44
1259069 TTAATCCGTT
* * * * *
1259079 CCACTGTAACTTCAGGGAGGTAGGATTAGTAACTTTAATCTGCT
1 CCACTGTAACTTCAGGGAGATAAGATTAGTAACTTCAACCTGCC
* *
1259123 CCACTGTAACTTTAGGGAGATAAGACTT-GTATCTTCAACCTGCC
1 CCACTGTAACTTCAGGGAGATAAGA-TTAGTAACTTCAACCTGCC
** * * * *
1259167 CCACTACAACTTCATGGG-GATAAGGTTTGCT-ATTTCAACCTGCT
1 CCACTGTAACTTCA-GGGAGATAAGATTAG-TAACTTCAACCTGCC
* * *
1259211 CTACTGCAACTTCAGAGAGA
1 CCACTGTAACTTCAGGGAGA
1259231 CAAAATTTGA
Statistics
Matches: 86, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
43 4 0.05
44 76 0.88
45 6 0.07
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
CCACTGTAACTTCAGGGAGATAAGATTAGTAACTTCAACCTGCC
Found at i:1259286 original size:41 final size:41
Alignment explanation
Indices: 1259206--1259287 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
1259196 CTATTTCAAC
*
1259206 CTGCTCTACTGCAACTTCAGAGAGACAAAATTTGATATGAT
1 CTGCTCTACTGCAACTTCAGAGAGACAAAATCTGATATGAT
* * * *
1259247 CTGCTCTACTGCAACTTTAGAGAGACGAGATCTGTTATGAT
1 CTGCTCTACTGCAACTTCAGAGAGACAAAATCTGATATGAT
1259288 AGATTTAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (41 bp):
CTGCTCTACTGCAACTTCAGAGAGACAAAATCTGATATGAT
Found at i:1260992 original size:69 final size:69
Alignment explanation
Indices: 1260910--1261162 Score: 398
Period size: 69 Copynumber: 3.7 Consensus size: 69
1260900 TTTGTACTAA
1260910 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
1 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
**
1260975 TATG
66 GCTG
*
1260979 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACGTATAT
1 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
1261044 GCTG
66 GCTG
* * * *
1261048 CCCATTTGTTGTGTATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTATGTATAT
1 CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
1261113 GCTG
66 GCTG
* * * *
1261117 CCCATTTGTTGTATATAAGTTGTCCAAATTTTGGTGTATAAATGTT
1 CCCATTTGTTGTATATATGCTGT-TAAATTTTGGTGTAAAAATGTT
1261163 TTTTAATTTG
Statistics
Matches: 169, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
69 150 0.89
70 19 0.11
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (69 bp):
CCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATAT
GCTG
Found at i:1261114 original size:23 final size:23
Alignment explanation
Indices: 1261023--1261117 Score: 75
Period size: 23 Copynumber: 4.1 Consensus size: 23
1261013 GTAAAAATAT
* *
1261023 TGCTCAATTTGGTACGTATATGC
1 TGCTAAATTTGGTATGTATATGC
** * *
1261046 TGC-CCATTTGTTGTGTATATGC
1 TGCTAAATTTGGTATGTATATGC
* * ** *
1261068 TGTTAAATTTTGGTGTAAAAATGC
1 TGCTAAA-TTTGGTATGTATATGC
1261092 TGCTAAATTTGGTATGTATATGC
1 TGCTAAATTTGGTATGTATATGC
1261115 TGC
1 TGC
1261118 CCATTTGTTG
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
22 17 0.31
23 19 0.35
24 18 0.33
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (23 bp):
TGCTAAATTTGGTATGTATATGC
Found at i:1261133 original size:22 final size:22
Alignment explanation
Indices: 1260913--1261156 Score: 57
Period size: 24 Copynumber: 10.5 Consensus size: 22
1260903 GTACTAACCC
* *
1260913 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATATATGCTG-CAA
* * * *
1260936 ATTTTGGTGTAAAAATGTTGCTCA
1 A-TTTGGTGTATATATGCTGC-AA
*
1260960 ATTTGGTACGTATATTATGC--C-C
1 ATTTGGT--GTATA-TATGCTGCAA
* *
1260982 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATATATGCTG-CAA
*
1261005 ATTTTGGTGTAAAAATATTGCT-C-A
1 A-TTTGGTGT--ATATA-TGCTGCAA
*** **
1261029 ATTTGGTACGTATATGCTGCCC
1 ATTTGGTGTATATATGCTGCAA
* * *
1261051 ATTTGTTGTGTATATGCTGTTAA
1 ATTTGGTGTATATATGCTG-CAA
* *
1261074 ATTTTGGTGTAAAAATGCTGCTAA
1 A-TTTGGTGTATATATGCTGC-AA
* * **
1261098 ATTTGGTATGTATATGCTGCCC
1 ATTTGGTGTATATATGCTGCAA
* * *
1261120 ATTTGTTGTATATAAGTTGTCCAA
1 ATTTGGTGTATATATGCTG--CAA
1261144 ATTTTGGTGTATA
1 A-TTTGGTGTATA
1261157 AATGTTTTTT
Statistics
Matches: 154, Mismatches: 46, Indels: 40
0.64 0.19 0.17
Matches are distributed among these distances:
19 5 0.03
20 9 0.06
21 4 0.03
22 36 0.23
23 30 0.19
24 45 0.29
25 14 0.09
26 7 0.05
27 4 0.03
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.45
Consensus pattern (22 bp):
ATTTGGTGTATATATGCTGCAA
Found at i:1261201 original size:138 final size:137
Alignment explanation
Indices: 1260923--1261202 Score: 355
Period size: 138 Copynumber: 2.0 Consensus size: 137
1260913 ATTTGTTGTA
* * *
1260923 TATATGCTGTTAAATTTTGGTGTAAAAATGTTGCTCAATTTGGTACGTATATTATGCCCATTTGT
1 TATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTACGTATATGATGCCCATTTGT
* * * * * *
1260988 TGTATATATGCTGTTAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACGTATATGCTGCCCAT
66 TGTATATAAGCTGTCAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACATAAATGCTGCCAAA
*
1261053 TTGTTGTG
131 TTG-TATG
* *
1261061 TATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTATGTATATGCTGCCCATTTGT
1 TATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTACGTATATGATGCCCATTTGT
* * * ** * *
1261126 TGTATATAAGTTGTCCAAATTTTGGTGTATAAATGTTTTTTAATTTGGTATATAAATGCTGTCCA
66 TGTATATAAGCTGT-CAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACATAAATGCTG-CCA
1261191 AATTG-ATG
129 AATTGTATG
1261199 TATA
1 TATA
1261203 AGAGCTGTCC
Statistics
Matches: 121, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
138 78 0.64
139 37 0.31
140 6 0.05
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (137 bp):
TATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTAAATTTGGTACGTATATGATGCCCATTTGT
TGTATATAAGCTGTCAAATTTTGGTGTAAAAATATTGCTCAATTTGGTACATAAATGCTGCCAAA
TTGTATG
Found at i:1265356 original size:18 final size:18
Alignment explanation
Indices: 1265335--1265372 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1265325 AGTTCAAAAC
1265335 ATATGATTCTTAACGTGT
1 ATATGATTCTTAACGTGT
1265353 ATATGATTCTTAACGTGT
1 ATATGATTCTTAACGTGT
1265371 AT
1 AT
1265373 GTATTCTTCT
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:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (18 bp):
ATATGATTCTTAACGTGT
Found at i:1267683 original size:22 final size:21
Alignment explanation
Indices: 1267644--1267687 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
1267634 AAATTTTTAA
1267644 TAAATAAAAAATATTAAATAT
1 TAAATAAAAAATATTAAATAT
1267665 TAAATTAAAATAATA-TAAATAT
1 TAAA-TAAAA-AATATTAAATAT
1267687 T
1 T
1267688 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 13 0.62
23 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATAAAAAATATTAAATAT
Found at i:1270767 original size:2 final size:2
Alignment explanation
Indices: 1270760--1270798 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1270750 TAAATATCTC
1270760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1270799 AGTTATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1273256 original size:2 final size:2
Alignment explanation
Indices: 1273249--1273286 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1273239 CAATAAATAA
1273249 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
1273287 TATGTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1273809 original size:24 final size:26
Alignment explanation
Indices: 1273781--1273836 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
1273771 TTGATTAAAA
*
1273781 ATAAAAAT-AAAAATATATATTTGAT
