Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008821.1 Hibiscus syriacus cultivar Beakdansim tig00111989_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: 1271541
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:991883 original size:14 final size:14
Alignment explanation
Indices: 991866--991899 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
991856 ATTATTTATC
*
991866 ATATTTATTAATTA
1 ATATTTAATAATTA
991880 ATATTTAATAATTA
1 ATATTTAATAATTA
*
991894 CTATTT
1 ATATTT
991900 CTCCTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTTAATAATTA
Found at i:995319 original size:22 final size:21
Alignment explanation
Indices: 995294--995355 Score: 88
Period size: 22 Copynumber: 2.9 Consensus size: 21
995284 ATGAAATTTA
*
995294 TCCCGAAGGACCTGTGAATATG
1 TCCCGAAGGACCTATGAAT-TG
*
995316 TCCCGAAGGACCTATGAGTTG
1 TCCCGAAGGACCTATGAATTG
995337 TCCCCGAAGGACCTATGAA
1 T-CCCGAAGGACCTATGAA
995356 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 3 0.08
22 33 0.92
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (21 bp):
TCCCGAAGGACCTATGAATTG
Found at i:995655 original size:14 final size:15
Alignment explanation
Indices: 995628--995656 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
995618 ATATCATATA
995628 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
995643 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
995657 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:1001197 original size:16 final size:16
Alignment explanation
Indices: 1001176--1001208 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1001166 GTTAACTAAC
1001176 TATAAATGTATGTTGA
1 TATAAATGTATGTTGA
1001192 TATAAATGTATGTTGA
1 TATAAATGTATGTTGA
1001208 T
1 T
1001209 GACGTAACAC
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:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TATAAATGTATGTTGA
Found at i:1004425 original size:37 final size:37
Alignment explanation
Indices: 1004375--1004449 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1004365 CTCAAAGAAC
1004375 TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
1 TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
1004412 TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
1 TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
1004449 T
1 T
1004450 CTTGTCATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (37 bp):
TGCAAAAGACAGAAACAATCTAGTTACAATTTTACAT
Found at i:1008231 original size:27 final size:27
Alignment explanation
Indices: 1008191--1008248 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1008181 AAATACCCTT
* *
1008191 AATCGAATTGTTTTTAACTGTTAATTG
1 AATCGAATTGTTTTTAACTATTAACTG
* *
1008218 AATCGAATTTTTTTTAAGTATTAACTG
1 AATCGAATTGTTTTTAACTATTAACTG
1008245 AATC
1 AATC
1008249 AAATAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.47
Consensus pattern (27 bp):
AATCGAATTGTTTTTAACTATTAACTG
Found at i:1008371 original size:16 final size:16
Alignment explanation
Indices: 1008343--1008382 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
1008333 ATAGTTTATA
1008343 ATTAATT-TAAATAAT
1 ATTAATTATAAATAAT
1008358 ATTAATTATAAATAAT
1 ATTAATTATAAATAAT
1008374 ATATAATTA
1 AT-TAATTA
1008383 ATTTGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAATTATAAATAAT
Found at i:1011427 original size:18 final size:17
Alignment explanation
Indices: 1011395--1011428 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1011385 TCACCCGGTT
1011395 CGGTTTGAACGGTTCAA
1 CGGTTTGAACGGTTCAA
*
1011412 CGGTTCTGATCGGTTCA
1 CGGTT-TGAACGGTTCA
1011429 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAA
Found at i:1018814 original size:21 final size:20
Alignment explanation
Indices: 1018786--1018824 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1018776 CATTGCAGGA
*
1018786 ATTTATGGCTTCGACAAAAG
1 ATTTATGGCTTCAACAAAAG
*
1018806 ATTTCATGGTTTCAACAAA
1 ATTT-ATGGCTTCAACAAA
1018825 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
ATTTATGGCTTCAACAAAAG
Found at i:1023450 original size:16 final size:16
Alignment explanation
Indices: 1023429--1023465 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1023419 TTATTTCACA
1023429 TATTTCTATTTCTATT
1 TATTTCTATTTCTATT
* *
1023445 TATTTCTATTTTTCTT
1 TATTTCTATTTCTATT
1023461 TATTT
1 TATTT
1023466 AATGAACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTCTATTTCTATT
Found at i:1027066 original size:8 final size:8
Alignment explanation
Indices: 1027052--1027110 Score: 57
Period size: 8 Copynumber: 7.1 Consensus size: 8
1027042 AAGACAAATC
1027052 AAAACAAAG
1 AAAA-AAAG
*
1027061 AAACAAGAAA
1 AAA-AA-AAG
1027071 AAAAAAAG
1 AAAAAAAG
1027079 AAAAAAAG
1 AAAAAAAG
*
1027087 AAAAGAA-
1 AAAAAAAG
*
1027094 AAACAAAG
1 AAAAAAAG
1027102 AAAAAAAG
1 AAAAAAAG
1027110 A
1 A
1027111 TGACAAAGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
7 5 0.12
8 24 0.59
9 6 0.15
10 6 0.15
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1027090 original size:13 final size:12
Alignment explanation
Indices: 1027068--1027108 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1027058 AAGAAACAAG
1027068 AAAAAAAAAAGA
1 AAAAAAAAAAGA
1027080 AAAAAAGAAAAG-
1 AAAAAA-AAAAGA
*
1027092 -AAAAACAAAGA
1 AAAAAAAAAAGA
1027103 AAAAAA
1 AAAAAA
1027109 GATGACAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
10 4 0.16
11 5 0.20
12 11 0.44
13 5 0.20
ACGTcount: A:0.88, C:0.02, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1027986 original size:22 final size:21
Alignment explanation
Indices: 1027960--1028026 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 21
1027950 TCAAAAGGGG
1027960 TAATATTTTCAAACTTTTGAT
1 TAATATTTTCAAACTTTTGAT
*
1027981 TAAATATTTTTCAAAACTCTTTTAAT
1 T-AATA-TTTTC-AAA--CTTTTGAT
* *
1028007 TGATATTTTCATACTTTTGA
1 TAATATTTTCAAACTTTTGA
1028027 AAATACAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
21 7 0.19
22 4 0.11
23 7 0.19
24 8 0.22
25 3 0.08
26 8 0.22
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.52
Consensus pattern (21 bp):
TAATATTTTCAAACTTTTGAT
Found at i:1028877 original size:107 final size:106
Alignment explanation
Indices: 1028621--1028894 Score: 317
Period size: 107 Copynumber: 2.6 Consensus size: 106
1028611 ATAAATCTCA
* * *
1028621 TCTCATTTGAGGCATTTTTCACTTGAGAATACAAATTT-GAATTTGTTTCACATTAAAC-AAAGT
1 TCTCATTTGAGACATTTTTCATTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAAAT
* * *
1028684 TGATATCATTTGAGATCGCTTTCTTAAAAAAACAAACTTCG
66 TAATATCATTTAAGATCGATTTCTTAAAAAAACAAACTTCG
** * * *
1028725 TCTTGTTTGAGACATTTTTTTCCTTTGA-CATACAAATTTCGAATTTGATTCAC-TTGAAACAAA
1 TCTCATTTGAGACA--TTTTTCATTTGAGAATACAAATTTCGAATTTGTTTCACATT-AAACAAA
* * * *
1028788 AATTAATCTCATTTAAGATTGTTATTTCTTTCAAAATA-AAA-TTCG
63 AATTAATATCATTTAAGATCG--ATTTC-TTAAAAAAACAAACTTCG
1028833 TCTCATTTGAGACATTTTTCATTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAA
1 TCTCATTTGAGACATTTTTCATTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAA
1028895 GTTGATCTCA
Statistics
Matches: 140, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
104 11 0.08
105 12 0.09
106 37 0.26
107 48 0.34
108 18 0.13
109 7 0.05
110 7 0.05
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.41
Consensus pattern (106 bp):
TCTCATTTGAGACATTTTTCATTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAAAT
TAATATCATTTAAGATCGATTTCTTAAAAAAACAAACTTCG
Found at i:1029007 original size:35 final size:35
Alignment explanation
Indices: 1028888--1029023 Score: 143
Period size: 36 Copynumber: 3.8 Consensus size: 35
1028878 GTTTCACATT
* **
1028888 AAACAAAGTTGATCTCACTTGAGATCGTTTTCTC-AA
1 AAACAAATTTG-TCTCACTTGAGA-CAATTTCTCTAA
* *
1028924 AAACAAACTTTGTCTCGCTTGAGATAATTT-TCCTAA
1 AAACAAA-TTTGTCTCACTTGAGACAATTTCT-CTAA
* *
1028960 AAACAATTTTGTCTC-TTTGAGACAATTTCTCTAA
1 AAACAAATTTGTCTCACTTGAGACAATTTCTCTAA
1028994 AAACAAATGTTGTCTCACTTGAGACAATTT
1 AAACAAAT-TTGTCTCACTTGAGACAATTT
1029024 TACAAATTAT
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
34 23 0.27
35 20 0.24
36 38 0.45
37 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (35 bp):
AAACAAATTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:1029263 original size:63 final size:63
Alignment explanation
Indices: 1029195--1029367 Score: 156
Period size: 63 Copynumber: 2.7 Consensus size: 63
1029185 GAAAAAAATC
1029195 TTTGAGTATATTTCTTT-AATAACAAAATATTGTCTCTTTTGAGAAAGTTTC-TTTTGAAAGAAT
1 TTTGAGTATATTTCTTTGAA-AACAAAATATTGTCTCTTTTGAGAAAG-TTCATTTTGAAAGAAT
* * * * * * *
1029258 TTTGAGTATGTTTTTTTGGAAACACAATTTTGTCTCTTTTGAGACAGTTCATTTTGAAGAAAAAT
1 TTTGAGTATATTTCTTTGAAAACAAAATATTGTCTCTTTTGAGAAAGTTCATTTTG-A-AAGAAT
* * * *
1029323 CTTTAAGTCTGTTT-TTATGAAAAC-AAATGTTTGTCTCTTTTGAGA
1 -TTTGAGTATATTTCTT-TGAAAACAAAAT-ATTGTCTCTTTTGAGA
1029368 CAATTTCTCT
Statistics
Matches: 92, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
62 3 0.03
63 44 0.48
64 2 0.02
65 10 0.11
66 33 0.36
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (63 bp):
TTTGAGTATATTTCTTTGAAAACAAAATATTGTCTCTTTTGAGAAAGTTCATTTTGAAAGAAT
Found at i:1029361 original size:66 final size:63
Alignment explanation
Indices: 1029215--1029375 Score: 182
Period size: 66 Copynumber: 2.5 Consensus size: 63
1029205 TTTCTTTAAT
* * * * * * *
1029215 AACAAAATATTGTCTCTTTTGAGAAAGTTTCTTTTGAAAGAATTTTGAGTATGTTTTTTTGGA
1 AACACAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAAAAATTTTAAGTATGTTTTTATGAA
*
1029278 AACACAATTTTGTCTCTTTTGAGACAG-TTCATTTTGAAGAAAAATCTTTAAGTCTGTTTTTATG
1 AACACAATTTTGTCTCTTTTGAGACAGTTTC-TTTTG-A-AAAAAT-TTTAAGTATGTTTTTATG
1029342 AA
62 AA
*
1029344 AACA-AATGTTTGTCTCTTTTGAGACAATTTCT
1 AACACAAT-TTTGTCTCTTTTGAGACAGTTTCT
