Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_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: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 17
Found at i:1016952 original size:24 final size:24
Alignment explanation
Indices: 1016924--1016971 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1016914 ACAAAGGAAA
1016924 AAACACATATTTCCTTCTTATTAT
1 AAACACATATTTCCTTCTTATTAT
*
1016948 AAACACATGTTTCCTTCTTATTAT
1 AAACACATATTTCCTTCTTATTAT
1016972 TTCACAGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.02, T:0.46
Consensus pattern (24 bp):
AAACACATATTTCCTTCTTATTAT
Found at i:1023026 original size:32 final size:31
Alignment explanation
Indices: 1022985--1023054 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
1022975 ACATAATATA
*
1022985 TGGTCACTTTCGTTTTTTATTTAATTAAGCTT
1 TGGTCACTTTCG-GTTTTATTTAATTAAGCTT
* * * *
1023017 TGGTTACTTTTGGTTTTATTTAATTAAGATA
1 TGGTCACTTTCGGTTTTATTTAATTAAGCTT
1023048 TGGTCAC
1 TGGTCAC
1023055 CATGGGTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 22 0.69
32 10 0.31
ACGTcount: A:0.21, C:0.10, G:0.16, T:0.53
Consensus pattern (31 bp):
TGGTCACTTTCGGTTTTATTTAATTAAGCTT
Found at i:1024379 original size:2 final size:2
Alignment explanation
Indices: 1024374--1024410 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1024364 ATATATCTTT
1024374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1024411 TAAAAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1025949 original size:20 final size:20
Alignment explanation
Indices: 1025924--1025961 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1025914 AGAGTTTGAG
1025924 TATCGATACTGGATGAATAA
1 TATCGATACTGGATGAATAA
*
1025944 TATCGATACTGGTTGAAT
1 TATCGATACTGGATGAAT
1025962 CAGGGCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
TATCGATACTGGATGAATAA
Found at i:1026035 original size:15 final size:15
Alignment explanation
Indices: 1026011--1026096 Score: 120
Period size: 15 Copynumber: 5.8 Consensus size: 15
1026001 TTACCAGGGA
1026011 GAGTATCAATACTGT
1 GAGTATCAATACTGT
* *
1026026 GAGTACCAATATTGT
1 GAGTATCAATACTGT
*
1026041 TAGTATCAATACTGT
1 GAGTATCAATACTGT
* *
1026056 GAGTACCAATACTAT
1 GAGTATCAATACTGT
1026071 GAGTATCAATACTGT
1 GAGTATCAATACTGT
1026086 GAGTA-CAATAC
1 GAGTATCAATAC
1026097 CAATACTCTT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
14 6 0.10
15 55 0.90
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (15 bp):
GAGTATCAATACTGT
Found at i:1026046 original size:30 final size:30
Alignment explanation
Indices: 1026011--1026096 Score: 138
Period size: 30 Copynumber: 2.9 Consensus size: 30
1026001 TTACCAGGGA
* *
1026011 GAGTATCAATACTGTGAGTACCAATATTGT
1 GAGTATCAATACTGTGAGTACCAATACTAT
*
1026041 TAGTATCAATACTGTGAGTACCAATACTAT
1 GAGTATCAATACTGTGAGTACCAATACTAT
1026071 GAGTATCAATACTGTGAGTA-CAATAC
1 GAGTATCAATACTGTGAGTACCAATAC
1026097 CAATACTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 6 0.12
30 46 0.88
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (30 bp):
GAGTATCAATACTGTGAGTACCAATACTAT
Found at i:1031084 original size:20 final size:20
Alignment explanation
Indices: 1031059--1031129 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
1031049 GATGCAATCA
*
1031059 GTATCGATACCTAGAGAGAG
1 GTATCGATACCGAGAGAGAG
1031079 GTATCGATACCGAGAGAGAG
1 GTATCGATACCGAGAGAGAG
** *
1031099 GTATCGATATTGTGAG-GAAG
1 GTATCGATACCGAGAGAG-AG
1031119 GTATCGATACC
1 GTATCGATACC
1031130 ATTAAAAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (20 bp):