1 ATAAAAATAAAAAATATATATTTAAT
1273806 -TAAAAATAAAAAATATATATTTAAT
1 ATAAAAATAAAAAATATATATTTAAT
1273831 ATAAAA
1 ATAAAA
1273837 TTCGAGCCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 7 0.25
25 16 0.57
26 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
ATAAAAATAAAAAATATATATTTAAT
Found at i:1273817 original size:25 final size:27
Alignment explanation
Indices: 1273762--1273836 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 27
1273752 AAATATATAT
1273762 AATATATATTTGATTAAAAATAAAAATAAA
1 AATATATATTTGATTAAAAAT---AATAAA
1273792 AATATATATTTGATTAAAAAT-A-AAA
1 AATATATATTTGATTAAAAATAATAAA
*
1273817 AATATATATTTAATATAAAA
1 AATATATATTTGAT-TAAAA
1273837 TTCGAGCCGG
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
25 16 0.37
26 6 0.14
30 21 0.49
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
AATATATATTTGATTAAAAATAATAAA
Found at i:1280543 original size:2 final size:2
Alignment explanation
Indices: 1280536--1280566 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1280526 CTTTTTATTC
1280536 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 A
1280567 AATTAGTCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1282775 original size:21 final size:21
Alignment explanation
Indices: 1282751--1282790 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1282741 GAAACACAGA
*
1282751 GATTCAAATGAAAGGCAGCGT
1 GATTCAAATGAAAAGCAGCGT
1282772 GATTCAAATGAAAAGCAGC
1 GATTCAAATGAAAAGCAGC
1282791 AACAAAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.17
Consensus pattern (21 bp):
GATTCAAATGAAAAGCAGCGT
Found at i:1284355 original size:4 final size:4
Alignment explanation
Indices: 1284341--1284386 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
1284331 TGAAAATATA
*
1284341 ATAC TTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1284387 TTACAAATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:1291318 original size:22 final size:22
Alignment explanation
Indices: 1291284--1291325 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1291274 ATTTAAACAA
* *
1291284 AAAAAAATTAAATATCAAATTG
1 AAAAAAATCAAATACCAAATTG
*
1291306 AAAAAACTCAAATACCAAAT
1 AAAAAAATCAAATACCAAAT
1291326 CTAATATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAAAATCAAATACCAAATTG
Found at i:1291343 original size:31 final size:32
Alignment explanation
Indices: 1291308--1291373 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
1291298 TCAAATTGAA
* *
1291308 AAAACTCAAATACCAAATCT-AATATT-AAATC
1 AAAACTAAAATACCAAAT-TAAACATTAAAATC
*
1291339 AAAACTAAAATACTAAATTAAACATTAAAATC
1 AAAACTAAAATACCAAATTAAACATTAAAATC
1291371 AAA
1 AAA
1291374 CTCTTAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 21 0.70
32 8 0.27
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (32 bp):
AAAACTAAAATACCAAATTAAACATTAAAATC
Found at i:1294632 original size:15 final size:15
Alignment explanation
Indices: 1294612--1294644 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1294602 AAAACAATAT
1294612 AAACAATGAATACTA
1 AAACAATGAATACTA
*
1294627 AAACAATGAATGCTA
1 AAACAATGAATACTA
1294642 AAA
1 AAA
1294645 TAACTCTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.18
Consensus pattern (15 bp):
AAACAATGAATACTA
Found at i:1297620 original size:3 final size:3
Alignment explanation
Indices: 1297612--1297637 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1297602 GAGGAAATTA
1297612 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1297638 AGGATATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1298611 original size:16 final size:17
Alignment explanation
Indices: 1298592--1298625 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1298582 AAAGATTATG
1298592 AAATAAAAA-AGTTTAA
1 AAATAAAAATAGTTTAA
1298608 AAATAAAAATAGTTTAA
1 AAATAAAAATAGTTTAA
1298625 A
1 A
1298626 TCTAAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
AAATAAAAATAGTTTAA
Found at i:1302060 original size:17 final size:17
Alignment explanation
Indices: 1302030--1302067 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1302020 ATTTGATTTG
1302030 TTAT-TATCGCATAGAA
1 TTATATATCGCATAGAA
*
1302046 TTATATATCGTATAGAA
1 TTATATATCGCATAGAA
1302063 TTATA
1 TTATA
1302068 CAAAGTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (17 bp):
TTATATATCGCATAGAA
Found at i:1313162 original size:16 final size:15
Alignment explanation
Indices: 1313143--1313173 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1313133 CTATAATATA
1313143 ATATATATATATGTGC
1 ATATATAT-TATGTGC
1313159 ATATATATTATGTGC
1 ATATATATTATGTGC
1313174 TCTTATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
ATATATATTATGTGC
Found at i:1327188 original size:19 final size:19
Alignment explanation
Indices: 1327164--1327210 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1327154 AATCAGCAAT
1327164 AATACATAAATGTCAAGTA
1 AATACATAAATGTCAAGTA
1327183 AATACATAAATGTCAAGTA
1 AATACATAAATGTCAAGTA
*
1327202 AATGCATAA
1 AATACATAA
1327211 CATAGCAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
AATACATAAATGTCAAGTA
Found at i:1330890 original size:13 final size:13
Alignment explanation
Indices: 1330872--1330897 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1330862 TGACTTTGCA
1330872 CGCTGAAATAGAC
1 CGCTGAAATAGAC
1330885 CGCTGAAATAGAC
1 CGCTGAAATAGAC
1330898 AATCCCAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
CGCTGAAATAGAC
Found at i:1337459 original size:18 final size:19
Alignment explanation
Indices: 1337420--1337459 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1337410 TAAATGGTAG
1337420 CAAAACAGTGAGAAAACAA
1 CAAAACAGTGAGAAAACAA
1337439 CAAAACAGT-A-AAAATCAA
1 CAAAACAGTGAGAAAA-CAA
1337457 CAA
1 CAA
1337460 GAAAACAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 9 0.45
ACGTcount: A:0.65, C:0.17, G:0.10, T:0.07
Consensus pattern (19 bp):
CAAAACAGTGAGAAAACAA
Found at i:1340885 original size:351 final size:350
Alignment explanation
Indices: 1340238--1340917 Score: 1191
Period size: 351 Copynumber: 1.9 Consensus size: 350
1340228 TTTATATGGG
1340238 TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
1 TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
*
1340303 GGTAGAATGTATCTTTTTTTAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAGG
66 GGTAGAATGTATCTTTTTATAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAGG
1340368 ATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATTT
131 ATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATTT
*
1340433 ATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAATTTTGTG
196 ATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAAATTTGTG
* *
1340498 AATTAAATATATTCTTAAAGCAGAATGTGTGTTATTATGTATGTTTTGAGTAAGTCCCTGATTCA
261 AATTAAATATATTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATTCA
1340563 TTTTGCCTGTATGTTTAAGGTTTCT
326 TTTTGCCTGTATGTTTAAGGTTTCT
* * *
1340588 TTTCATTTTTTCTGTAATTTATTTTTGGGAAATATGTAAAATGTGGCTTCATATTTGAAGTTTGG
1 TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
* *
1340653 GGTGGAATGTATCTTTTTCATAGAGCTACAAAGTTAGGCATTTTGGGTTTTTGGTAAGGT-AAAG
66 GGTAGAATGTATCTTTTT-ATAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAG
1340717 AGATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACAT
130 -GATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACAT
* * * * * *
1340782 TTATCGTGCAACATTTTTTTACCACAGTTTGACTGCTTTAGTTCATTTTCTTGACTTCAAATTTG
194 TTATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAAATTTG
*
1340847 TGAATTAAATATGTTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATT
259 TGAATTAAATATATTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATT
1340912 CATTTT
324 CATTTT
1340918 TGCTTTCTGC
Statistics
Matches: 312, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
350 83 0.27
351 229 0.73
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (350 bp):
TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
GGTAGAATGTATCTTTTTATAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAGG
ATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATTT
ATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAAATTTGTG
AATTAAATATATTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATTCA
TTTTGCCTGTATGTTTAAGGTTTCT
Found at i:1352841 original size:71 final size:71
Alignment explanation
Indices: 1352725--1352866 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
1352715 ACCAATTTGA
1352725 CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
1 CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
1352790 TTAGTG
66 TTAGTG
1352796 CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
1 CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
1352861 TTAGTG
66 TTAGTG
1352867 TCGCGGTTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (71 bp):
CAAAACATGTAAACATCGCAAACTAAATTTATTGTTATACCAATTAAAATTATGTACTGAATATA
TTAGTG
Found at i:1354119 original size:38 final size:38
Alignment explanation
Indices: 1354068--1354143 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1354058 CGTTAGATTA
1354068 ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
1 ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
1354106 ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
1 ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
1354144 TATTGATCCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (38 bp):
ACTTGGATCTAAGGCATGTTTTCCTACTCGTTGTTGGG
Found at i:1360153 original size:43 final size:43
Alignment explanation
Indices: 1360088--1360174 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
1360078 TCATCACCTA
*
1360088 TTTGGTTTAAAGAATTTGTTTTTAAT-GTTCTTTTTTATAATTTT
1 TTTGGTTTAAAGAATTTATTTTTAATGGTTC-TTTTTAT-ATTTT
1360132 TTTGG-TTAAAGAATTTATTTTTAATGGTTCTTTTTATATTTT
1 TTTGGTTTAAAGAATTTATTTTTAATGGTTCTTTTTATATTTT
1360174 T
1 T
1360175 AGAATTTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
42 6 0.15
43 26 0.63
44 9 0.22
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.63
Consensus pattern (43 bp):
TTTGGTTTAAAGAATTTATTTTTAATGGTTCTTTTTATATTTT
Found at i:1365080 original size:20 final size:20
Alignment explanation
Indices: 1365057--1365236 Score: 55
Period size: 20 Copynumber: 8.9 Consensus size: 20
1365047 TAAAGTATTT
1365057 AAAAATATATAAAAATTGTA
1 AAAAATATATAAAAATTGTA
* * *
1365077 AAAAA-AAATAATTAAATTATT
1 AAAAATATATAA--AAATTGTA
* * * *
1365098 AAAAA-AT-CAAATACTGTT
1 AAAAATATATAAAAATTGTA
* * * *
1365116 AAAAAGATTTTAAATTTGTA
1 AAAAATATATAAAAATTGTA
* *
1365136 AAAAATCTTATTAAAAATTATA
1 AAAAAT-ATA-TAAAAATTGTA
* * **
1365158 AAACATTATTTAAATTTTGTA
1 AAA-AATATATAAAAATTGTA
* *
1365179 AAAATTAT-TTAAAATTGT-
1 AAAAATATATAAAAATTGTA
* * *
1365197 AAATATTTATTAAAAGTTGTA
1 AAAAATATA-TAAAAATTGTA
* *
1365218 AAAATTATTTAAAAATTGT
1 AAAAATATATAAAAATTGT
1365237 GAACCAATAG
Statistics
Matches: 111, Mismatches: 39, Indels: 20
0.65 0.23 0.12
Matches are distributed among these distances:
18 15 0.14
19 14 0.13
20 39 0.35
21 29 0.26
22 12 0.11
23 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAAATATATAAAAATTGTA
Found at i:1365207 original size:40 final size:39
Alignment explanation
Indices: 1365124--1365236 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 39
1365114 TTAAAAAGAT
* *
1365124 TTTAAATTTGTAAAAAATCTTATTAAAAATTATAAAACATTA
1 TTTAAATTTGT-AAAAA--TTATTTAAAATTGTAAAACATTA
*
1365166 TTTAAATTTTGTAAAAATTATTTAAAATTGTAAATA-TTTA
1 TTTAAA-TTTGTAAAAATTATTTAAAATTGTAAA-ACATTA
* *
1365206 TTAAAAGTTGTAAAAATTATTTAAAAATTGT
1 TTTAAATTTGTAAAAATTATTT-AAAATTGT
1365237 GAACCAATAG
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
39 15 0.24
40 31 0.49
41 1 0.02
42 11 0.17
43 5 0.08
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (39 bp):
TTTAAATTTGTAAAAATTATTTAAAATTGTAAAACATTA
Found at i:1365456 original size:10 final size:10
Alignment explanation
Indices: 1365441--1365511 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
1365431 GATTATTTCC
1365441 AATTTTTAAT
1 AATTTTTAAT
*
1365451 AATTTTTAACA
1 AATTTTTAA-T
** *
1365462 AAAATTAAAT
1 AATTTTTAAT
*
1365472 AATGTTTAAT
1 AATTTTTAAT
*
1365482 GATTTTTAAT
1 AATTTTTAAT
1365492 AAATTTTTTAA-
1 -AA-TTTTTAAT
1365503 AATTTTTAA
1 AATTTTTAA
1365512 ATATTTTAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
9 7 0.15
10 26 0.55
11 7 0.15
12 7 0.15
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:1365517 original size:10 final size:10
Alignment explanation
Indices: 1365491--1365620 Score: 51
Period size: 9 Copynumber: 13.1 Consensus size: 10
1365481 TGATTTTTAA
1365491 TAAAT-TTTT
1 TAAATATTTT
1365500 TAAA-ATTTT
1 TAAATATTTT
1365509 TAAATATTTT
1 TAAATATTTT
*
1365519 AAACAATATTTT
1 -TA-AATATTTT
*
1365531 ATAAATTATTTA
1 -TAAA-TATTTT
*
1365543 TAAAT-TTTC
1 TAAATATTTT
*** *
1365552 TCCTTTTTTT
1 TAAATATTTT
*
1365562 TAGA-ATTTT
1 TAAATATTTT
1365571 TAAATATTTT
1 TAAATATTTT
*
1365581 T-AATGTTTT
1 TAAATATTTT
*
1365590 CT-AATA-ATT
1 -TAAATATTTT
1365599 TAAATATTGTT
1 TAAATATT-TT
1365610 TACAAT-TTTT
1 TA-AATATTTT
1365620 T
1 T
1365621 TGATTTGGTC
Statistics
Matches: 92, Mismatches: 17, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
8 1 0.01
9 37 0.40
10 23 0.25
11 13 0.14
12 18 0.20
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (10 bp):
TAAATATTTT
Found at i:1384611 original size:27 final size:27
Alignment explanation
Indices: 1384581--1384635 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1384571 CCATATTATT
1384581 TTTTATTTTTT-TATAATAAAAATTTTA
1 TTTTATTTTTTAT-TAATAAAAATTTTA
* *
1384608 TTTTATTTTTTATTTATTAAAATTTTA
1 TTTTATTTTTTATTAATAAAAATTTTA
1384635 T
1 T
1384636 ATTCATGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTATTTTTTATTAATAAAAATTTTA
Found at i:1384736 original size:5 final size:5
Alignment explanation
Indices: 1384726--1384834 Score: 209
Period size: 5 Copynumber: 21.8 Consensus size: 5
1384716 TATATGATAC
1384726 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1384776 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
1384826 GTAAT ATAA
1 ATAAT ATAA
1384835 ACTTAGAGAA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 102 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:1401760 original size:32 final size:32
Alignment explanation
Indices: 1401719--1401780 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1401709 CACCACTATT
1401719 ATTTTTAATCTTACTAAAGATAAATGCACTGC
1 ATTTTTAATCTTACTAAAGATAAATGCACTGC
*
1401751 ATTTTTAATCTTACTGAAGATAAATGCACT
1 ATTTTTAATCTTACTAAAGATAAATGCACT