1029376 CTTAAAACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
62 3 0.04
63 29 0.35
64 1 0.01
65 8 0.10
66 39 0.47
67 3 0.04
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (63 bp):
AACACAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAAAAATTTTAAGTATGTTTTTATGAA
Found at i:1029427 original size:33 final size:33
Alignment explanation
Indices: 1029388--1029450 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1029378 TAAAACAAAC
1029388 ATCTTTGAGATTGTTTCCCTTGAAACAAAATTT
1 ATCTTTGAGATTGTTTCCCTTGAAACAAAATTT
* *
1029421 ATCTTTGAGTTTGTTTCTCTTGAAACAAAA
1 ATCTTTGAGATTGTTTCCCTTGAAACAAAA
1029451 ACGTCTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (33 bp):
ATCTTTGAGATTGTTTCCCTTGAAACAAAATTT
Found at i:1030121 original size:40 final size:40
Alignment explanation
Indices: 1030051--1030127 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
1030041 CTAAAGATGG
* * *
1030051 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCTCGA
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCTCGA
* * *
1030091 CCAGATCTCCTCATCGCGTAGGAGCTGTGTCACCCCT
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCT
1030128 AGATAACCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (40 bp):
CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCTCGA
Found at i:1030248 original size:135 final size:134
Alignment explanation
Indices: 1029906--1030265 Score: 510
Period size: 134 Copynumber: 2.7 Consensus size: 134
1029896 AATCATTATC
* * *
1029906 CCTAAAGATGGCTAGAACTCTTCATCACGTATGAGTCA-TGTCATCTC-CTGACCAGATCTCTTT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAG-CAGTGTCATCTCTC-GACCAGATCTCCTC
* * *
1029969 ATCACGTAGGAG-TCGTGTCACCTCTAGATAACCAGACGTCCTCATCACGTGGGAACCGTGTTAT
64 ATCACGTAGGAGCT-GTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTAT
*
1030033 CGCCCTT
128 CACCCTT
* *
1030040 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCTCGACCAGATCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCTCTCGACCAGATCTCCTCAT
* * * *
1030105 CGCGTAGGAGCTGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAATCGAGTTATCAC
66 CACGTAGGAGCTGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCAC
1030170 CCTT
131 CCTT
*
1030174 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCTCTCGACCAGATTTCCTCA
1 CCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCAGTGTCATCTCTCGACCAGATCTCCTCA
* * *
1030239 TCACGTAGGAACCGTGTCACCCTTAGA
65 TCACGTAGGAGCTGTGTCACCCCTAGA
1030266 CGACCCAAAC
Statistics
Matches: 202, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
133 1 0.00
134 128 0.63
135 73 0.36
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (134 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCTCTCGACCAGATCTCCTCAT
CACGTAGGAGCTGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCAC
CCTT
Found at i:1030299 original size:43 final size:40
Alignment explanation
Indices: 1030188--1030299 Score: 102
Period size: 40 Copynumber: 2.7 Consensus size: 40
1030178 AAGATGGCCA
*
1030188 AGAACTCTTCATCACGTATGAGCAGTGTCATCTCTCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCACCTCTCGACC
** * * * *
1030228 AGATTTCCTCATCACGTAGGAACCGTGTCACC-CTTAGACGACCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCACCTC-T---CGA-CC
1030272 A-AACTCTTCATCACGTATGAGCAGTGTC
1 AGAACTCTTCATCACGTATGAGCAGTGTC
1030300 GTCCCCAACA
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
39 1 0.02
40 26 0.48
43 24 0.44
44 3 0.06
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCACCTCTCGACC
Found at i:1043619 original size:62 final size:62
Alignment explanation
Indices: 1043499--1043643 Score: 139
Period size: 62 Copynumber: 2.3 Consensus size: 62
1043489 GGTACATTCC
* * * *
1043499 TTAATGGGTGTATCGATACACTACCTGTGTATCGGTACCCAAATTACATTCGAAGTTTTCATT
1 TTAAAGGGTGTATCGATACACTAACTGTGTATCGATACACAAATTACATTCGAAGTTTT-ATT
* * ** * **
1043562 TTAAAGGG-GTATCGATATACTAACTGTGTATTGATACACTTATTGCATTCGTTGTTTTATTT
1 TTAAAGGGTGTATCGATACACTAACTGTGTATCGATACACAAATTACATTCGAAGTTTTA-TT
* *
1043624 ATTCAAGAGTGTATCGATAC
1 -TTAAAGGGTGTATCGATAC
1043644 CTGTTGAATG
Statistics
Matches: 65, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
61 1 0.02
62 42 0.65
63 13 0.20
64 9 0.14
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (62 bp):
TTAAAGGGTGTATCGATACACTAACTGTGTATCGATACACAAATTACATTCGAAGTTTTATT
Found at i:1051116 original size:15 final size:15
Alignment explanation
Indices: 1051096--1051142 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1051086 GCGCATGCCT
1051096 CATCAACGTGTGCTC
1 CATCAACGTGTGCTC
* *
1051111 CATCAACATCTGCTC
1 CATCAACGTGTGCTC
*
1051126 CATCAACGTGTGTTC
1 CATCAACGTGTGCTC
1051141 CA
1 CA
1051143 CCATCTTCGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (15 bp):
CATCAACGTGTGCTC
Found at i:1054594 original size:13 final size:13
Alignment explanation
Indices: 1054573--1054627 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
1054563 TGCGTCATAA
1054573 ATTTATGACGCAC
1 ATTTATGACGCAC
* * *
1054586 ATATATGACACGC
1 ATTTATGACGCAC
1054599 ATTTATGACGCAC
1 ATTTATGACGCAC
*
1054612 ATTTATGACGCTC
1 ATTTATGACGCAC
1054625 ATT
1 ATT
1054628 GCGCATCATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:1059933 original size:16 final size:15
Alignment explanation
Indices: 1059907--1059936 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1059897 CGTTTTGGAC
1059907 AAAAGGAAAAAGGGA
1 AAAAGGAAAAAGGGA
1059922 AAAAGAGAAAAAGGG
1 AAAAG-GAAAAAGGG
1059937 GAAGCATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAAGGAAAAAGGGA
Found at i:1062730 original size:12 final size:13
Alignment explanation
Indices: 1062710--1062756 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
1062700 TACATATATA
*
1062710 TATATATTTTTTT
1 TATATATTTTATT
1062723 TA-ATATTTTATT
1 TATATATTTTATT
1062735 TATATATCTATTATT
1 TATATAT-T-TTATT
*
1062750 AATATAT
1 TATATAT
1062757 ATATATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
13 6 0.21
14 1 0.03
15 11 0.38
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATATTTTATT
Found at i:1063023 original size:28 final size:27
Alignment explanation
Indices: 1062986--1063052 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
1062976 TTTCCCATAT
* *
1062986 TTTACTTATTTCATTTT-TTTCTTTTG
1 TTTATTTATTTCATTTTATTTATTTTG
*
1063012 TCTCTATTTATTTTTATTTTATTTATTTTG
1 T-T-TATTTA-TTTCATTTTATTTATTTTG
1063042 TTTATTTATTT
1 TTTATTTATTT
1063053 TGTTTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 1 0.03
27 4 0.12
28 11 0.32
29 9 0.26
30 9 0.26
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTATTTATTTCATTTTATTTATTTTG
Found at i:1063047 original size:13 final size:13
Alignment explanation
Indices: 1063029--1063061 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1063019 TTATTTTTAT
1063029 TTTATTTATTTTG
1 TTTATTTATTTTG
1063042 TTTATTTATTTTG
1 TTTATTTATTTTG
1063055 TTTATTT
1 TTTATTT
1063062 TTCTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTATTTATTTTG
Found at i:1063071 original size:22 final size:23
Alignment explanation
Indices: 1063023--1063073 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
1063013 CTCTATTTAT
*
1063023 TTTTATTTTATTTATTTTGTTTA
1 TTTTATTTTATTTATTTTGTCTA
*
1063046 -TTTATTTTGTTTATTTT-TCTA
1 TTTTATTTTATTTATTTTGTCTA
1063067 TTTTATT
1 TTTTATT
1063074 CATGTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTATTTTATTTATTTTGTCTA
Found at i:1063090 original size:26 final size:26
Alignment explanation
Indices: 1063042--1063095 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1063032 ATTTATTTTG
* * *
1063042 TTTATTTATTTTGTTTATTTTTCTAT
1 TTTATTCATTTTCTTTATTTTTCAAT
1063068 TTTATTCATGTTTCTTTA-TTTTCAAT
1 TTTATTCAT-TTTCTTTATTTTTCAAT
1063094 TT
1 TT
1063096 GCTTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTATTCATTTTCTTTATTTTTCAAT
Found at i:1066332 original size:16 final size:18
Alignment explanation
Indices: 1066311--1066347 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1066301 ATATTTTGCA
1066311 TTTTATA-TTT-CATGTT
1 TTTTATATTTTCCATGTT
1066327 TTTTATATTTTCCATGTT
1 TTTTATATTTTCCATGTT
1066345 TTT
1 TTT
1066348 ACATTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 3 0.16
18 9 0.47
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTATATTTTCCATGTT
Found at i:1068734 original size:65 final size:68
Alignment explanation
Indices: 1068630--1068763 Score: 247
Period size: 65 Copynumber: 2.0 Consensus size: 68
1068620 CCACGAAGGC
1068630 CCCATACATCAAAGTAGACGAGGAAGCGATAGAATATTCATTCTGCTCCTT-GAG-TT-TGAATG
1 CCCATACATCAAAGTAGACGAGGAAGCGATAGAATATTCATTCTGCTCCTTGGAGTTTGTGAATG
1068692 CCA
66 CCA
1068695 CCCATACATCAAAGTAGACGAGGAAGCGATAGAATATTCATTCTGCTCCTTGGAGTTTGTGAATG
1 CCCATACATCAAAGTAGACGAGGAAGCGATAGAATATTCATTCTGCTCCTTGGAGTTTGTGAATG
1068760 CCA
66 CCA
1068763 C
1 C
1068764 ATTTGTGGAA
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
65 51 0.77
66 3 0.05
67 2 0.03
68 10 0.15
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (68 bp):
CCCATACATCAAAGTAGACGAGGAAGCGATAGAATATTCATTCTGCTCCTTGGAGTTTGTGAATG
CCA
Found at i:1078132 original size:90 final size:87
Alignment explanation
Indices: 1077971--1078140 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 87
1077961 CCTAATACAC
*
1077971 CATTTTATAGCCAAGTTACCCTAATCATATTAGGTTTTATTATTTCAAATTAATTAAATCTATAT
1 CATTTTATAGCCAAGTTACCCTAATCATATTAGGTTTTATTATTTCAAATTAATTAAATATATAT
1078036 TTAATTAATTAGAATTTAGTAAT
66 TTAATTAATT-GAATTTAGTAAT
* *
1078059 CATTTTATATCCAAGTTACCCTAATTATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
1 CATTTTATAGCCAAGTTACCCTAATCATATTA-GG-TTTTATTATTTCAAATTAATTAAATATAT