GTATCGATACCGAGAGAGAG
Found at i:1031637 original size:57 final size:57
Alignment explanation
Indices: 1031549--1031732 Score: 287
Period size: 57 Copynumber: 3.2 Consensus size: 57
1031539 ATGATAATTT
* *
1031549 GTGTATGAATTTTCATATGGGAACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAA
1 GTGTATGAATTTCCATATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAA
* *
1031606 GTGTATGAATTTCCATATGGGCACTTTGTGTGCAAAAAGTTAAAAAATTCATTCTAA
1 GTGTATGAATTTCCATATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAA
* * * * *
1031663 GTGTATGAATTTCCGTGTGGGCACTTTGTGTGCAAAACGTTAAGAGATTAATACTAA
1 GTGTATGAATTTCCATATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAA
1031720 GTGTATGAATTTC
1 GTGTATGAATTTC
1031733 TGTATGGGAA
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 116 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (57 bp):
GTGTATGAATTTCCATATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAA
Found at i:1037547 original size:22 final size:23
Alignment explanation
Indices: 1037517--1037591 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 23
1037507 TTTATTTATT
1037517 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
*
1037540 TATT-ATATTTTTAATATTATATAAAA
1 TATTAATATTTATAATA--ATAT--AA
1037566 TAATTAATTATATTATAATAATATAA
1 T-ATTAA-TAT-TTATAATAATATAA
1037592 GATTTTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
22 11 0.26
23 4 0.10
24 4 0.10
26 5 0.12
27 3 0.07
28 5 0.12
29 3 0.07
30 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:1037644 original size:30 final size:30
Alignment explanation
Indices: 1037599--1037686 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
1037589 TAAGATTTTA
1037599 TATTTTTAT-TTTAATAATATATAATAAAT
1 TATTTTTATATTTAATAATATATAATAAAT
*
1037628 TTTTTTTATATTTAATAATGA-ATAAT--AT
1 TATTTTTATATTTAATAAT-ATATAATAAAT
* *
1037656 TATTTATATATTTAAATAATATTTTAATAAA
1 TATTTTTATATTT-AATAATA-TATAATAAA
1037687 GATATTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
28 14 0.29
29 14 0.29
30 18 0.38
31 1 0.02
32 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
TATTTTTATATTTAATAATATATAATAAAT
Found at i:1037706 original size:23 final size:20
Alignment explanation
Indices: 1037680--1037727 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
1037670 AATAATATTT
1037680 TAATAAAGATATTTTAAATATA
1 TAATAAAGAT-TTTTAAA-ATA
* *
1037702 CTAATTAATATTTTTAAAATA
1 -TAATAAAGATTTTTAAAATA
1037723 TAATA
1 TAATA
1037728 TAACACTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 3 0.14
22 7 0.32
23 8 0.36
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TAATAAAGATTTTTAAAATA
Found at i:1038059 original size:14 final size:14
Alignment explanation
Indices: 1038025--1038060 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1038015 AAATGTAATT
*
1038025 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
1038039 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
*
1038053 CGTTTTCC
1 CATTTTCC
1038061 AAAAATGTAA
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:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:1038088 original size:14 final size:15
Alignment explanation
Indices: 1038067--1038108 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1038057 TTCCAAAAAT
1038067 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
1038082 G-AATTCAAATTCTA
1 GTAATTCATTTTCCA
1038096 GTAATTCATTTTC
1 GTAATTCATTTTC
1038109 GAGTTCCAGT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:1038124 original size:36 final size:35