1401781 ACACATCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (32 bp):
ATTTTTAATCTTACTAAAGATAAATGCACTGC
Found at i:1407570 original size:25 final size:25
Alignment explanation
Indices: 1407536--1407585 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1407526 TCAACTATTC
1407536 GTTACTACAAATTTGAATCTTGATA
1 GTTACTACAAATTTGAATCTTGATA
1407561 GTTACTACAAATTTGAATCTTGATA
1 GTTACTACAAATTTGAATCTTGATA
1407586 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (25 bp):
GTTACTACAAATTTGAATCTTGATA
Found at i:1409155 original size:31 final size:29
Alignment explanation
Indices: 1409082--1409157 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
1409072 CTGAAATTTG
* *
1409082 AAATTTAAAAAGTAGAGAGACTAAATTCCT
1 AAATTT-AAAAGTACAGAGACCAAATTCCT
** *
1409112 AAAAATACAAGTACAGAGACCAAATTCCT
1 AAATTTAAAAGTACAGAGACCAAATTCCT
1409141 AATATTTGAAAAGTACA
1 AA-ATTT-AAAAGTACA
1409158 AATACTATAG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 22 0.61
30 6 0.17
31 8 0.22
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.24
Consensus pattern (29 bp):
AAATTTAAAAGTACAGAGACCAAATTCCT
Found at i:1409494 original size:6 final size:6
Alignment explanation
Indices: 1409482--1409519 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1409472 AAATAATAAT
* *
1409482 TTTATA ATTATA ATTATA TTTATA TTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TT
1409520 AAATCACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTTATA
Found at i:1410437 original size:24 final size:24
Alignment explanation
Indices: 1410405--1410454 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1410395 ATTAGAAAGA
*
1410405 GAGAGAACTCTAGAAGGCAATGAT
1 GAGAGAACTCTAGAAGGCAACGAT
1410429 GAGAGAACTCTAGAAGGCAACGAT
1 GAGAGAACTCTAGAAGGCAACGAT
1410453 GA
1 GA
1410455 TATTAGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.14, G:0.30, T:0.14
Consensus pattern (24 bp):
GAGAGAACTCTAGAAGGCAACGAT
Found at i:1412591 original size:33 final size:32
Alignment explanation
Indices: 1412520--1412595 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
1412510 GTGTTTATAT
* * * *
1412520 GTAAGACCATAGATGGGTTATGGCATTCTGAT
1 GTAAGACCATAGATGAGTTATGGCACTATGAC
1412552 GATAAGACCATA-ACTGAGTTATGGCACTATGAAC
1 G-TAAGACCATAGA-TGAGTTATGGCACTATG-AC
1412586 GTAAGACCAT
1 GTAAGACCAT
1412596 GATTGGATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 2 0.05
33 33 0.89
34 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (32 bp):
GTAAGACCATAGATGAGTTATGGCACTATGAC
Found at i:1416136 original size:2 final size:2
Alignment explanation
Indices: 1416129--1416157 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1416119 TGATTTTCAA
1416129 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
1416158 NNNNNNNNNN
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:1421372 original size:3 final size:3
Alignment explanation
Indices: 1421364--1421404 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1421354 CTATAATTTG
1421364 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1421405 AGAACCTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1424626 original size:18 final size:18
Alignment explanation
Indices: 1424589--1424627 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1424579 ATCTAAATAT
*
1424589 AATTAATTAATTAATTAA
1 AATTAATTAATTAATAAA
*
1424607 AATTAATTAATTGATAAA
1 AATTAATTAATTAATAAA
1424625 AAT
1 AAT
1424628 AGTAGCAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AATTAATTAATTAATAAA
Found at i:1432325 original size:3 final size:3
Alignment explanation
Indices: 1432319--1432361 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1432309 CGTCGTCGTC
1432319 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1432362 CTTAGGCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1433940 original size:4 final size:4
Alignment explanation
Indices: 1433931--1433957 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1433921 ATTAGACCTA
1433931 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1433958 GAATAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1436726 original size:18 final size:18
Alignment explanation
Indices: 1436692--1436726 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1436682 TTTAAAGTAT
**
1436692 TTTTAAAATACTTTTTTA
1 TTTTAAAATACAATTTTA
1436710 TTTTAAAATACAATTTT
1 TTTTAAAATACAATTTT
1436727 GGTGTTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAAATACAATTTTA
Found at i:1437751 original size:15 final size:16
Alignment explanation
Indices: 1437726--1437756 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1437716 TAAATTTTTA
1437726 AAAATATTCAAAAAAT
1 AAAATATTCAAAAAAT
1437742 AAAA-ATTCAAAAAAT
1 AAAATATTCAAAAAAT
1437757 TAGCATAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATTCAAAAAAT
Found at i:1439867 original size:3 final size:3
Alignment explanation
Indices: 1439861--1439924 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
1439851 ATTTATTATG
*
1439861 TTA TTA TT- GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1439908 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
1439925 GCATTACCCA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 57 0.98
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1442440 original size:34 final size:35
Alignment explanation
Indices: 1442396--1442462 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1442386 CAGTAAAATA
*
1442396 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
1442430 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
1442463 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:1442577 original size:20 final size:19
Alignment explanation
Indices: 1442552--1442599 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1442542 CATATATTGA
1442552 TATATATATTAATAATTTT
1 TATATATATTAATAATTTT
*
1442571 T-TATATATTAAATTATTTT
1 TATATATATT-AATAATTTT
*
1442590 TACATATATT
1 TATATATATT
1442600 GCAATGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATATATTAATAATTTT
Found at i:1442584 original size:16 final size:19
Alignment explanation
Indices: 1442554--1442589 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1442544 TATATTGATA
1442554 TATATATTAATAATT-TTT
1 TATATATTAATAATTATTT
1442572 TATATATT-A-AATTATTT
1 TATATATTAATAATTATTT
1442589 T
1 T
1442590 TACATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATATTAATAATTATTT
Found at i:1443288 original size:19 final size:19
Alignment explanation
Indices: 1443265--1443307 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1443255 TTAATGGTTA
* *
1443265 AATTTATGTTTATATTTTT
1 AATTTAGGTTAATATTTTT
*
1443284 TATTTAGGTTAATATTTTT
1 AATTTAGGTTAATATTTTT
1443303 AATTT
1 AATTT
1443308 GAATTTTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
AATTTAGGTTAATATTTTT
Found at i:1458217 original size:58 final size:58
Alignment explanation
Indices: 1458082--1458197 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
1458072 ACATCATCAC
1458082 TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
1 TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
1458140 TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
1 TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