1078124 ATTTAATTAATTGAATT
64 ATTTAATTAATTGAATT
1078141 AAATATTTAG
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
88 30 0.39
89 7 0.09
90 40 0.52
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.46
Consensus pattern (87 bp):
CATTTTATAGCCAAGTTACCCTAATCATATTAGGTTTTATTATTTCAAATTAATTAAATATATAT
TTAATTAATTGAATTTAGTAAT
Found at i:1078133 original size:20 final size:21
Alignment explanation
Indices: 1078108--1078176 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
1078098 TATTATTTCA
1078108 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* * *
1078128 AATTAATTGAATTAAATATTT
1 AATTAATTAAAATATATATTT
*
1078149 AGGATT-ATTAAAACATATATTT
1 A--ATTAATTAAAATATATATTT
1078171 AATTAA
1 AATTAA
1078177 ATCTAGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
20 11 0.28
21 12 0.31
22 13 0.33
23 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:1081127 original size:20 final size:18
Alignment explanation
Indices: 1081087--1081129 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1081077 CCCTAAATTG
* *
1081087 GAAAAAAAATAAAAAAGA
1 GAAAAAAAACAAAAAAAA
1081105 GAAAAAAGAACAAAAGAAAA
1 GAAAAAA-AACAAAA-AAAA
1081125 GAAAA
1 GAAAA
1081130 TAAGTGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (18 bp):
GAAAAAAAACAAAAAAAA
Found at i:1081646 original size:14 final size:14
Alignment explanation
Indices: 1081629--1081655 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1081619 GATCAGAACT
1081629 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
1081643 TCAAGATTCCAGA
1 TCAAGATTCCAGA
1081656 CATGCAACCG
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:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:1082075 original size:43 final size:43
Alignment explanation
Indices: 1082022--1082122 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
1082012 ATGAAGGGGC
* **
1082022 CATCCGCGATTTCAACCCCATGACGGAGGATATCATACCCATA
1 CATCCACGATTTCAACCCCACAACGGAGGATATCATACCCATA
* * *
1082065 CATCCACGATTTCAACTCCACAATGGAGGATATCGTACCCATA
1 CATCCACGATTTCAACCCCACAACGGAGGATATCATACCCATA
1082108 CATCCACGATTTCAA
1 CATCCACGATTTCAA
1082123 ATCCACGATG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACCCCACAACGGAGGATATCATACCCATA
Found at i:1082128 original size:43 final size:43
Alignment explanation
Indices: 1082046--1082143 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
1082036 ACCCCATGAC
* *
1082046 GGAGGATATCATACCCATACATCCACGATTTCAACTCCACAAT
1 GGAGGATATCGTACCCATACATCCACGATTTCAAATCCACAAT
*
1082089 GGAGGATATCGTACCCATACATCCACGATTTCAAATCCACGAT
1 GGAGGATATCGTACCCATACATCCACGATTTCAAATCCACAAT
*
1082132 GGAAGATATCGT
1 GGAGGATATCGT
1082144 GCTATTTGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (43 bp):
GGAGGATATCGTACCCATACATCCACGATTTCAAATCCACAAT
Found at i:1082388 original size:111 final size:110
Alignment explanation
Indices: 1082185--1082389 Score: 268
Period size: 111 Copynumber: 1.9 Consensus size: 110
1082175 GCTTCCCAGT
* * * * *
1082185 TTCAGAGCTAATTTTAACTTCACAACGAATGATATTGGATTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCTAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAAAACAAGCTCAACTTCA
* *
1082250 TAACAAATGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAACAAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
* * *
1082295 TTCAGAG-TCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAAAAACAAGTTCAACTT
1 TTCAGAGCT-AATTTCAACTTCACAACGAAGGATATTAGACTCAAGAC-AAAACAAGCTCAACTT
* * *
1082359 CACAGCGAAGGGGCGACTGGTTGTCAACAAA
64 CACAACAAAGGGGCGACTGATTGTCAACAAA
1082390 TAATTTCCCA
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
109 1 0.01
110 39 0.49
111 40 0.50
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (110 bp):
TTCAGAGCTAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAAAACAAGCTCAACTTCA
CAACAAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
Found at i:1082443 original size:107 final size:106
Alignment explanation
Indices: 1082177--1082444 Score: 263
Period size: 111 Copynumber: 2.5 Consensus size: 106
1082167 ACGAAGGGGC
* * * * * * *
1082177 TTCCCAGTTTCAGAGCTAATTTTAACTTCACAACGAATGATATTGGATTCAAGACAACACAAGCT
1 TTCCCAATTCCAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCAAGACAAAACAAGCT
* *
1082242 CAACTTCATAACAAATGGGCGACTGATTGTCAACAAACAACT
65 CAACTTCACAACAAAGGGGCGACTGATTGTCAACAAACAACT
* * * * *
1082284 TT-TCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAAAAAC
1 TTCCCA-ATTC---CAGAGCCAATTTCAACTTCACA-CGAAGGATATTGGACTCAAGAC-AAAAC
* * * * *
1082348 AAGTTCAACTTCACAGCGAAGGGGCGACTGGTTGTCAACAAATAA-T
60 AAGCTCAACTTCACAACAAAGGGGCGACTGATTGTCAACAAACAACT
1082394 TTCCCAATTCCAGAGCCAATTTCAACTTCACGAC-AGAGGATATTGGACTCA
1 TTCCCAATTCCAGAGCCAATTTCAACTTCAC-ACGA-AGGATATTGGACTCA
1082445 GAACAATACA
Statistics
Matches: 129, Mismatches: 23, Indels: 18
0.76 0.14 0.11
Matches are distributed among these distances:
106 3 0.02
107 38 0.29
108 1 0.01
109 1 0.01
110 42 0.33
111 44 0.34
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (106 bp):
TTCCCAATTCCAGAGCCAATTTCAACTTCACACGAAGGATATTGGACTCAAGACAAAACAAGCTC
AACTTCACAACAAAGGGGCGACTGATTGTCAACAAACAACT
Found at i:1083194 original size:13 final size:13
Alignment explanation
Indices: 1083176--1083205 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1083166 TTTGTTATTA
1083176 ATATTGTATAATT
1 ATATTGTATAATT
1083189 ATATTGTATAATT
1 ATATTGTATAATT
1083202 ATAT
1 ATAT
1083206 ATATAATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
ATATTGTATAATT
Found at i:1084755 original size:25 final size:25
Alignment explanation
Indices: 1084717--1084766 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1084707 TTCCCTACTT
** *
1084717 CTGTACTTGGTTGCCTGTCTCTAAG
1 CTGTACTTCCTTGCCTGTATCTAAG
1084742 CTGTACTTCCTTGCCTGTATCTAAG
1 CTGTACTTCCTTGCCTGTATCTAAG
1084767 TAGGTATGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (25 bp):
CTGTACTTCCTTGCCTGTATCTAAG
Found at i:1086123 original size:2 final size:2
Alignment explanation
Indices: 1086114--1086294 Score: 170
Period size: 2 Copynumber: 96.0 Consensus size: 2
1086104 GTACACACAC
1086114 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1086155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * * * *
1086195 AT AT AA AT AT -T AT AT AT TT TT GT TT CGT -T AT TT CT TT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
*
1086236 A- AT -T AT -T AT AT CT A- AT -T A- AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1086271 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
1086295 TTCCATTTAT
Statistics
Matches: 152, Mismatches: 14, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
1 12 0.08
2 139 0.91
3 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1086511 original size:13 final size:13
Alignment explanation
Indices: 1086480--1086521 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1086470 TCTATTTATT
* *
1086480 TTTATTTTATCTA
1 TTTATTTTGTTTA
*
1086493 TCTATTTTGTTTA
1 TTTATTTTGTTTA
1086506 TTTATTTTGTTTA
1 TTTATTTTGTTTA
1086519 TTT
1 TTT
1086522 TTCTATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTATTTTGTTTA
Found at i:1095535 original size:43 final size:45
Alignment explanation
Indices: 1095474--1095587 Score: 196
Period size: 45 Copynumber: 2.6 Consensus size: 45
1095464 TTCATCTTGT
1095474 CATGGTAGTGAGTAAGGTGAGTAAAGCCTTA-TT-TACACATTGC
1 CATGGTAGTGAGTAAGGTGAGTAAAGCCTTATTTATACACATTGC
1095517 CATGGTAGTGAGTAAGGTGAGTAAAGCCTTATTTATACACATTGC
1 CATGGTAGTGAGTAAGGTGAGTAAAGCCTTATTTATACACATTGC
* *
1095562 CATGGTAATGAGTAAGGTGATTAAAG
1 CATGGTAGTGAGTAAGGTGAGTAAAG
1095588 TCGACTATAA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
43 31 0.46
44 2 0.03
45 34 0.51
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (45 bp):
CATGGTAGTGAGTAAGGTGAGTAAAGCCTTATTTATACACATTGC
Found at i:1095859 original size:17 final size:18
Alignment explanation
Indices: 1095832--1095870 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1095822 TCCACCTTTG
1095832 TCTTATCTTTTTTCTTCA
1 TCTTATCTTTTTTCTTCA
*
1095850 TCTT-TCTTTTTTCTTCT
1 TCTTATCTTTTTTCTTCA
1095867 TCTT
1 TCTT
1095871 CATTCTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (18 bp):
TCTTATCTTTTTTCTTCA
Found at i:1096375 original size:20 final size:20
Alignment explanation
Indices: 1096347--1096385 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1096337 TTATGGGTTT
*
1096347 TAGTGTCAACATTGTTCATG
1 TAGTATCAACATTGTTCATG
*
1096367 TAGTATCAATATTGTTCAT
1 TAGTATCAACATTGTTCAT
1096386 ATTCTGGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TAGTATCAACATTGTTCATG
Found at i:1104403 original size:2 final size:2
Alignment explanation
Indices: 1104349--1104389 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1104339 GATGTGCATA
1104349 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1104390 GTACGCATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1106072 original size:21 final size:21
Alignment explanation
Indices: 1106046--1106101 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1106036 TGTTATATGT
1106046 GGTCCTTCGGGACATCTACAG
1 GGTCCTTCGGGACATCTACAG
1106067 GGTCCTTCGGGACATCTACAG
1 GGTCCTTCGGGACATCTACAG
*
1106088 GGTCCTTCGAGACA
1 GGTCCTTCGGGACA
1106102 GTTTTACATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.23
Consensus pattern (21 bp):
GGTCCTTCGGGACATCTACAG
Found at i:1108677 original size:22 final size:22
Alignment explanation
Indices: 1108652--1108696 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1108642 AAAAAATTTG
1108652 AAAAT-GAAAATTATTTTCTAAA
1 AAAATAGAAAA-TATTTTCTAAA
1108674 AAAATAGAAAATATTTTCTAAA
1 AAAATAGAAAATATTTTCTAAA
1108696 A
1 A