Alignment explanation
Indices: 1038077--1038144 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 35
1038067 GTAATTCATT
*
1038077 TTCCAGAATTCAAATTCTAGTAATTCATTTTCGAG
1 TTCCAGAATTCAAATTCCAGTAATTCATTTTCGAG
*
1038112 TTCCAGTAATTCAAATTCCAGTAATTTATTTTC
1 TTCCAG-AATTCAAATTCCAGTAATTCATTTTC
1038145 CGAAAAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 6 0.20
36 24 0.80
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.43
Consensus pattern (35 bp):
TTCCAGAATTCAAATTCCAGTAATTCATTTTCGAG
Found at i:1039419 original size:57 final size:57
Alignment explanation
Indices: 1039230--1039421 Score: 276
Period size: 57 Copynumber: 3.4 Consensus size: 57
1039220 ATGAAACTTT
* * * * *
1039230 GTGTATGAATTTCCATATGAGAACTTTGAGTGCAAAAAGTTAAGAAATTCATATTAA
1 GTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAA
* * *
1039287 GTGTATGAATTTCCATATTGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATTCTAA
1 GTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAA
* *
1039344 GTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAATGTTAAGAGATTCATACTAA
1 GTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAA
**
1039401 GTGTATGAATTTTTGTATGGG
1 GTGTATGAATTTCCGTATGGG
1039422 AACTATATGT
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 122 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (57 bp):
GTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAA
Found at i:1044342 original size:55 final size:55
Alignment explanation
Indices: 1044277--1044387 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
1044267 TTGTCAGATG
* *
1044277 TCCTATGCAGATTTGAAAAGAAAGGAAATAGAATATCAAGAGGGAGATAAAGTAT
1 TCCTATGCAGATTTGAAAAGAAAGGAAATAAAATATCAAGAGGGAGACAAAGTAT
*
1044332 TCCTATGCAGATTTGAAACGAAAGGAAATAAAATATCAAGAGGGAGACAAAGTAT
1 TCCTATGCAGATTTGAAAAGAAAGGAAATAAAATATCAAGAGGGAGACAAAGTAT
1044387 T
1 T
1044388 TTTGAAAGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.22
Consensus pattern (55 bp):
TCCTATGCAGATTTGAAAAGAAAGGAAATAAAATATCAAGAGGGAGACAAAGTAT
Found at i:1046799 original size:20 final size:20
Alignment explanation
Indices: 1046747--1046801 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
1046737 ATGCAAAAAT
* *
1046747 GGTATCGATACCATAGTATG
1 GGTATCGATACTATAGTAAG
* *
1046767 GTAGTATCAATACTATGGTAAG
1 G--GTATCGATACTATAGTAAG
1046789 GGTATCGATACTA
1 GGTATCGATACTA
1046802 AAGAACCAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 12 0.43
22 16 0.57
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.31
Consensus pattern (20 bp):
GGTATCGATACTATAGTAAG
Found at i:1050278 original size:2 final size:2
Alignment explanation
Indices: 1050271--1050296 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1050261 TTAAAAATTA
1050271 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
1050297 GATAAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1051681 original size:14 final size:14
Alignment explanation
Indices: 1051662--1051712 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1051652 TTTAAAAGGA
1051662 CTGAAATGTAGATG
1 CTGAAATGTAGATG
* * *
1051676 CTGAAATTTAAAAGG
1 CTGAAATGT-AGATG
1051691 ACTGAAATGTAGATG
1 -CTGAAATGTAGATG
1051706 CTGAAAT
1 CTGAAAT
1051713 TTAAAAGGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 15 0.52
15 6 0.21
16 8 0.28
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (14 bp):
CTGAAATGTAGATG
Found at i:1051684 original size:30 final size:30
Alignment explanation
Indices: 1051634--1051720 Score: 147