1458198 GTCAGTAAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (58 bp):
TGCCACATAACAAAACGAAATTGGGCTTAGATGACAGGCCGTTATTTGGTCGTGCAAT
Found at i:1465709 original size:19 final size:18
Alignment explanation
Indices: 1465676--1465712 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1465666 TGTTCATATA
1465676 ATAAAAATTAAAATTAAT
1 ATAAAAATTAAAATTAAT
*
1465694 ATAAAAACTTAGAATTAAT
1 ATAAAAA-TTAAAATTAAT
1465713 TATATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAAAAATTAAAATTAAT
Found at i:1474246 original size:23 final size:23
Alignment explanation
Indices: 1474215--1474268 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1474205 CTCCTATATA
*
1474215 TGCTCACTGAGTTCCTAATAATT
1 TGCTTACTGAGTTCCTAATAATT
* *
1474238 TGCTTACTGATTTCGTAATAATT
1 TGCTTACTGAGTTCCTAATAATT
*
1474261 TACTTACT
1 TGCTTACT
1474269 CTGCTCGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (23 bp):
TGCTTACTGAGTTCCTAATAATT
Found at i:1474402 original size:2 final size:2
Alignment explanation
Indices: 1474395--1474425 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1474385 TAAATCGAAA
1474395 AG AG AG 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 AG AG AG A
1474426 AGATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1476241 original size:27 final size:29
Alignment explanation
Indices: 1476207--1476265 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
1476197 AACTCTTTAT
*
1476207 AAAAAAT-AATAATATTAATTTGA-ATTA
1 AAAAAATAAATAATATTAAATTGAGATTA
* *
1476234 AAAAAATAAATTATTTTAAATTGAGATTA
1 AAAAAATAAATAATATTAAATTGAGATTA
1476263 AAA
1 AAA
1476266 TATCAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 13 0.48
29 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAAATAAATAATATTAAATTGAGATTA
Found at i:1476255 original size:23 final size:25
Alignment explanation
Indices: 1476208--1476255 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
1476198 ACTCTTTATA
*
1476208 AAAAATAATAATATTAATTTGAATT
1 AAAAATAATAATATTAATTTAAATT
*
1476233 AAAAA-AATAA-ATTATTTTAAATT
1 AAAAATAATAATATTAATTTAAATT
1476256 GAGATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
24 5 0.24
25 5 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAAATAATAATATTAATTTAAATT
Found at i:1482804 original size:21 final size:21
Alignment explanation
Indices: 1482750--1482806 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
1482740 TAGGTGCAAA
*
1482750 ATTAATATAATT-TTATATTT
1 ATTAATATAATTGTTAAATTT
* *
1482770 TTTTATAATTAATTGTTAAATTT
1 ATTAAT-A-TAATTGTTAAATTT
1482793 ATTAATATAATTGT
1 ATTAATATAATTGT
1482807 ATTTATTATG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.14
21 8 0.28
22 6 0.21
23 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTAATATAATTGTTAAATTT
Found at i:1487920 original size:26 final size:26
Alignment explanation
Indices: 1487865--1487921 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1487855 TATACGATAA
* * * *
1487865 AAGTAAATTTAATTTATTTTTATTTC
1 AAGTAAATATAATTAATTTATATGTC
1487891 AAGTAAATATAATTAATTGTATATGT-
1 AAGTAAATATAATTAATT-TATATGTC
1487917 AAGTA
1 AAGTA
1487922 GGCAAAAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (26 bp):
AAGTAAATATAATTAATTTATATGTC
Found at i:1494224 original size:27 final size:28
Alignment explanation
Indices: 1494168--1494229 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
1494158 AATTCTAAAC
* * * *
1494168 TTTGGGTTCGATGTTCAAGGTTTAATG-
1 TTTGGGTTCAATATTCAAGGTTCAAAGT
*
1494195 TTTGGGTTCAATATTCAATGTTCAAAGT
1 TTTGGGTTCAATATTCAAGGTTCAAAGT
1494223 TTTGGGT
1 TTTGGGT
1494230 ATGGGGTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.45
Consensus pattern (28 bp):
TTTGGGTTCAATATTCAAGGTTCAAAGT
Found at i:1497231 original size:6 final size:6
Alignment explanation
Indices: 1497220--1497246 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1497210 TTGTAAGGAT
1497220 GGGAAG GGGAAG GGGAAG GGGAAG GGG
1 GGGAAG GGGAAG GGGAAG GGGAAG GGG
1497247 TTGTTCGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:1498227 original size:11 final size:11
Alignment explanation
Indices: 1498211--1498260 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
1498201 TTGCTTCTTC
1498211 TTCTTCTTTCT
1 TTCTTCTTTCT
1498222 TTCTTCTTTCT
1 TTCTTCTTTCT
*
1498233 TTCTTCTCTCT
1 TTCTTCTTTCT
* *
1498244 CTC-TCTCTC-
1 TTCTTCTTTCT
1498253 TTCTTCTT
1 TTCTTCTT
1498261 CCCCCACCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 2 0.06
10 9 0.26
11 23 0.68
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (11 bp):
TTCTTCTTTCT
Found at i:1503956 original size:43 final size:43
Alignment explanation
Indices: 1503895--1503979 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
1503885 TCATTACAAT
1503895 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
1 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
1503938 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAA
1 GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAA
1503980 AAATATCATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (43 bp):
GGTTTGAAAAAGAAAGAATTGAAGATATTTTTATTAGTTCAAC
Found at i:1511559 original size:2 final size:2
Alignment explanation
Indices: 1511552--1511591 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1511542 AACTCAAGCT
1511552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1511592 AATTAATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1513790 original size:30 final size:30
Alignment explanation
Indices: 1513750--1513812 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1513740 ACTTAATAAG
*
1513750 TAAATATTTTTAAAATAATAATAAAATTAA
1 TAAATATTTTTAAAATAAAAATAAAATTAA
*
1513780 TAAATGTTTTTAAAATAAAAATAAAATTAA
1 TAAATATTTTTAAAATAAAAATAAAATTAA
1513810 TAA
1 TAA
1513813 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
TAAATATTTTTAAAATAAAAATAAAATTAA
Found at i:1513814 original size:33 final size:33
Alignment explanation
Indices: 1513724--1513816 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 33
1513714 TTTTGTATAA
* * *
1513724 TTTTAAAATATATAT-AACTTAATAAGTAAATAT
1 TTTTAAAATAAAAATAAAATTAATAA-TAAATAT
* *
1513757 TTTTAAAATAATAATAAAA-T--TAATAAATGT
1 TTTTAAAATAAAAATAAAATTAATAATAAATAT
1513787 TTTTAAAATAAAAATAAAATTAATAATAAA
1 TTTTAAAATAAAAATAAAATTAATAATAAA
1513817 ATAAATTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
30 24 0.48
31 4 0.08
33 20 0.40
34 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (33 bp):
TTTTAAAATAAAAATAAAATTAATAATAAATAT
Found at i:1514158 original size:12 final size:11
Alignment explanation
Indices: 1514136--1514196 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
1514126 TAAATATTTT
1514136 TAAAATAATAA
1 TAAAATAATAA
1514147 TAAAAT--TAA
1 TAAAATAATAA
**
1514156 T-AAAT-ATCTT
1 TAAAATAAT-AA
1514166 TAAAATAATAA
1 TAAAATAATAA
1514177 TAAAATTAATAA
1 TAAAA-TAATAA
1514189 TAAAATAA
1 TAAAATAA
1514197 ATTTTATAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 4 0.10
9 5 0.12
10 1 0.02
11 18 0.44
12 13 0.32
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:1514162 original size:30 final size:30
Alignment explanation
Indices: 1514126--1514188 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
1514116 ACTTAACAAG
*
1514126 TAAATATTTTTAAAATAATAATAAAATTAA
1 TAAATATCTTTAAAATAATAATAAAATTAA