1108697 CCAAACATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAATAGAAAATATTTTCTAAA
Found at i:1111771 original size:7 final size:7
Alignment explanation
Indices: 1111759--1111783 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1111749 ACTAATTCAC
1111759 AAATCCA
1 AAATCCA
1111766 AAATCCA
1 AAATCCA
1111773 AAATCCA
1 AAATCCA
1111780 AAAT
1 AAAT
1111784 TTAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATCCA
Found at i:1112103 original size:28 final size:27
Alignment explanation
Indices: 1112049--1112102 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1112039 CTATTAGATT
*
1112049 TATGGGATTTGAGGTATTTGTTAAAAA
1 TATGAGATTTGAGGTATTTGTTAAAAA
1112076 TATGAGATTTGAGGT-TATTGTTAAAAA
1 TATGAGATTTGAGGTAT-TTGTTAAAAA
1112103 AAATCTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (27 bp):
TATGAGATTTGAGGTATTTGTTAAAAA
Found at i:1113745 original size:19 final size:19
Alignment explanation
Indices: 1113721--1113762 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1113711 TATCTATCTA
**
1113721 CAGTCCCATCGGATGCACT
1 CAGTCCCATAAGATGCACT
1113740 CAGTCCCATAAGATGCACT
1 CAGTCCCATAAGATGCACT
1113759 CAGT
1 CAGT
1113763 AAGTGCATAC
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:0.26, C:0.33, G:0.19, T:0.21
Consensus pattern (19 bp):
CAGTCCCATAAGATGCACT
Found at i:1113886 original size:2 final size:2
Alignment explanation
Indices: 1113879--1113917 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1113869 CCATTCTTAA
1113879 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
1113918 GTAGTCGTAA
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:1119555 original size:17 final size:18
Alignment explanation
Indices: 1119533--1119573 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1119523 ATGGAATTGG
*
1119533 ATTCCAATT-CATGACAT
1 ATTCCAATTCCATCACAT
*
1119550 ATTCCAATTCCTTCACAT
1 ATTCCAATTCCATCACAT
1119568 ATTCCA
1 ATTCCA
1119574 TTTTATTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.37
Consensus pattern (18 bp):
ATTCCAATTCCATCACAT
Found at i:1124564 original size:666 final size:649
Alignment explanation
Indices: 1123624--1124977 Score: 1971
Period size: 666 Copynumber: 2.1 Consensus size: 649
1123614 TAAACTTTTT
* **
1123624 TCATTTTTATTGGAAAATTCAACTTATCTCTCCCTTTTTAGTAGAACTAAACTTACAATTTAATT
1 TCATTTTTATTGGAAAACTCAACTTATCTCTCCCTTTTTAGTAGAACTAAACGCACAATTTAATT
* *
1123689 CAAAAAAATAAAATTAAGTTCAACTCAATTCAAAAATTTATGAGTTTAAAATTATTAAACTCAAA
66 CAAAAAAATAAAATTAAATTCAACTCAATTCAAAAATTTATAAGTTTAAAATTATTAAACTCAAA
* ** * ** *
1123754 ACAAAAAATTAAAATTCAACTCGAGTTAGAGTCTATAAGAGAGAACACCTTGAGTGATTTCTTAA
131 ACAAAAAATTAAAATTCAACTCGAGCTAGAAACTATAAGAGAGAACACCCTGAGCAATTACTTAA
* * *
1123819 GGGCCTCACTTTCTATTTTTATAGTTACGAATTCTTAACTTTTTCAATTTTATAAAATAGCACCA
196 GGGCCCCACTTTCTACTTTTATAGTTACGAATTCTTAACTTTTTCAATTTTATAAAACAGCACCA
* *
1123884 ACTTTTATTGTTATGACTGAAAATCCATAATTTAATCAATGTTATTTGGTTTATTGATATAATAT
261 ACTTTTATTGTTATGACTGAAAACCCATAATTTAATCAATGTTATTTGGTTTATTAATATAATAT
*
1123949 TAAAATAATTATTCAAAATAATAAAATATATTTATGTTCTATAGGGTCTATCTTTAAATTTTTGA
326 TAAAATAATTATTCAAAATAATAAAATATATTTACGTTCTATAGGGTCTATCTTTAAATTTTT-A
* * *
1124014 -TCAAGGTTTATAATTAATATCCCTATTTTTTT-ATTTTATAAAATAGTCCTTACTTTCTATCTT
390 CCCAAGGTTTATAATTAATACCCCTATTTTTTTAATTTTATAAAATAATCCTTACTTTCTATCTT
1124077 TACAACTAAGAGCCCATAATGTAATCATTTTCTATAGTTTTATTAATACAATATTAAATTAAATG
455 TACAACTAAGAGCCCATAATGTAATCATTTT-TATAGTTTTATTAATACAATATTAAATTAAATG
*
1124142 TTCAAAATAATAAAATATATTTTCGTT-TATATGACTTATTTTTTAATTTTCGCTTAAGGTTTAT
519 TTAAAAATAAT-AAATATATTTTCGTTCTATATGACTTATTTTTTAATTTTCGCTTAAGGTTTAT
** * *
1124206 ATA-TGAGGGCTCCTAATTTTTTTTTAATTTTATAAGATAGTTCCTATTTTATACAGCACTATAA
583 A-ACTGAGGGCTCCTAA--TTTTTAAAATTTTATAAGATAGTCCCTATTTTATACAACACTATAA
*
1124270 TTTAT
645 TTTAA
* * * **
1124275 TTATTTTTATTGGGAAACTCAAATTATCTCTCCCTTTTTAGTAGGGCTAAACGCACAATTTAATT
1 TCATTTTTATTGGAAAACTCAACTTATCTCTCCCTTTTTAGTAGAACTAAACGCACAATTTAATT
** * * * *
1124340 CAAAAAGTTTAAAATTAAATTCGATTCAATTCAAAAATTTTTAAGTTTAAATTTATTAAACTCGA
66 CAAAAA-AATAAAATTAAATTCAACTCAATTCAAAAATTTATAAGTTTAAAATTATTAAACTC-A
* *
1124405 CTTAAATTCAAAAAAGTAATTAAAGTTTAACTCGAGCTAGAACCAACTATAAGAGAGAACACCCT
129 ---AAA--C--AAAA--AATTAAAATTCAACTCGAGCTAG-A--AACTATAAGAGAGAACACCCT
* *
1124470 GAGCAATTACTTAAGGGCCCCCACTTTCTACTTTTATAGTTATGGATTCTTAACTTTTTCAATTT
182 GAGCAATTACTTAAGGG-CCCCACTTTCTACTTTTATAGTTACGAATTCTTAACTTTTTCAATTT
* * * *
1124535 TTTAAAACAGTC-CCTACTTTTATTGTTATGACTGAAAGCCCATAATTTAATCAATTTTATTTGG
246 TATAAAACAG-CACCAACTTTTATTGTTATGACTGAAAACCCATAATTTAATCAATGTTATTTGG
* *
1124599 TTTATTAATATAATATTAAAATGATTATTCAAAATAATAGAATATATTTACGTTCTATAGGGTCT
310 TTTATTAATATAATATTAAAATAATTATTCAAAATAATAAAATATATTTACGTTCTATAGGGTCT
*
1124664 ATTTTTAAATTTTTACCCAAGGTTTATAATTAATACCCCTATTTTTTTAATTTTATAAAATAATC
375 ATCTTTAAATTTTTACCCAAGGTTTATAATTAATACCCCTATTTTTTTAATTTTATAAAATAATC
* ** *
1124729 CTTACTTTCTATCTTTACAACTAAGGGTTCATAATGTAATCATTTTTATAGTTTTATTAATATAA
440 CTTACTTTCTATCTTTACAACTAAGAGCCCATAATGTAATCATTTTTATAGTTTTATTAATACAA
*
1124794 TATTAAATTAATTGTTAAAAATAATAAATATATTTTCGTTCTATATGACTTATTTTTTAATTTTC
505 TATTAAATTAAATGTTAAAAATAATAAATATATTTTCGTTCTATATGACTTATTTTTTAATTTTC
*
1124859 GCTTAAGGTTTATAACTGAGGGCTCCTAATTTTTAAAATTTTATAAGATAGTCCCTATTTTCTAC
570 GCTTAAGGTTTATAACTGAGGGCTCCTAATTTTTAAAATTTTATAAGATAGTCCCTATTTTATAC
1124924 AACACTATAATTTAA
635 AACACTATAATTTAA
*
1124939 TCATTTTTATTGGAAAACTCAACTTATCTCTCCCCTTTT
1 TCATTTTTATTGGAAAACTCAACTTATCTCTCCCTTTTT
1124978 GCACAATTTA
Statistics
Matches: 624, Mismatches: 59, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
651 63 0.10
652 48 0.08
653 1 0.00
656 3 0.00
658 1 0.00
660 4 0.01
662 20 0.03
663 1 0.00
664 80 0.13
665 49 0.08
666 295 0.47
667 59 0.09
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (649 bp):
TCATTTTTATTGGAAAACTCAACTTATCTCTCCCTTTTTAGTAGAACTAAACGCACAATTTAATT
CAAAAAAATAAAATTAAATTCAACTCAATTCAAAAATTTATAAGTTTAAAATTATTAAACTCAAA
ACAAAAAATTAAAATTCAACTCGAGCTAGAAACTATAAGAGAGAACACCCTGAGCAATTACTTAA
GGGCCCCACTTTCTACTTTTATAGTTACGAATTCTTAACTTTTTCAATTTTATAAAACAGCACCA
ACTTTTATTGTTATGACTGAAAACCCATAATTTAATCAATGTTATTTGGTTTATTAATATAATAT
TAAAATAATTATTCAAAATAATAAAATATATTTACGTTCTATAGGGTCTATCTTTAAATTTTTAC
CCAAGGTTTATAATTAATACCCCTATTTTTTTAATTTTATAAAATAATCCTTACTTTCTATCTTT
ACAACTAAGAGCCCATAATGTAATCATTTTTATAGTTTTATTAATACAATATTAAATTAAATGTT
AAAAATAATAAATATATTTTCGTTCTATATGACTTATTTTTTAATTTTCGCTTAAGGTTTATAAC
TGAGGGCTCCTAATTTTTAAAATTTTATAAGATAGTCCCTATTTTATACAACACTATAATTTAA
Found at i:1134801 original size:21 final size:21
Alignment explanation
Indices: 1134777--1134819 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1134767 GGCTTCGGAT
*
1134777 TATAAGAAT-TTATTTTCAAAA
1 TATAAGAATGATA-TTTCAAAA
1134798 TATAAGAATGATATTTCAAAA
1 TATAAGAATGATATTTCAAAA
1134819 T
1 T
1134820 TGAAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (21 bp):
TATAAGAATGATATTTCAAAA
Found at i:1134828 original size:21 final size:21
Alignment explanation
Indices: 1134790--1134829 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1134780 AAGAATTTAT
*
1134790 TTTCAAAATATAAGAATGATA
1 TTTCAAAATATAAAAATGATA
1134811 TTTCAAAAT-TGAAAAATGA
1 TTTCAAAATAT-AAAAATGA
1134830 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
TTTCAAAATATAAAAATGATA
Found at i:1138728 original size:23 final size:22
Alignment explanation
Indices: 1138646--1138725 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
1138636 ACACTAGCTA
1138646 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* *
1138669 GTGCATCGATACAT-CATGAA-
1 GTGCATCGATGCATCCTTGAAT
* *
1138689 GATACACCGATGCACTCCTTGAAT
1 G-TGCATCGATGCA-TCCTTGAAT
1138713 GTGCATCGATGCA
1 GTGCATCGATGCA
1138726 CTCTGCTGTG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.02
21 14 0.31
22 1 0.02
23 28 0.62
24 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:1140973 original size:19 final size:19
Alignment explanation
Indices: 1140949--1140986 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1140939 AAAGGGGGAA
1140949 AAGATGTATTATAGTAAGG
1 AAGATGTATTATAGTAAGG
1140968 AAGATGTATTATAGTAAGG
1 AAGATGTATTATAGTAAGG
1140987 GGGAGTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (19 bp):
AAGATGTATTATAGTAAGG
Found at i:1143763 original size:18 final size:20
Alignment explanation
Indices: 1143740--1143784 Score: 67
Period size: 18 Copynumber: 2.3 Consensus size: 20
1143730 TCAAAAACCA
1143740 TTTTTTCCA-TTT-TTCTTT
1 TTTTTTCCACTTTGTTCTTT
1143758 TTTTTTCCACTTTGTTCTTT
1 TTTTTTCCACTTTGTTCTTT
1143778 TCTTTTT
1 T-TTTTT
1143785 TTTGAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.38
19 3 0.12
20 7 0.29
21 5 0.21
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTTCCACTTTGTTCTTT
Found at i:1143817 original size:18 final size:17
Alignment explanation
Indices: 1143791--1143825 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1143781 TTTTTTTGAA
1143791 CTTTCTTTATTATTTTTC
1 CTTTCTTTATT-TTTTTC
*
1143809 CTTTTTTTATTTTTTTC
1 CTTTCTTTATTTTTTTC
1143826 TTCGTGGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (17 bp):
CTTTCTTTATTTTTTTC
Found at i:1148968 original size:34 final size:34
Alignment explanation
Indices: 1148925--1148993 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1148915 GCTTGATATC
1148925 TACACAATCATACATTCCAAGTATTATAATTCAA
1 TACACAATCATACATTCCAAGTATTATAATTCAA
1148959 TACACAATCATACATTCCAAGTATTATAATTCAA
1 TACACAATCATACATTCCAAGTATTATAATTCAA
1148993 T
1 T
1148994 CCTTAATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (34 bp):
TACACAATCATACATTCCAAGTATTATAATTCAA
Found at i:1158015 original size:32 final size:31
Alignment explanation