Period size: 30 Copynumber: 2.9 Consensus size: 30
1051624 GAAACAAGCA
* * *
1051634 GAAAAGTAAATGCTGGAATTTAAAAGGACT
1 GAAATGTAGATGCTGAAATTTAAAAGGACT
1051664 GAAATGTAGATGCTGAAATTTAAAAGGACT
1 GAAATGTAGATGCTGAAATTTAAAAGGACT
1051694 GAAATGTAGATGCTGAAATTTAAAAGG
1 GAAATGTAGATGCTGAAATTTAAAAGG
1051721 CAGGAATGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.25
Consensus pattern (30 bp):
GAAATGTAGATGCTGAAATTTAAAAGGACT
Found at i:1054244 original size:27 final size:27
Alignment explanation
Indices: 1054187--1054244 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1054177 TCTGTTTTTT
* ***
1054187 AAAAAAACCGGTTTTTTATCCGGTTTG
1 AAAAAAACCGGTTTTTAATCCGGTAAA
1054214 AAAAAAACCGGTTTTTAATCCGGTAAA
1 AAAAAAACCGGTTTTTAATCCGGTAAA
1054241 AAAA
1 AAAA
1054245 TCGGTCGTTC
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:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (27 bp):
AAAAAAACCGGTTTTTAATCCGGTAAA
Found at i:1056606 original size:26 final size:26
Alignment explanation
Indices: 1056563--1056669 Score: 160
Period size: 26 Copynumber: 4.1 Consensus size: 26
1056553 ACTAAGTGCA
*
1056563 TATGGTGGACACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
* *
1056589 TATGGTGGGCATGGCCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
* * *
1056615 TATGGTGGGAAGGACCTTATGTATAT
1 TATGGTGGGCACGACCTTATGTGTAT
1056641 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATGTGTAT
1056667 TAT
1 TAT
1056670 CACTTTGGTG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.36
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTATGTGTAT
Found at i:1057728 original size:2 final size:2
Alignment explanation
Indices: 1057721--1057751 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1057711 AGTAATCATA
1057721 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1057752 GTCCATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1069152 original size:81 final size:81
Alignment explanation
Indices: 1069039--1069369 Score: 450
Period size: 81 Copynumber: 4.1 Consensus size: 81
1069029 AATCCTTTAG
* * * *
1069039 TCTTTTACCCAAAGGTATTTAGCCTTTCATCTAACTTCCATGATTGGCACATTTCTGCCAAATGC
1 TCTTTTACCCAAAGGTATTTAACCTTTCATCTAACTGCCATAATTGACACATTTCTGCCAAATGC
1069104 ATAACTAGGCTATTAA
66 ATAACTAGGCTATTAA
* *
1069120 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTGCCATAATTGACATC-TTTCTGCCAAATG
1 TCTTTTACCCAAAGGTATTTAACCTTTCATCTAACTGCCATAATTGACA-CATTTCTGCCAAATG
1069184 CACT-ACTAGGCTATTAA
65 CA-TAACTAGGCTATTAA
* * **
1069201 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTATCAAATGC
1 TCTTTTACCCAAAGGTATTTAACCTTTCATCTAACTGCCATAATTGACACATTTCTGCCAAATGC
* *
1069266 ACAGCTAGGCTATTAA
66 ATAACTAGGCTATTAA
* ** * * * *
1069282 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGATATATTTATGTCAAATGC
1 TCTTTTACCCAAAGGTATTTAACCTTTCATCTAACTGCCATAATTGACACATTTCTGCCAAATGC
*
1069347 ATAGCTAGGCTATTAA
66 ATAACTAGGCTATTAA
1069363 TCTTTTA
1 TCTTTTA
1069370 TTTAGAACAG
Statistics
Matches: 228, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
80 1 0.00
81 225 0.99
82 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (81 bp):
TCTTTTACCCAAAGGTATTTAACCTTTCATCTAACTGCCATAATTGACACATTTCTGCCAAATGC
ATAACTAGGCTATTAA
Found at i:1069882 original size:20 final size:17
Alignment explanation
Indices: 1069857--1069903 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1069847 TGTATCAATG
1069857 GTATTGATACCTTCTCCAAA
1 GTATTGATACC--C-CCAAA
*
1069877 GTATTGATACCCCCTAA
1 GTATTGATACCCCCAAA