1514156 TAAATATCTTTAAAATAATAATAAAATTAA
1 TAAATATCTTTAAAATAATAATAAAATTAA
1514186 TAA
1 TAA
1514189 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
TAAATATCTTTAAAATAATAATAAAATTAA
Found at i:1514190 original size:33 final size:33
Alignment explanation
Indices: 1514101--1514192 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 33
1514091 GAAAATAAAT
* * *
1514101 TTTAAAA-AAT-ATATAACTTAACAAGTAAATATT
1 TTTAAAATAATAATA-AAATTAATAA-TAAATATC
1514134 TTTAAAATAATAATAAAA-T--TAATAAATATC
1 TTTAAAATAATAATAAAATTAATAATAAATATC
1514164 TTTAAAATAATAATAAAATTAATAATAAA
1 TTTAAAATAATAATAAAATTAATAATAAA
1514193 ATAAATTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
30 25 0.49
31 3 0.06
33 15 0.29
34 5 0.10
35 3 0.06
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (33 bp):
TTTAAAATAATAATAAAATTAATAATAAATATC
Found at i:1515147 original size:9 final size:9
Alignment explanation
Indices: 1515133--1515165 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
1515123 TGTGAAAGAT
1515133 AATATTAAA
1 AATATTAAA
1515142 AATATTAAA
1 AATATTAAA
1515151 AATATTAAA
1 AATATTAAA
1515160 AATATT
1 AATATT
1515166 CAGATCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AATATTAAA
Found at i:1518385 original size:44 final size:45
Alignment explanation
Indices: 1518325--1518416 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 45
1518315 TATTACAACA
* *
1518325 TCTATTCCATTTAACCAAAC-ATAAGAATT-TTATTACAGCTCTAT
1 TCTATTCCATTCAACCAAACAAT-AGAATTATGATTACAGCTCTAT
* *
1518369 TCTATTTCATTCAACCAAACAATTGAATTACTGATTACAGCTCTAT
1 TCTATTCCATTCAACCAAACAATAGAATTA-TGATTACAGCTCTAT
1518415 TC
1 TC
1518417 AATTAGAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 23 0.56
45 2 0.05
46 16 0.39
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (45 bp):
TCTATTCCATTCAACCAAACAATAGAATTATGATTACAGCTCTAT
Found at i:1523680 original size:15 final size:15
Alignment explanation
Indices: 1523660--1523701 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1523650 TCAATCTCTT
**
1523660 AATAAATAATTTTTA
1 AATAAATAATTTAAA
1523675 AATAAATAATTTAAA
1 AATAAATAATTTAAA
1523690 AATAAAATAATT
1 AAT-AAATAATT
1523702 ATATAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAAATAATTTAAA
Found at i:1523870 original size:9 final size:9
Alignment explanation
Indices: 1523858--1523903 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
1523848 AATTTTATAA
1523858 ATATATATT
1 ATATATATT
1523867 ATATATATT
1 ATATATATT
* *
1523876 A-AGA-ATA
1 ATATATATT
1523883 ATATATATT
1 ATATATATT
*
1523892 ATAGATATT
1 ATATATATT
1523901 ATA
1 ATA
1523904 AAATTTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
7 3 0.10
8 4 0.13
9 23 0.77
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (9 bp):
ATATATATT
Found at i:1528667 original size:11 final size:11
Alignment explanation
Indices: 1528651--1528684 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1528641 TGGGTTCTTT
1528651 TACAAAAATAA
1 TACAAAAATAA
1528662 TACAAAAA-AA
1 TACAAAAATAA
*
1528672 TACTAAAATAA
1 TACAAAAATAA
1528683 TA
1 TA
1528685 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (11 bp):
TACAAAAATAA
Found at i:1528970 original size:152 final size:153
Alignment explanation
Indices: 1528784--1529132 Score: 516
Period size: 149 Copynumber: 2.3 Consensus size: 153
1528774 GTATTTTGAC
1528784 CCTTTGTTCGTATTTTTTCCCAAATTTTATTACTTTTAATAAAAATATATTATTTT-TATATTTT
1 CCTTTGTTCGTATTTTTTCCCAAATTTTATTACTTTTAATAAAAATATATTATTTTCTA-ATTTT
*
1528848 ATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTA-CT-TTTTTTAAATAAA
65 ATTATTTTACATTATTTTAATACATTATATTTGAAATGTATTAATTTAGCTGTTTTTTAAATAAA
*
1528911 -TTTTAAAAAAA-TCTTATTTCGG
130 TTTTTAAAAAAACTCTTATTTCAG
*
1528933 CTCTTTGTTCGTATTTTTTTCCCAAGAGTTTATTAC-TTT-A-AAAAATATATTATTTTCTAATT
1 C-CTTTGTTCGTA-TTTTTTCCCAA-ATTTTATTACTTTTAATAAAAATATATTATTTTCTAATT
* * *
1528995 TTATTATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAAT
63 TTATTATTTTACATTATTTTAATACATTATATTTGAAATGTATTAATTTAG-CTGTTTTTTAAAT
1529060 AAATTTTTAAAAAAACTCTTATTTCAG
127 AAATTTTTAAAAAAACTCTTATTTCAG
* *
1529087 CCATTTGTTCATATTTTTTCCCAAATTTTATTACTTTCAATAAAAA
1 CC-TTTGTTCGTATTTTTTCCCAAATTTTATTACTTTTAATAAAAA
1529133 AAGCCTAAAT
Statistics
Matches: 178, Mismatches: 9, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
149 67 0.38
150 14 0.08
151 15 0.08
152 31 0.17
153 25 0.14
154 21 0.12
155 5 0.03
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.53
Consensus pattern (153 bp):
CCTTTGTTCGTATTTTTTCCCAAATTTTATTACTTTTAATAAAAATATATTATTTTCTAATTTTA
TTATTTTACATTATTTTAATACATTATATTTGAAATGTATTAATTTAGCTGTTTTTTAAATAAAT
TTTTAAAAAAACTCTTATTTCAG
Found at i:1530913 original size:3 final size:3
Alignment explanation
Indices: 1530905--1530929 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1530895 ACATGCATAT
1530905 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1530930 AGAAACCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1537642 original size:108 final size:108
Alignment explanation
Indices: 1537453--1537669 Score: 416
Period size: 108 Copynumber: 2.0 Consensus size: 108
1537443 TTTTGGATAA
*
1537453 AAAAAATTATATTTACATATTTCAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
1 AAAAAATTATATATACATATTTCAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
1537518 TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
66 TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
*
1537561 AAAAAATTATATATACATATTTTAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
1 AAAAAATTATATATACATATTTCAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
1537626 TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
66 TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
1537669 A
1 A
1537670 TAACCGACTC
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (108 bp):
AAAAAATTATATATACATATTTCAATATTAGAAGCCGGCTATGTAAGTTGGTTTGGTTAAAAAAA
TTCATAATCGATAACTATGCACTACAAGACCACTTTAACCATC
Found at i:1538784 original size:27 final size:27
Alignment explanation
Indices: 1538752--1538807 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1538742 AGAATAAGCA
1538752 TCTCTAGCATATTAAAGAAAATGTCAT
1 TCTCTAGCATATTAAAGAAAATGTCAT
1538779 TCTCTAGCATATTAAAGAAAATGTCAT
1 TCTCTAGCATATTAAAGAAAATGTCAT
1538806 TC
1 TC
1538808 ATACCTGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (27 bp):
TCTCTAGCATATTAAAGAAAATGTCAT
Found at i:1544534 original size:86 final size:85
Alignment explanation
Indices: 1544428--1544603 Score: 246
Period size: 86 Copynumber: 2.1 Consensus size: 85
1544418 CTGTTATAGA
* *
1544428 AAAGTGGTTAAAAACATATAAGAGCTGTATGAATTATTGTTTTTATGTAAAT-TTTTATTTTACA
1 AAAGTGGTTAAAAACATATAAAAGCTGCATGAATTATTGTTTTTATG-AAATATTTTATTTTACA
*
1544492 TTCTTCTACACGATTAACTAT
65 TTCTTCCACACGATTAACTAT
* * * * *
1544513 AAAGTGGTTAAAAAACGTATAAAAGGTGCATGAATTATTGTTTTTATGCATTATTTTATTTTGCA
1 AAAGTGGTT-AAAAACATATAAAAGCTGCATGAATTATTGTTTTTATGAAATATTTTATTTTACA
*
1544578 TTCTTCCACACGATTAATTAT
65 TTCTTCCACACGATTAACTAT
1544599 AAAGT
1 AAAGT
1544604 TCATAAGTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
85 11 0.14
86 69 0.86
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (85 bp):
AAAGTGGTTAAAAACATATAAAAGCTGCATGAATTATTGTTTTTATGAAATATTTTATTTTACAT