Indices: 1157979--1158070 Score: 121
Period size: 32 Copynumber: 2.9 Consensus size: 31
1157969 CATACACAAT
*
1157979 GGAGTACCTTAGGGCCTTAGAGCCTACCTAAG
1 GGAGTACCTTAGGGCCTAAGAGCCTACC-AAG
* *
1158011 GGAGTACCTTGGGGCCTAAGAACCTATCCAAG
1 GGAGTACCTTAGGGCCTAAGAGCCTA-CCAAG
* *
1158043 TGAGTAACTTAGGGCCTAAGAGCCTACC
1 GGAGTACCTTAGGGCCTAAGAGCCTACC
1158071 CAATGATCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 2 0.04
32 48 0.92
33 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (31 bp):
GGAGTACCTTAGGGCCTAAGAGCCTACCAAG
Found at i:1159359 original size:22 final size:22
Alignment explanation
Indices: 1159334--1159386 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1159324 CATCTCAATG
1159334 GTCTTTCAGATCATTTCATCCA
1 GTCTTTCAGATCATTTCATCCA
* *
1159356 GTCTTTTAGATCATTTCATCCG
1 GTCTTTCAGATCATTTCATCCA
1159378 GTTCTTTCA
1 G-TCTTTCA
1159387 TATGAATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.45
Consensus pattern (22 bp):
GTCTTTCAGATCATTTCATCCA
Found at i:1162927 original size:34 final size:35
Alignment explanation
Indices: 1162831--1163093 Score: 255
Period size: 34 Copynumber: 7.3 Consensus size: 35
1162821 CTTGAAAAAA
* * *
1162831 ATATAATATATAGTTTTTAGAAAACGGTTTTTGAAAAC
1 ATATATTATATAG-TTTT-GAAAACGATTTTTG-AAAT
* * * *
1162869 ATATAATATATACTTTTTAAAAAATCGGTTTTTGAAA-
1 ATATATTATATA-GTTTT-GAAAA-CGATTTTTGAAAT
* **
1162906 GTATA-TATATAGTTTTGAAAATAATTTTTGAAAT
1 ATATATTATATAGTTTTGAAAACGATTTTTGAAAT
* *
1162940 ATATATTATATATTTTTGAAAACAATTTTTGAAAAT
1 ATATATTATATAGTTTTGAAAACGATTTTTG-AAAT
1162976 ATATATTATATAGTTTTGAAAACGATTTTTGAAA-
1 ATATATTATATAGTTTTGAAAACGATTTTTGAAAT
*
1163010 ATATATTATATAGTTTTGAAAATGATTTTTGAAA-
1 ATATATTATATAGTTTTGAAAACGATTTTTGAAAT
* ** *
1163044 ATATATTATATAATTTTGAAAAATAATTTGTGAATAT
1 ATATATTATATAGTTTTG-AAAACGATTTTTGAA-AT
1163081 ATATATATATATA
1 ATATAT-TATATA
1163094 TATATATATA
Statistics
Matches: 199, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
33 9 0.05
34 58 0.29
35 43 0.22
36 40 0.20
37 10 0.05
38 30 0.15
39 9 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (35 bp):
ATATATTATATAGTTTTGAAAACGATTTTTGAAAT
Found at i:1163084 original size:2 final size:2
Alignment explanation
Indices: 1163077--1163110 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1163067 TAATTTGTGA
1163077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1163111 GTTTTGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1163103 original size:55 final size:52
Alignment explanation
Indices: 1163044--1163145 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 52
1163034 ATTTTTGAAA
*
1163044 ATATAT-TA-TATAATTTTGAAAAATAATTTGTGAATATATATATATATATATAT
1 ATATATATATTATAATTTTG-AAAATAATTT-TGAAAATATATA-ATATATATAT
*
1163097 ATATATATATTATAGTTTTGAAAATAATTTTGAAAATATATAATATATA
1 ATATATATATTATAATTTTGAAAATAATTTTGAAAATATATAATATATA
1163146 GTTTTTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
52 7 0.16
53 17 0.38
54 12 0.27
55 9 0.20
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (52 bp):
ATATATATATTATAATTTTGAAAATAATTTTGAAAATATATAATATATATAT
Found at i:1163146 original size:35 final size:38
Alignment explanation
Indices: 1163095--1163169 Score: 111
Period size: 35 Copynumber: 2.1 Consensus size: 38
1163085 ATATATATAT
*
1163095 ATATATATATATTATAGTTTTGAAAATA-ATTTTGAAA
1 ATATATATATATTATAGTTTTGAAAAGAGATTTTGAAA
*
1163132 ATATATA-ATA-TATAGTTTTTAAAAGAGATTTTGAAA
1 ATATATATATATTATAGTTTTGAAAAGAGATTTTGAAA
1163168 AT
1 AT
1163170 GATAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 14 0.40
36 14 0.40
37 7 0.20
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (38 bp):
ATATATATATATTATAGTTTTGAAAAGAGATTTTGAAA
Found at i:1166801 original size:15 final size:15
Alignment explanation
Indices: 1166781--1166811 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1166771 TTCCCTCTGA
1166781 GCTAGAGATAGCAAG
1 GCTAGAGATAGCAAG
1166796 GCTAGAGATAGCAAG
1 GCTAGAGATAGCAAG
1166811 G
1 G
1166812 AAAGAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.35, T:0.13
Consensus pattern (15 bp):
GCTAGAGATAGCAAG
Found at i:1182006 original size:15 final size:15
Alignment explanation
Indices: 1181986--1182017 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1181976 TTTGCTCCAA
1181986 TTGCTCTGACATCAT
1 TTGCTCTGACATCAT
1182001 TTGCTCTGACATCAT
1 TTGCTCTGACATCAT
1182016 TT
1 TT
1182018 CTATACCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (15 bp):
TTGCTCTGACATCAT
Found at i:1183576 original size:201 final size:199
Alignment explanation
Indices: 1183231--1183807 Score: 695
Period size: 201 Copynumber: 2.9 Consensus size: 199
1183221 CATTCACAGA
* *
1183231 ATAGCTCAAGGCAAGAAGGGTTATATGTCAATGAAAACTTTCGAGTTCGATTCCATTCAGCTCGA
1 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAA-GAAAACTTTCGAGTTCGATTCCATTCAGCTCGA
** * * ** * * ** *
1183296 GAACTTATCAGCCACATGGTAGCAGCGATGAATTACTTTTTGGTTGAAGTTTAAACTAAGGTCTT
65 GGGCATATCAACCACATGGTAG-AATGAGGAACTACTTTCCGGTTGAAGTTTAAACTGAGGTCTT
* ** *
1183361 TAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAATGAACTATCTCCCAGTCAAATT
129 TAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACCAAAGT
* **
1183426 TACGGC
194 CACAAC
* * *
1183432 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACTTTCGAGTTTGATTCAATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAA-GAAAACTTTCGAGTTCGATTCCATTCAGCTCGA
* * *
1183497 GGGCACATCAACCGCATGGTAGTAATGAGGAACTACTTTCCAGTTGAAGTTTAAACTGAGGTCTT
65 GGGCATATCAACCACATGGTAG-AATGAGGAACTACTTTCCGGTTGAAGTTTAAACTGAGGTCTT
* * *
1183562 TAAGTCAAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTATCTCCTAACCTAAGT
129 TAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACCAAAGT
*
1183627 CATAAC
194 CACAAC
* * * *
1183633 ATAGCTCAAGGTGAGAAGGGTTATCTGTCAATAAAAATCTTCGAGTTCGATTCCATTCAGCTTGA
1 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAAGAAAACT-TTCGAGTTCGATTCCATTCAGCTCGA
* * *
1183698 GGGAATATCAACCACATGGTAGCATCGAGGAACTACTTTCCGGTTGAATTTTCAAACTGAGGTCT
65 GGGCATATCAACCACATGGTAGAAT-GAGGAACTACTTTCCGGTTGAAGTTT-AAACTGAGGTCT
** * * * * *
1183763 TTAAACCGAGAAGAAGACCAAGGTTGACTACGATTTGGCAACAAG
128 TTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAG
1183808 AAGCCACCTT
Statistics
Matches: 320, Mismatches: 53, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
200 7 0.02
201 264 0.82
202 49 0.15
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (199 bp):
ATAGCTCAAGGCGAGAAGGGTTATCTGTCAAGAAAACTTTCGAGTTCGATTCCATTCAGCTCGAG
GGCATATCAACCACATGGTAGAATGAGGAACTACTTTCCGGTTGAAGTTTAAACTGAGGTCTTTA
AGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAACCAAAGTCA
CAAC
Found at i:1184207 original size:38 final size:36
Alignment explanation
Indices: 1184132--1184357 Score: 118
Period size: 34 Copynumber: 6.5 Consensus size: 36
1184122 AGTATAGTTC
* * *
1184132 TTGAAAAAATATAATATAATTTTTAGAAAACGGTTT
1 TTGAAAACATATAATATAATTTTTAAAAAACGATTT
1184168 TTGAAAACATATAATATATACTTTTTAAAAAATC-ATTT
1 TTGAAAACATATAATATA-A-TTTTTAAAAAA-CGATTT
* * * * *
1184206 TTGAAAGC--ATAGTAT-AGTTTT-GAAAACAATTT
1 TTGAAAACATATAATATAATTTTTAAAAAACGATTT
* * * * *
1184238 TTGAAAATATATTATAT-A-GTTT-GAAAACGATAT
1 TTGAAAACATATAATATAATTTTTAAAAAACGATTT
* * * *
1184271 TTGAAAATATATTATAT-AGTTTT-GAAAACGATTT
1 TTGAAAACATATAATATAATTTTTAAAAAACGATTT
* * * *
1184305 TTGAAAATATATTATATAGTTTTGAAAAATA--A-TT
1 TTGAAAACATATAATATAATTTTTAAAAA-ACGATTT
*
1184339 GTGAAAACATATATATATA
1 TTGAAAACATATA-ATATA
1184358 TATATATATA
Statistics
Matches: 156, Mismatches: 23, Indels: 23
0.77 0.11 0.11
Matches are distributed among these distances:
31 1 0.01
32 14 0.09
33 34 0.22
34 49 0.31
35 9 0.06
36 26 0.17
37 2 0.01
38 20 0.13
39 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (36 bp):
TTGAAAACATATAATATAATTTTTAAAAAACGATTT
Found at i:1184300 original size:34 final size:34
Alignment explanation
Indices: 1184218--1184357 Score: 196
Period size: 34 Copynumber: 4.1 Consensus size: 34
1184208 GAAAGCATAG
* *
1184218 TATAGTTTTGAAAACAATTTTTGAAAATATATTA
1 TATAGTTTTGAAAACGATATTTGAAAATATATTA
1184252 TATAG-TTTGAAAACGATATTTGAAAATATATTA
1 TATAGTTTTGAAAACGATATTTGAAAATATATTA
*
1184285 TATAGTTTTGAAAACGATTTTTGAAAATATATTA
1 TATAGTTTTGAAAACGATATTTGAAAATATATTA
*
1184319 TATAGTTTTGAAAA--ATAATTGTGAAAACATATATA
1 TATAGTTTTGAAAACGAT-ATT-TGAAAATATAT-TA
1184354 TATA
1 TATA
1184358 TATATATATA
Statistics
Matches: 97, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
32 2 0.02
33 33 0.34
34 56 0.58
35 6 0.06
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (34 bp):
TATAGTTTTGAAAACGATATTTGAAAATATATTA
Found at i:1184305 original size:67 final size:69
Alignment explanation
Indices: 1184218--1184357 Score: 216
Period size: 67 Copynumber: 2.1 Consensus size: 69
1184208 GAAAGCATAG
*
1184218 TATAGTTTTGAAAACAATTTTTGAAAATATATTATATAG-TTTGAAAACGAT-ATT-TGAAAATA
1 TATAGTTTTGAAAACAATTTTTGAAAATATATTATATAGTTTTGAAAA--ATAATTGTGAAAACA
1184280 TAT-TA
64 TATATA
*
1184285 TATAGTTTTGAAAACGATTTTTGAAAATATATTATATAGTTTTGAAAAATAATTGTGAAAACATA
1 TATAGTTTTGAAAACAATTTTTGAAAATATATTATATAGTTTTGAAAAATAATTGTGAAAACATA
1184350 TATA
66 TATA
1184354 TATA
1 TATA
1184358 TATATATATA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
66 2 0.03
67 41 0.61
68 18 0.27
69 6 0.09
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (69 bp):
TATAGTTTTGAAAACAATTTTTGAAAATATATTATATAGTTTTGAAAAATAATTGTGAAAACATA
TATA
Found at i:1184354 original size:2 final size:2
Alignment explanation
Indices: 1184347--1184428 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
1184337 TTGTGAAAAC