1069894 GTATTGATAC
1 GTATTGATAC
1069904 TAATTGCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.54
18 1 0.04
20 11 0.42
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (17 bp):
GTATTGATACCCCCAAA
Found at i:1071681 original size:29 final size:30
Alignment explanation
Indices: 1071643--1071705 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1071633 AACCCATTAA
1071643 TTTTCTAAAA-TTACCAAATTGGTCCCCAAC
1 TTTTCTAAAACTTACCAAA-TGGTCCCCAAC
* *
1071673 TTTTC-AAAACTTACCAAATGGTCCTCAAT
1 TTTTCTAAAACTTACCAAATGGTCCCCAAC
1071702 TTTT
1 TTTT
1071706 TTTATGGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (30 bp):
TTTTCTAAAACTTACCAAATGGTCCCCAAC
Found at i:1078626 original size:26 final size:26
Alignment explanation
Indices: 1078590--1078693 Score: 163
Period size: 26 Copynumber: 4.0 Consensus size: 26
1078580 TAAGTGCATC
1078590 TGGTGGGCACGACCTTATGTGTATTA
1 TGGTGGGCACGACCTTATGTGTATTA
*
1078616 TGGTGGGCACGACCTTATTTGTATTA
1 TGGTGGGCACGACCTTATGTGTATTA
* * *
1078642 TGGTGGGCACAACTTTATGTATATTA
1 TGGTGGGCACGACCTTATGTGTATTA
*
1078668 TGGTGGGCATGACCTTATGTGTATTA
1 TGGTGGGCACGACCTTATGTGTATTA
1078694 GCACTTTGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.38
Consensus pattern (26 bp):
TGGTGGGCACGACCTTATGTGTATTA
Found at i:1080957 original size:2 final size:2
Alignment explanation
Indices: 1080950--1081003 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1080940 AATATTTTGC
1080950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1080992 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1081004 AAGTGTAAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1081492 original size:39 final size:39
Alignment explanation
Indices: 1081372--1081494 Score: 158
Period size: 39 Copynumber: 3.2 Consensus size: 39
1081362 AAGATACCTA
* *
1081372 GTGCATAA-GGTGGACGCAACCTTATGTGTAAGCACTTCA
1 GTGCA-AATGGTGGACGCAACCTTATGTGTAAACACTTCG
* * *
1081411 GTGCAAATGGTGGACACAACTTTATCTGTAAACACTTCG
1 GTGCAAATGGTGGACGCAACCTTATGTGTAAACACTTCG
* * *
1081450 GTGCAAATGTTGGACGCAACCTTATGTGTAATCACTTTG
1 GTGCAAATGGTGGACGCAACCTTATGTGTAAACACTTCG
1081489 GTGCAA
1 GTGCAA
1081495 CTTGAATACG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
38 2 0.03
39 70 0.97
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (39 bp):
GTGCAAATGGTGGACGCAACCTTATGTGTAAACACTTCG
Found at i:1083041 original size:25 final size:25
Alignment explanation
Indices: 1083013--1083069 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
1083003 TCTTTAATGT
1083013 ATATTTAATTTGAATTAA-T-TAAATA
1 ATATTTAATTT--ATTAATTCTAAATA
*
1083038 ATATTTTATTTATTAATTCTAAATA
1 ATATTTAATTTATTAATTCTAAATA
1083063 A-ATTTAA
1 ATATTTAA
1083070 AAACCCTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 5 0.18
24 6 0.21
25 17 0.61
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
ATATTTAATTTATTAATTCTAAATA
Found at i:1089979 original size:2 final size:2
Alignment explanation
Indices: 1089972--1090017 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1089962 AATATTTTGC
1089972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1090014 TA TA
1 TA TA
1090018 AAAGTGTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1090468 original size:39 final size:39
Alignment explanation
Indices: 1090356--1090469 Score: 156
Period size: 39 Copynumber: 2.9 Consensus size: 39
1090346 AGTGCATAAG
* *
1090356 GTGGATGCAACCTTATGCGTAAGCACTTCGATGCAAATA
1 GTGGACGCAACCTTATGCGTAAGCACTTCGGTGCAAATA
* * * * *
1090395 GTGGACACAACCTTATGTGTAAGTAATTCAGTGCAAATA