TCTTCCACACGATTAACTAT
Found at i:1545573 original size:21 final size:19
Alignment explanation
Indices: 1545547--1545601 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
1545537 TCAAATTTAG
*
1545547 AATTTTAATATTATTTATTTT
1 AATTTTAAT-TTATTTA-ATT
1545568 AATTTTAATTTTAATTTAATT
1 AATTTTAA-TTT-ATTTAATT
*
1545589 AATTTCAATTTAT
1 AATTTTAATTTAT
1545602 CAGTTTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 3 0.10
21 19 0.63
22 6 0.20
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTTAATTTATTTAATT
Found at i:1545592 original size:15 final size:14
Alignment explanation
Indices: 1545547--1545601 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
1545537 TCAAATTTAG
1545547 AATTTTAATATTATT
1 AATTTTAAT-TTATT
*
1545562 TATTTTAA-TT-TT
1 AATTTTAATTTATT
1545574 AATTTTAATTTAATT
1 AATTTTAATTT-ATT
*
1545589 AATTTCAATTTAT
1 AATTTTAATTTAT
1545602 CAGTTTACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 9 0.26
13 4 0.12
14 2 0.06
15 19 0.56
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTTTAATTTATT
Found at i:1546374 original size:167 final size:167
Alignment explanation
Indices: 1546098--1546435 Score: 491
Period size: 167 Copynumber: 2.0 Consensus size: 167
1546088 ATTGGGTTTG
* * *
1546098 GGTAAAACTAGACCTGTCTATAGGGCGGATCACTCGACTCGAAAGCCTACCCAAAAAGTAGGAGG
1 GGTAAAACTAGACCTGTCCATAGGGCGGATCACCCGACCCGAAAGCCTACCCAAAAAGTAGGAGG
* ** *
1546163 GTTTGGATAAAATATAGGCCTGAAAAATGAGCTTTGGGCAAAAAATAAGGCCCGTTTGAAAAACG
66 GTTTAGATAAAATATAGGCCCAAAAAATGAGCTTGGGGCAAAAAATAAGGCCCGTTTGAAAAACG
*
1546228 GGTCAAGTAT-TGGGTAAGACTTTTTTGGTCTTGAGTA
131 GGTCAAGCATCT-GGTAAGACTTTTTTGGTCTTGAGTA
* * * ** *
1546265 GGTAAAACTAGACCTGTCCATGGGGCAGG-TCACCCGACCCGAAAGCTTGCCTGAAAAGTGGGAG
1 GGTAAAACTAGACCTGTCCATAGGGC-GGATCACCCGACCCGAAAGCCTACCCAAAAAGTAGGAG
*
1546329 GGTTTAGATAAAATATAGGCCCAAAAAATGAGCTTGGGGCAAAAAATAAGGCTCGTTTGAAAAAC
65 GGTTTAGATAAAATATAGGCCCAAAAAATGAGCTTGGGGCAAAAAATAAGGCCCGTTTGAAAAAC
* *
1546394 GGGTCAAGCATCTTGTAAGACTTTTTTGGTCTTGAGTG
130 GGGTCAAGCATCTGGTAAGACTTTTTTGGTCTTGAGTA
1546432 GGTA
1 GGTA
1546436 TGACTAGGGG
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
167 149 0.98
168 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (167 bp):
GGTAAAACTAGACCTGTCCATAGGGCGGATCACCCGACCCGAAAGCCTACCCAAAAAGTAGGAGG
GTTTAGATAAAATATAGGCCCAAAAAATGAGCTTGGGGCAAAAAATAAGGCCCGTTTGAAAAACG
GGTCAAGCATCTGGTAAGACTTTTTTGGTCTTGAGTA
Found at i:1546658 original size:13 final size:13
Alignment explanation
Indices: 1546640--1546669 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1546630 AGCCCAAACT
*
1546640 CAATTATCCAACC
1 CAATTACCCAACC
1546653 CAATTACCCAACC
1 CAATTACCCAACC
1546666 CAAT
1 CAAT
1546670 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:1546847 original size:9 final size:9
Alignment explanation
Indices: 1546808--1546864 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
1546798 TAAAAAAAAT
*
1546808 TTCGGGCAA
1 TTCGGGTAA
*
1546817 TTCGGGTATTT
1 TTCGGGTA--A
1546828 TTC-GGTAA
1 TTCGGGTAA
*
1546836 TTCGGTTAA
1 TTCGGGTAA
1546845 TTCGGGTAA
1 TTCGGGTAA
1546854 TTCGGGTAA
1 TTCGGGTAA
1546863 TT
1 TT
1546865 TTTAACCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 3 0.08
9 30 0.75
10 4 0.10
11 3 0.08
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.40
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:1547259 original size:20 final size:21
Alignment explanation
Indices: 1547234--1547278 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1547224 CTGTTGAATT
*
1547234 TTTTTTACTGTTTTCTTAC-A
1 TTTTTTACTGTTTTATTACTA
*
1547254 TTTTTTATTGTTTTATTACTA
1 TTTTTTACTGTTTTATTACTA
1547275 TTTT
1 TTTT
1547279 CTTGTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTTTACTGTTTTATTACTA
Found at i:1547283 original size:19 final size:20
Alignment explanation
Indices: 1547236--1547284 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1547226 GTTGAATTTT
* * *
1547236 TTTTACTGTTTTCTTACATT
1 TTTTATTGTTTTATTACATA
1547256 TTTTATTGTTTTATTAC-TA
1 TTTTATTGTTTTATTACATA
*
1547275 TTTTCTTGTT
1 TTTTATTGTT
1547285 ATTTTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.14, C:0.10, G:0.06, T:0.69
Consensus pattern (20 bp):
TTTTATTGTTTTATTACATA
Found at i:1550224 original size:16 final size:16
Alignment explanation
Indices: 1550183--1550217 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1550173 ACGAGATTGT
*
1550183 AACCTCTTCAACTAAC
1 AACCACTTCAACTAAC
1550199 AACCACTTCAACTAAC
1 AACCACTTCAACTAAC
1550215 AAC
1 AAC
1550218 TAGTTCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (16 bp):
AACCACTTCAACTAAC
Found at i:1551205 original size:61 final size:61
Alignment explanation
Indices: 1551101--1551215 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
1551091 AAGTCTACCT
* * * *
1551101 AACTCTAGTGACCTAAATCTCATTACAAATATTGAATTAAATAACTAACTCAACGTAATTC
1 AACTCTAATGACCCAAATCTCATTACAAATATCGAAATAAATAACTAACTCAACGTAATTC
* * *
1551162 AACTCTAATTACCCAAATCTCATTACAAGTA-CGAAATAGAATAATTAACTCAAC
1 AACTCTAATGACCCAAATCTCATTACAAATATCGAAATA-AATAACTAACTCAAC
1551216 TCTAATTGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 5 0.11
61 41 0.89
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (61 bp):
AACTCTAATGACCCAAATCTCATTACAAATATCGAAATAAATAACTAACTCAACGTAATTC
Found at i:1552788 original size:2 final size:2
Alignment explanation
Indices: 1552781--1552809 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1552771 AGATGGATCC
1552781 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1552810 TAATGCCAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1561546 original size:5 final size:5
Alignment explanation
Indices: 1561536--1561566 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1561526 GTCATTTTCA
1561536 ATAAT ATAAT ATAAT ATAAT ATTAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT
1561567 GATTCCTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:1562026 original size:18 final size:18
Alignment explanation
Indices: 1561990--1562034 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1561980 AGCTTTTAAG
*
1561990 AAATACTTTTGGGACAAA
1 AAATACTTTTGAGACAAA
* *
1562008 AAATGCTTTTGAGA-GAA
1 AAATACTTTTGAGACAAA
1562025 AAATACTTTT
1 AAATACTTTT
1562035 CAAACGCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (18 bp):
AAATACTTTTGAGACAAA
Found at i:1567645 original size:17 final size:17
Alignment explanation
Indices: 1567578--1567645 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
1567568 TATGTGAATG
*
1567578 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
1567594 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
1567613 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
1567632 TAAAATTATTAATT
1 TAAAATTATTAATT
1567646 GTTAGTACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:1567668 original size:116 final size:116
Alignment explanation
Indices: 1567464--1567702 Score: 417
Period size: 116 Copynumber: 2.1 Consensus size: 116
1567454 TAAGTTTGTG
*
1567464 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
** *
1567529 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTA
66 TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
1567580 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
1567644 TTGTTAGTACCAGGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
66 TTGTTAGTACCA-GAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
*
1567696 ACATTAT
1 AAATTAT
1567703 GAGTTTAGTT
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
115 41 0.35
116 76 0.65
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
Found at i:1569299 original size:2 final size:2
Alignment explanation
Indices: 1569292--1569332 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1569282 TTGTATGTAA
*
1569292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
1569333 AATTTAAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1570628 original size:18 final size:18
Alignment explanation
Indices: 1570590--1570629 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1570580 GACTCGGAAA
* *
1570590 AGGATACATATAAGGGTT
1 AGGATACATATAAAGGCT
*
1570608 AGGATGCATATAAAGGCT
1 AGGATACATATAAAGGCT
1570626 AGGA
1 AGGA
1570630 AACGCAACTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAAGGCT
Found at i:1571481 original size:19 final size:19
Alignment explanation
Indices: 1571447--1571494 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1571437 AGAAAAATTG
*
1571447 TTATTGTTTTTTTCACCT-TT
1 TTATTG-TTATTTCA-CTATT
1571467 TTATTGTTATTTCACTATT
1 TTATTGTTATTTCACTATT
*
1571486 ATATTGTTA
1 TTATTGTTA
1571495 CTATTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.68
20 6 0.24
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (19 bp):
TTATTGTTATTTCACTATT
Found at i:1571514 original size:14 final size:14
Alignment explanation
Indices: 1571480--1571515 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1571470 TTGTTATTTC
*
1571480 ACTATTATATTGTT
1 ACTATTTTATTGTT
1571494 ACTATTTTATTGTT
1 ACTATTTTATTGTT
*
1571508 ATTATTTT
1 ACTATTTT
1571516 GATATTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (14 bp):
ACTATTTTATTGTT
Found at i:1573709 original size:2 final size:2
Alignment explanation
Indices: 1573702--1573732 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1573692 ACTTTATTGA
1573702 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 A
1573733 AGCTACATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1580228 original size:40 final size:40
Alignment explanation
Indices: 1580184--1580316 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
1580174 GCTCCTACGA
* *
1580184 GGACGCGGTTTGCTGACACATCAGCAAAGCGCGCTGACGT
1 GGACGCGATTTGCTGACACATCAACAAAGCGCGCTGACGT
*
1580224 GGACGCGATTTACTGACACATCAACAAAGCGCGCTGACGT
1 GGACGCGATTTGCTGACACATCAACAAAGCGCGCTGACGT
* ** * *
1580264 GGACGCGATTTGCTGACACGTCCCCTGACATCGCGCTGACGT
1 GGACGCGATTTGCTGACACATCAAC--AAAGCGCGCTGACGT
1580306 GGACGCGATTT
1 GGACGCGATTT
1580317 CGGGGAAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 58 0.71
42 24 0.29
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.20
Consensus pattern (40 bp):
GGACGCGATTTGCTGACACATCAACAAAGCGCGCTGACGT
Found at i:1582992 original size:18 final size:19
Alignment explanation
Indices: 1582952--1582993 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1582942 TTTTTTTACT
* *
1582952 TTTTTTATTAACTTTTGTC
1 TTTTTTATTAACTTTTATA
*
1582971 TTTTTT-TTAAGTTTTATA
1 TTTTTTATTAACTTTTATA
1582989 TTTTT
1 TTTTT
1582994 CTTATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTTATTAACTTTTATA
Found at i:1583016 original size:23 final size:22
Alignment explanation
Indices: 1582990--1583032 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
1582980 AGTTTTATAT
1582990 TTTTC-TTATTTTATTTTATTTTA
1 TTTTCTTTA-TTTA-TTTATTTTA
*
1583013 TTTTGTTTATTTATTTATTT
1 TTTTCTTTATTTATTTATTT
1583033 ATTGTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 8 0.44
24 3 0.17
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTCTTTATTTATTTATTTTA
Found at i:1583031 original size:8 final size:9
Alignment explanation
Indices: 1582995--1583048 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
1582985 TATATTTTTC
1582995 TTATTTTATT
1 TTATTTTA-T
1583005 TTATTTTAT
1 TTATTTTAT
1583014 TT-TGTTTAT
1 TTAT-TTTAT
1583023 TTA-TTTAT
1 TTATTTTAT
1583031 TTATTGTTAT
1 TTATT-TTAT
*
1583041 TAATTTTA
1 TTATTTTA
1583049 AAAAAATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
8 9 0.23
9 14 0.36
10 16 0.41
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (9 bp):
TTATTTTAT
Found at i:1583120 original size:11 final size:11
Alignment explanation
Indices: 1583089--1583133 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1583079 TTATAATATA
1583089 TATTTTTAAA-
1 TATTTTTAAAT
* *
1583099 AATTTTAAAAT
1 TATTTTTAAAT
1583110 TATTTTTAAAT
1 TATTTTTAAAT
1583121 TATTTTTTAAAT
1 TA-TTTTTAAAT
1583133 T
1 T
1583134 TTGAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 8 0.28
11 11 0.38
12 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAT
Found at i:1583125 original size:32 final size:33
Alignment explanation
Indices: 1583088--1583157 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
1583078 TTTATAATAT
1583088 ATATTTTTAAAAATTTT-AAAATTA-TTTTTAAA
1 ATATTTTT-AAAATTTTGAAAATTATTTTTTAAA
* * *
1583120 TTATTTTTTAAATTTTGAATATTATTTTTTAAA
1 ATATTTTTAAAATTTTGAAAATTATTTTTTAAA
1583153 ATATT
1 ATATT
1583158 AAATAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 7 0.22
32 13 0.41
33 12 0.38
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
ATATTTTTAAAATTTTGAAAATTATTTTTTAAA
Found at i:1583145 original size:21 final size:20
Alignment explanation
Indices: 1583111--1583152 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1583101 TTTTAAAATT
*
1583111 ATTTTTAAATTATTTTTTAA
1 ATTTTGAAATTATTTTTTAA
1583131 ATTTTGAATATTATTTTTTAA
1 ATTTTGAA-ATTATTTTTTAA
1583152 A
1 A
1583153 ATATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTGAAATTATTTTTTAA
Found at i:1583162 original size:22 final size:21
Alignment explanation
Indices: 1583119--1583162 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1583109 TTATTTTTAA
* *
1583119 ATTATTTTTTAAATTTTGAAT
1 ATTATTTTTTAAATATTAAAT
1583140 ATTATTTTTTAAAATATTAAAT
1 ATTATTTTTT-AAATATTAAAT
1583162 A
1 A
1583163 AAAAAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTATTTTTTAAATATTAAAT
Found at i:1583723 original size:62 final size:63
Alignment explanation
Indices: 1583646--1583769 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 63
1583636 CTTTAAAAAC
* ** * **
1583646 TTAAAGAAATTAAATATATTAAAAAATGTTATGTATAGTCAATTTTAAAATTTTAATATATTT
1 TTAAAGAAATTAAATATATTAAAAAATGTTAAGTATAACCAATATTAAAATTACAATATATTT
1583709 TTAAA-AAATTAAATATATTAAAAAATGTTAAGTATAACCAATATTAAAATTACAATATATT
1 TTAAAGAAATTAAATATATTAAAAAATGTTAAGTATAACCAATATTAAAATTACAATATATT
1583770 AAATATATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 50 0.91
63 5 0.09
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (63 bp):
TTAAAGAAATTAAATATATTAAAAAATGTTAAGTATAACCAATATTAAAATTACAATATATTT
Found at i:1583861 original size:17 final size:17
Alignment explanation
Indices: 1583839--1583872 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1583829 AAAAATGATT
1583839 TTTTAATATAT-TTAAAA
1 TTTTAA-ATATGTTAAAA
1583856 TTTTAAATATGTTAAAA
1 TTTTAAATATGTTAAAA
1583873 GAAAATGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTTAAATATGTTAAAA
Done.