1184347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1184389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1184429 GTTTCGAAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1184526 original size:9 final size:9
Alignment explanation
Indices: 1184512--1184543 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1184502 ACATAGTTAG
1184512 TTATTTATA
1 TTATTTATA
1184521 TTATTTATA
1 TTATTTATA
1184530 TTATTTA-A
1 TTATTTATA
1184538 TTATTT
1 TTATTT
1184544 CACTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATTTATA
Found at i:1184570 original size:13 final size:13
Alignment explanation
Indices: 1184512--1184570 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
1184502 ACATAGTTAG
1184512 TTATTTATA-TTAT
1 TTATTT-TACTTAT
* * *
1184525 TTATATTATTTAA
1 TTATTTTACTTAT
*
1184538 TTATTTCACTTAT
1 TTATTTTACTTAT
*
1184551 TTATTTTACTTTT
1 TTATTTTACTTAT
1184564 TTATTTT
1 TTATTTT
1184571 CGTTTTTAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
12 2 0.05
13 35 0.95
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTACTTAT
Found at i:1185658 original size:22 final size:21
Alignment explanation
Indices: 1185633--1185693 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
1185623 TTTTATTTTA
*
1185633 TTTTTTAACCTTTTTTAAATTC
1 TTTTTTAACATTTTTT-AATTC
*
1185655 TTTTTAAAAGCATTTTTT-ATTC
1 TTTTT-TAA-CATTTTTTAATTC
*
1185677 TCTTTTAACATTTTTTA
1 TTTTTTAACATTTTTTA
1185694 TATTTTTCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 8 0.25
21 2 0.06
22 13 0.41
23 2 0.06
24 7 0.22
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATTTTTTAATTC
Found at i:1185697 original size:22 final size:21
Alignment explanation
Indices: 1185634--1185697 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
1185624 TTTATTTTAT
* *
1185634 TTTTTAACCTTTTTTAAATTC
1 TTTTTAACATTTTTTATATTC
1185655 TTTTTAAAAGCA-TTTTT-TATTC
1 TTTTT--AA-CATTTTTTATATTC
1185677 TCTTTTAACATTTTTTATATT
1 T-TTTTAACATTTTTTATATT
1185698 TTTCCCTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
20 2 0.06
21 12 0.34
22 9 0.26
23 11 0.31
24 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTAACATTTTTTATATTC
Found at i:1185849 original size:4 final size:4
Alignment explanation
Indices: 1185840--1185878 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
1185830 GCTATTCACT
1185840 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1185879 TTATTTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1191296 original size:16 final size:17
Alignment explanation
Indices: 1191246--1191296 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1191236 AAAATAAATA
1191246 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
1191263 AATTT-AAA-TTAGGGGT
1 AATTTGAAAGTTA-GAGT
1191279 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
1191295 AA
1 AA
1191297 CTAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 3 0.10
16 15 0.52
17 8 0.28
18 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:1194183 original size:13 final size:13
Alignment explanation
Indices: 1194165--1194190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1194155 TGAAATCAGG
1194165 ATCTCCCTCTATT
1 ATCTCCCTCTATT
1194178 ATCTCCCTCTATT
1 ATCTCCCTCTATT
1194191 TTGATTTAAT
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:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (13 bp):
ATCTCCCTCTATT
Found at i:1195564 original size:3 final size:3
Alignment explanation
Indices: 1195558--1195612 Score: 56
Period size: 3 Copynumber: 16.3 Consensus size: 3
1195548 CCCCCAGGTT
1195558 TTC TTC TTC TTCC TTC TTTC TTTC TTC TTTC TTTC TTC TTTC TTC TTC
1 TTC TTC TTC TT-C TTC -TTC -TTC TTC -TTC -TTC TTC -TTC TTC TTC
1195606 TTC TTC T
1 TTC TTC T
1195613 AAGTTTTAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 28 0.58
4 20 0.42
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1195584 original size:11 final size:11
Alignment explanation
Indices: 1195557--1195607 Score: 79
Period size: 11 Copynumber: 4.8 Consensus size: 11
1195547 ACCCCCAGGT
1195557 TTTCTTC-TTC
1 TTTCTTCTTTC
*
1195567 TTCCTTCTTTC
1 TTTCTTCTTTC
1195578 TTTCTTCTTTC
1 TTTCTTCTTTC
1195589 TTTCTTCTTTC
1 TTTCTTCTTTC
1195600 -TTCTTCTT
1 TTTCTTCTT
1195608 CTTCTAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 14 0.37
11 24 0.63
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:1197567 original size:12 final size:13
Alignment explanation
Indices: 1197533--1197567 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1197523 CAATTGCTTC
1197533 TTTGTGTGTTATT
1 TTTGTGTGTTATT
*
1197546 TTTGTATGTTATT
1 TTTGTGTGTTATT
1197559 TTTG-GTGTT
1 TTTGTGTGTT
1197568 TTGTGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.09, C:0.00, G:0.23, T:0.69
Consensus pattern (13 bp):
TTTGTGTGTTATT
Found at i:1201884 original size:6 final size:6
Alignment explanation
Indices: 1201873--1201924 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
1201863 GTACTCTCAA
1201873 CATCTC CATCTC CATCTC CATCTC CATCTC CATCTC CATCTC CATCTC
1 CATCTC CATCTC CATCTC CATCTC CATCTC CATCTC CATCTC CATCTC
1201921 CATC
1 CATC
1201925 CTTGGGTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
CATCTC
Found at i:1202308 original size:28 final size:29
Alignment explanation
Indices: 1202264--1202319 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1202254 ACAATTTCAT
*
1202264 TATTTTAATAGATAATA-AATATAAAAAA
1 TATTTTAATAGATAATATAAAATAAAAAA
*
1202292 TATTTTTATA-ATAAATATAAAATAAAAA
1 TATTTTAATAGAT-AATATAAAATAAAAA
1202320 TGTTACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 13 0.54
29 9 0.38
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
TATTTTAATAGATAATATAAAATAAAAAA
Found at i:1212876 original size:15 final size:16
Alignment explanation
Indices: 1212856--1212890 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1212846 TGTATAAGTT
*
1212856 TATATGTTAT-TGTTG
1 TATATGTTATGTGATG
1212871 TATATGTTATGTGATG
1 TATATGTTATGTGATG
1212887 TATA
1 TATA
1212891 CATGAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.54
Consensus pattern (16 bp):
TATATGTTATGTGATG
Found at i:1213134 original size:44 final size:44
Alignment explanation
Indices: 1213071--1213172 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
1213061 GGGTCTACGC
* * *
1213071 GGTGCTTCAGGATATATACAAAGGTCCTTCTGGACATATACAGA
1 GGTGCTTCAGGACATATACAAAGGTCCTTCGGGACAAATACAGA
* * *
1213115 GGTGCTTCGGGACATATACAGAGGTCCTTCGGGACAAATACATA
1 GGTGCTTCAGGACATATACAAAGGTCCTTCGGGACAAATACAGA
1213159 GGT-CATTCAGGACA
1 GGTGC-TTCAGGACA
1213173 AATTTCACAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 1 0.02
44 49 0.98
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (44 bp):
GGTGCTTCAGGACATATACAAAGGTCCTTCGGGACAAATACAGA
Found at i:1213175 original size:22 final size:22
Alignment explanation
Indices: 1213075--1213172 Score: 115
Period size: 22 Copynumber: 4.5 Consensus size: 22
1213065 CTACGCGGTG
* *
1213075 CTTCAGGATATATACAAAGGTC
1 CTTCAGGACATATACAGAGGTC
* *
1213097 CTTCTGGACATATACAGAGGTG
1 CTTCAGGACATATACAGAGGTC
*
1213119 CTTCGGGACATATACAGAGGTC
1 CTTCAGGACATATACAGAGGTC
* * *
1213141 CTTCGGGACAAATACATAGGTC
1 CTTCAGGACATATACAGAGGTC
*
1213163 ATTCAGGACA
1 CTTCAGGACA
1213173 AATTTCACAT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (22 bp):
CTTCAGGACATATACAGAGGTC
Found at i:1216153 original size:13 final size:13
Alignment explanation
Indices: 1216135--1216159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1216125 ACGACTCTAG
1216135 GCATGACATGGTC
1 GCATGACATGGTC
1216148 GCATGACATGGT
1 GCATGACATGGT
1216160 TTGACATGGC
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:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (13 bp):
GCATGACATGGTC
Found at i:1216495 original size:24 final size:25
Alignment explanation
Indices: 1216444--1216497 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
1216434 ATTTCTTTTC
*
1216444 TTTTATTTTATTTTCAAGTTTTCCT
1 TTTTATTTTATTTTCAAGTTTTACT
*
1216469 TTTTATTTTATTTT-AAGTTTTATT
1 TTTTATTTTATTTTCAAGTTTTACT
1216493 TTTTA
1 TTTTA
1216498 AACATGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTTATTTTATTTTCAAGTTTTACT
Found at i:1221911 original size:23 final size:23
Alignment explanation
Indices: 1221881--1221963 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
1221871 GTCGAGGGTT
*
1221881 CTATGTGGTTCTTCGGGATAAAA
1 CTATGTGGTCCTTCGGGATAAAA
**
1221904 CTATGTGGTCCTTCGGGATAATC
1 CTATGTGGTCCTTCGGGATAAAA
* * *
1221927 CTATATGGTCATTC-GGA-ACAA
1 CTATGTGGTCCTTCGGGATAAAA
1221948 CTATGTGG-CACTTCGG
1 CTATGTGGTC-CTTCGG
1221964 CTCAATTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.02
21 11 0.23
22 4 0.08
23 32 0.67
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGATAAAA
Found at i:1229887 original size:3 final size:3
Alignment explanation
Indices: 1229879--1230006 Score: 220
Period size: 3 Copynumber: 42.7 Consensus size: 3
1229869 TATATGTATT
*
1229879 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1229927 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1229975 TAA TAA TAA TAA TAA TAA TAA TTA TAG TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1230007 TGGATAAAAA
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1230570 original size:113 final size:113
Alignment explanation
Indices: 1230323--1230980 Score: 1182
Period size: 113 Copynumber: 5.9 Consensus size: 113
1230313 GAATTATGCC
* **
1230323 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * * *
1230388 GTGAA-CTTCTCCGG-AA--AAGAT-AATCAAGTGATGAATTCAAACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
1230431 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1230496 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