1 GTGGACGCAACCTTATGCGTAAGCACTTCGGTGCAAATA
*
1090434 GTGGACGCAACCTTATGCGTAAGCACTTTGGTGCAA
1 GTGGACGCAACCTTATGCGTAAGCACTTCGGTGCAA
1090470 CTCAAATACC
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (39 bp):
GTGGACGCAACCTTATGCGTAAGCACTTCGGTGCAAATA
Found at i:1091873 original size:117 final size:116
Alignment explanation
Indices: 1091390--1092088 Score: 426
Period size: 115 Copynumber: 6.0 Consensus size: 116
1091380 TGCTTATAGG
* * ** * * *
1091390 TTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTAGGAACTTTTTATTCATT-GGACAAGTTATTC
1 TTTGAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCATTAGGACGAGTTCTTT
* ** *
1091454 TCATTATGAAATCCTTTATTAGAAATGTTG-CTTCACCTCCTTCTGTGATGGA
65 TCATTATGAACTCCTCCATTAGAAATGTTGAC-CCACCTCCTTCTGTGATGGA
* * * * * * *
1091506 TTTGAACAAATGTTGGACAAGTTCTTCTCATTATGAACTTCTCCCTCATCA-GATGAGTTCTCCT
1 TTTGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCATTAGGACGAGTTCT-TT
* * ** ** *
1091570 T-ATTATGAAC-CCTTCCATTGGAAATTTTGA-TAACCTTTTTTTGTGATGGA
65 TCATTATGAACTCC-TCCATTAGAAATGTTGACCCACCTCCTTCTGTGATGGA
* * * * * * *
1091620 TTT-AGGACAGGTTGAACAAGTTCTTCTCATGATGAACTTCTTCTTCCCCTCTTGG-CGAGTTTT
1 TTTGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTT--CAT-TAGGACGAGTTCT
* * * * * *
1091683 TTCTCATTATGAACTCTTCTACTAGAAATGATGACCCACCTTCTTCTGTGATGAA
63 TT-TCATTATGAACTCCTCCATTAGAAATGTTGACCCACCTCCTTCTGTGATGGA
* * * * *
1091738 ATAG-GGAAA-GTTAAACAAGTTCTTCTCATTATGAACTT-TAACCTTCACTTAGGATGAGTTCT
1 TTTGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT--CCTTCA-TTAGGACGAGTTCT
* * *
1091800 TTTCATTATGAACTCC-CCGTTAGAAATGTTGACCCACCTCCTTCTATTATGGA
63 TTTCATTATGAACTCCTCCATTAGAAATGTTGACCCACCTCCTTCTGTGATGGA
* * * * * * * ** ***
1091853 TTTGAGCAAAGGTTGGACAAGTTATTTTTATTATGAACTTCTCCCTCATCA-TATAAGTTCTCCC
1 TTTGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCATTAGGACGAGTTCTTTT
* * * * * * *
1091917 CATTATGAAC-CATTACATTGGAAATGTTGATCCACATTCTTCTATGATGGA
66 CATTATGAACTC-CTCCATTAGAAATGTTGACCCACCTCCTTCTGTGATGGA
* * *
1091968 TTTG-G-ACAA-GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTGTAGG-CGAGTTC
1 TTTGAGCA-AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTT-C-AT-TAGGACGAGTTC
* * * * * * * * *
1092029 TTCTCATTATGAAATCTTCTACTGGACATGTTGATCCACATCCTTCTGTGATGGA
62 TTTTCATTATGAACTCCTCCATTAGAAATGTTGACCCACCTCCTTCTGTGATGGA
*
1092084 ATTGA
1 TTTGA
1092089 ACCAAATGGT
Statistics
Matches: 442, Mismatches: 112, Indels: 57
0.72 0.18 0.09
Matches are distributed among these distances:
113 64 0.14
114 43 0.10
115 133 0.30
116 94 0.21
117 83 0.19
118 25 0.06
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (116 bp):
TTTGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCATTAGGACGAGTTCTTTT
CATTATGAACTCCTCCATTAGAAATGTTGACCCACCTCCTTCTGTGATGGA
Found at i:1092325 original size:116 final size:116
Alignment explanation
Indices: 1092121--1092395 Score: 277
Period size: 116 Copynumber: 2.4 Consensus size: 116
1092111 AATCCTTATA
** ** * *
1092121 TGATAGACATGCCAAGGTTGAACAAACTCTTCTCATTATGAACTTTTTCTCCCTAATCGAACGAG
1 TGATAGACAAACCAAGGTTGAACAAGTTCTTCTCATTAAGAACTTTTTCTCCCTAATAGAACGAG
* * * * *
1092186 TTCTTCTCATTACAAACCCTTCCATTGA-AAATGTTGATCCACCT-CATTCTG
66 CTCTTATCATTACAAACCATTCCA-CGAGAAATGTTGACCCA-CTACATTCTG
* * * * *
1092237 TGATAGATAAACCAAGGTTGAACAAGTTCTTCACATTAGGAACTTTTTCTCCCTTATTAG-TCGA
1 TGATAGACAAACCAAGGTTGAACAAGTTCTTCTCATTAAGAACTTTTTCTCCC-TAATAGAACGA
* ** * * *
1092301 GCTCTTATTATTATGAACTATTCCACGAGAAATTTTGGCCCACTACATTCTG