1230544 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1230609 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
1230657 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1230722 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
*
1230770 AAAAGTTGAACAAGTTCTTCTCGTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1230835 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
66 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
1230883 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1230948 ATGAACCTTCTCTGGCAATGAATGATCCATCAA
66 ATGAACCTTCTCTGGCAATG-ATGATCCATCAA
1230981 GTGGATTTGA
Statistics
Matches: 533, Mismatches: 11, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
108 66 0.12
109 8 0.02
110 2 0.00
112 4 0.01
113 441 0.83
114 12 0.02
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
Found at i:1231780 original size:83 final size:83
Alignment explanation
Indices: 1231575--1231863 Score: 508
Period size: 83 Copynumber: 3.5 Consensus size: 83
1231565 CCTACTGAAT
* * *
1231575 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAC
* *
1231640 TGA-TCGTTCTGTCCAAC
66 TGATTGGTTCTGTTCAAC
*
1231657 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAC
1231722 TGATTGGTTCTGTTCAAC
66 TGATTGGTTCTGTTCAAC
*
1231740 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACATATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAC
1231805 TGATTGGTTCTGTTCAAC
66 TGATTGGTTCTGTTCAAC
1231823 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1231864 CTGTCTAATC
Statistics
Matches: 198, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
82 64 0.32
83 134 0.68
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAATTCAC
TGATTGGTTCTGTTCAAC
Found at i:1233190 original size:11 final size:11
Alignment explanation
Indices: 1233171--1233203 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
1233161 TTCCTTTTTT
1233171 TTTTCTTTTTCA
1 TTTT-TTTTTCA
1233183 TTTTTTTTTCA
1 TTTTTTTTTCA
1233194 TTTTTTTTTC
1 TTTTTTTTTC
1233204 TTCAAGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:1233198 original size:19 final size:18
Alignment explanation
Indices: 1233151--1233199 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1233141 CTTGACCCCC
*
1233151 TTTTTCTTTTTTCCTTTT
1 TTTTTCTTTTTTCATTTT
1233169 TTTTT-TCTTTTTCATTTT
1 TTTTTCT-TTTTTCATTTT
1233187 TTTTTCATTTTTT
1 TTTTTC-TTTTTT
1233200 TTTCTTCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.04
18 20 0.74
19 5 0.19
20 1 0.04
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTCTTTTTTCATTTT
Found at i:1246007 original size:3 final size:3
Alignment explanation
Indices: 1245999--1246089 Score: 164
Period size: 3 Copynumber: 30.3 Consensus size: 3
1245989 TATATGTATT
*
1245999 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1246047 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1246090 TATTATAGTA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1249839 original size:21 final size:23
Alignment explanation
Indices: 1249789--1249848 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1249779 GTCGAGGGTT
*
1249789 CTATGTGGTCCTTCAGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
1249812 CTATGTGGTCCTTCGGGAC-AAA
1 CTATGTGGTCCTTCGGGACAAAA
1249834 -TATGTGG-CACTTCGG
1 CTATGTGGTC-CTTCGG
1249849 TGCAATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 13 0.37
22 3 0.09
23 18 0.51
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:1252565 original size:28 final size:27
Alignment explanation
Indices: 1252511--1252565 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1252501 ATAATAATAT
** *
1252511 TATTATTTTAAATTCTTGTTATTAAAA
1 TATTATTTTAAATTCTTGCAAATAAAA
*
1252538 TATTATTTTATAATTTTTGCAAATAAAA
1 TATTATTTTA-AATTCTTGCAAATAAAA
1252566 GCACAGATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (27 bp):
TATTATTTTAAATTCTTGCAAATAAAA
Found at i:1262618 original size:20 final size:20
Alignment explanation
Indices: 1262524--1262892 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1262514 GATTTTCCAT
* ** *
1262524 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1262544 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1262564 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1262584 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1262604 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1262624 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1262644 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1262664 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1262684 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1262704 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1262724 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1262744 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1262764 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1262784 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1262804 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1262824 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1262844 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1262864 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1262884 AATCACAAC
1 AATCGCAAC
1262893 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1263589 original size:24 final size:24
Alignment explanation
Indices: 1263562--1263608 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1263552 AAATTTGGTC
1263562 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
1263586 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
1263609 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:1263794 original size:12 final size:12
Alignment explanation
Indices: 1263777--1263801 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1263767 ATATAATCCT
1263777 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1263789 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1263801 G
1 G
1263802 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1266154 original size:52 final size:50
Alignment explanation
Indices: 1266095--1266324 Score: 209
Period size: 52 Copynumber: 4.4 Consensus size: 50
1266085 CGGAAAATAC
* *
1266095 AATCGCAACGCGAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGCGAATGAAAATGCGAA-ATGAAAATCGCAATGC-GAAATGAA
* *
1266147 AATCGCAACGAGAGAATCG-CAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAC--GCGAAT-GAAAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * *
1266199 AATCGCAACGAGAGAATCG-CAATGCGAAATGAAAATCACAATGCGAAATGAA
1 AATCGCAAC--GCGAAT-GAAAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
1266251 AATCG-AAC-CGACAT-AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAACGCGA-ATGAA----AATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1266303 AATCGCAATGCGAAATGAAAAT
1 AATCGCAACGCG-AATGAAAAT
1266325 CGCAATGCGA
Statistics
Matches: 154, Mismatches: 11, Indels: 27
0.80 0.06 0.14
Matches are distributed among these distances:
48 2 0.01
49 2 0.01
51 6 0.04
52 107 0.69
53 18 0.12
54 15 0.10
55 4 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (50 bp):
AATCGCAACGCGAATGAAAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1266185 original size:19 final size:19
Alignment explanation
Indices: 1266122--1266400 Score: 346
Period size: 19 Copynumber: 15.7 Consensus size: 19
1266112 AAATCCCAAC
1266122 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGC-GAA
1266142 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
1266157 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
1266175 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
1266194 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
1266209 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
*
1266227 ATGAAAATCACAATGCGAA
1 ATGAAAATCGCAATGCGAA
* *
1266246 ATGAAAATCG-AA-CCGAC
1 ATGAAAATCGCAATGCGAA
1266263 AT---AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
* *
1266279 ATTAAAATCGCAATACGAA
1 ATGAAAATCGCAATGCGAA
1266298 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
1266317 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
1266336 ATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAA
1266353 A-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
1266369 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
1266388 ATGAAAATCGCAA
1 ATGAAAATCGCAA
1266401 CGAGATAATC
Statistics
Matches: 226, Mismatches: 13, Indels: 41
0.81 0.05 0.15
Matches are distributed among these distances:
14 33 0.15
15 4 0.02
16 15 0.07
17 14 0.06
18 5 0.02
19 142 0.63
20 13 0.06
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:1266249 original size:71 final size:71
Alignment explanation
Indices: 1266161--1266400 Score: 346
Period size: 71 Copynumber: 3.4 Consensus size: 71
1266151 GCAACGAGAG
*
1266161 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1266226 AATGAA
66 AATGAA
* * * *
1266232 AATCACAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
1266292 TACGAAATGAA
61 TGCGAAATGAA
1266303 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1266368 AATGAA
66 AATGAA
1266374 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1266401 CGAGATAATC
Statistics
Matches: 148, Mismatches: 11, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 111 0.75
72 2 0.01
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:1266328 original size:142 final size:138
Alignment explanation
Indices: 1266127--1266432 Score: 483
Period size: 142 Copynumber: 2.2 Consensus size: 138
1266117 CCAACATGAA
* *
1266127 AATCGCAATGCGGAAATGAAAATCGC-AACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
1 AATCGCAATGC-GAAATTAAAATCGCAAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGC
*
1266191 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAATGCGAAATGAAAATCG
65 GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCACAATGCGAAATGAAAATCG
1266256 -AACCGACAT
130 CAA-CGACAT
1266265 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATTAAAATCGCAA-ACG--A-GAAAATCGCAATGCGAAATGAAAATCGCAA
*
1266330 TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAA
62 TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCACAATGCGAAATGAAAA
*
1266395 TCGCAACGAGAT
127 TCGCAACGACAT
1266407 AATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATTA-AAATCGCA
1266433 TTGCGATTTT
Statistics
Matches: 156, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
137 13 0.08
138 12 0.08
139 3 0.02
141 1 0.01
142 122 0.78
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (138 bp):
AATCGCAATGCGAAATTAAAATCGCAAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCACAATGCGAAATGAAAATCGC
AACGACAT
Found at i:1266380 original size:52 final size:53
Alignment explanation
Indices: 1266161--1266422 Score: 278
Period size: 52 Copynumber: 4.9 Consensus size: 53
1266151 GCAACGAGAG
*
1266161 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATG--AATCGCAATGCGAAATGAA
* **
1266213 AATCGCAATGCGAAATGAAAATCACAATGCGAAATGAA----AAT-CGAACCGACA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATGAATCGCAATGCGAAATGA-A
*
1266264 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGC-A-ACGAAATG--AATCGCAATGCGAAATGAA
1266322 AATCGCAATGCGAAATGAAAATCGCAACGAAA-GAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAATGAA
*
1266374 AATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAAT
1266423 TATAAACGCA
Statistics
Matches: 185, Mismatches: 9, Indels: 32
0.82 0.04 0.14
Matches are distributed among these distances:
46 2 0.01
47 2 0.01
50 4 0.02
52 131 0.71
53 1 0.01
54 4 0.02
55 6 0.03
56 1 0.01
57 24 0.13
58 4 0.02
59 6 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAATGAA
Found at i:1266438 original size:71 final size:71
Alignment explanation
Indices: 1266095--1266438 Score: 283
Period size: 71 Copynumber: 4.9 Consensus size: 71
1266085 CGGAAAATAC
* * * *
1266095 AATCGCAACGCG-AATGAAAATCCCAA-C-ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--
1 AATCGCAATGCGAAATGAAAATCGCAACCGA-GATAATCGCAATGC-GAAATTAAAA-CGCAATG
*
1266155 CG--A-GAG
63 CGAAATGAA
* * * * *
1266161 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--GAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GATAATCGCAATGCGAAATTAAAACGCAAT
1266222 GCGAAATGAA
62 GCGAAATGAA
* * *
1266232 AATCACAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAAAATCGCAATACG
1 AATCGCAATGCGAAATGAAAATCGCAACCGAGATAATCGCAATGCGAAATTAAAA-CGCAATGCG
1266296 AAATGAA
65 AAATGAA
* * * *
1266303 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA--GAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GATAATCGCAATGCGAAATTAAAACGCAAT
1266364 GCGAAATGAA
62 GCGAAATGAA
*
1266374 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAACGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACCGAGATAATCGCAATGCGAAATTA-AAACGCAATGCG
1266438 A
65 A
1266439 TTTTCATTTC
Statistics
Matches: 227, Mismatches: 25, Indels: 47
0.76 0.08 0.16
Matches are distributed among these distances:
66 35 0.15
67 17 0.07
68 11 0.05
69 8 0.04
70 6 0.03
71 116 0.51
72 17 0.07
73 2 0.01
74 5 0.02
75 1 0.00
76 9 0.04
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACCGAGATAATCGCAATGCGAAATTAAAACGCAATGCGA
AATGAA
Found at i:1266538 original size:19 final size:19
Alignment explanation
Indices: 1266429--1266530 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1266419 AAATTATAAA
1266429 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1266448 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1266468 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1266484 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1266501 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1266520 CGCATTGCGAT
1 CGCATTGCGAT
1266531 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1266656 original size:14 final size:14
Alignment explanation
Indices: 1266637--1266673 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1266627 CATCAATTAC
1266637 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1266651 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1266665 ACAAATCAA
1 ACAAATCAA
1266674 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1268637 original size:14 final size:14
Alignment explanation
Indices: 1268618--1268674 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1268608 GCGAAATGAA
*
1268618 AATCGCAACGACAG
1 AATCGCAACGAAAG
1268632 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1268649 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1268665 AATCGCAACG
1 AATCGCAACG
1268675 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1268645 original size:33 final size:33
Alignment explanation
Indices: 1268599--1268691 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1268589 GCGAAACCAA
*
1268599 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1268632 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1268665 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1268692 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1268656 original size:19 final size:19
Alignment explanation
Indices: 1268562--1268696 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1268552 TAGTTTACTT
* *
1268562 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1268582 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1268601 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1268620 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1268634 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1268653 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1268667 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1268686 TCGCAATGCGA
1 TCGCAACGCGA
1268697 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1268714 original size:19 final size:19
Alignment explanation
Indices: 1268692--1268820 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1268682 AAAATCGCAA
1268692 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1268711 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1268725 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1268744 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1268758 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1268777 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1268796 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1268816 TGCGA
1 TGCGA
1268821 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1268734 original size:33 final size:33
Alignment explanation
Indices: 1268692--1268783 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1268682 AAAATCGCAA
1268692 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1268725 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1268758 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1268784 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1269173 original size:92 final size:93
Alignment explanation
Indices: 1268864--1269329 Score: 860
Period size: 92 Copynumber: 5.1 Consensus size: 93
1268854 TTGAATGGAT
1268864 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1268929 AGTTTAGC--AATT-GCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1268954 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1269019 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1269047 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAAT-CAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1269111 AGTTTAGCAGAATTGGCAGCAAACCGAAC
66 AGTTTAGCAGAATTGGCAGC-AACCGAAC
1269140 AAATTTACTTTC-ACCAAAAGACAAAACAAAGAC-AA-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1269201 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1269229 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1269293 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1269321 AAATTTACT
1 AAATTTACT
1269330 AAGCAATCTA
Statistics
Matches: 367, Mismatches: 0, Indels: 16
0.96 0.00 0.04
Matches are distributed among these distances:
89 58 0.16
90 102 0.28
91 3 0.01
92 110 0.30
93 94 0.26
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1269224 original size:182 final size:186
Alignment explanation
Indices: 1268864--1269329 Score: 860
Period size: 182 Copynumber: 2.5 Consensus size: 186
1268854 TTGAATGGAT
1268864 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1268929 AGTTTAGC--AATT-GCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1268991 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1269047 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAAT-CAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1269111 AGTTTAGCAGAATTGGCAGCAAACCGAACAAATTTACTTTC-ACCAAAAGACAAAACAAAGAC-A
66 AGTTTAGCAGAATTGGCAGC-AACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAA
1269174 A-A-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 ATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1269229 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1269293 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1269330 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 0, Indels: 12
0.96 0.00 0.04
Matches are distributed among these distances:
181 61 0.22
182 103 0.37
183 62 0.22
184 6 0.02
185 26 0.09
186 20 0.07
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Done.