65 GCTCTTATCATTACAAACCATTCCACGAGAAATGTTGACCCACTACATTCTG
* * *
1092353 TGATGGACGAACCAAGGTTGAACATGTTCTTCTCATTAAGAAC
1 TGATAGACAAACCAAGGTTGAACAAGTTCTTCTCATTAAGAAC
1092396 AAGTTGTTCT
Statistics
Matches: 129, Mismatches: 27, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
115 4 0.03
116 121 0.94
117 4 0.03
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (116 bp):
TGATAGACAAACCAAGGTTGAACAAGTTCTTCTCATTAAGAACTTTTTCTCCCTAATAGAACGAG
CTCTTATCATTACAAACCATTCCACGAGAAATGTTGACCCACTACATTCTG
Found at i:1092405 original size:20 final size:20
Alignment explanation
Indices: 1092372--1092409 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1092362 AACCAAGGTT
*
1092372 GAACATGTTCTTCTCATTAA
1 GAACAAGTTCTTCTCATTAA
*
1092392 GAACAAGTTGTTCTCATT
1 GAACAAGTTCTTCTCATT
1092410 GGATGACCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (20 bp):
GAACAAGTTCTTCTCATTAA
Found at i:1108841 original size:55 final size:55
Alignment explanation
Indices: 1108773--1109046 Score: 372
Period size: 55 Copynumber: 5.0 Consensus size: 55
1108763 ATGGGAACTG
*
1108773 TGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTA
1 TGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTA
* * * *
1108828 TATGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGAACTC
1 TGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTA
* * *
1108883 TGTGTGCAACCTCACGTAATTCATAATGAGTTTATGAAATTCCGTATTGGCACTA
1 TGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTA
* * * *
1108938 TGTGTGCAACCTCATGAAATTCATAATTAGTTTATAAACTTCCGTATTGGCACTA
1 TGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTA
* * * * *
1108993 TGTGTTCAACCCCACA-TAATTCATAACGAGTTTGTGAA-TTCCGTATTGGCACTA
1 TGTGTGCAACCTCA-AGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTA
1109047 CTTTTGATGT
Statistics
Matches: 195, Mismatches: 23, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
54 16 0.08
55 179 0.92
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (55 bp):
TGTGTGCAACCTCAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTA
Found at i:1110969 original size:15 final size:15
Alignment explanation
Indices: 1110949--1110980 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1110939 CATACAACAA
*
1110949 TATATATTGAGATAG
1 TATATATTGAAATAG
1110964 TATATATTGAAATAG
1 TATATATTGAAATAG
1110979 TA
1 TA
1110981 ATGATCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.41
Consensus pattern (15 bp):
TATATATTGAAATAG
Found at i:1112397 original size:27 final size:27
Alignment explanation
Indices: 1112360--1112415 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1112350 ATCATTTCAT
* *
1112360 ATGATGAGTATGACGTTTACACCCAAG
1 ATGATGAGTATGACATTTAAACCCAAG
*
1112387 ATGATGAGTATGTCATTTAAACCCAAG
1 ATGATGAGTATGACATTTAAACCCAAG
1112414 AT
1 AT
1112416 TTAGAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (27 bp):
ATGATGAGTATGACATTTAAACCCAAG
Found at i:1113078 original size:17 final size:17
Alignment explanation
Indices: 1113056--1113095 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1113046 CTTCCCTTTC
* * *
1113056 TTTGAGAGAAATTCTCT
1 TTTGAGAAAAAATCTCG
1113073 TTTGAGAAAAAATCTCG
1 TTTGAGAAAAAATCTCG
1113090 TTTGAG
1 TTTGAG
1113096 CAACAAACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (17 bp):
TTTGAGAAAAAATCTCG
Found at i:1117735 original size:13 final size:13
Alignment explanation
Indices: 1117726--1117768 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
1117716 GTTAGTACGA
1117726 CATATTAGTAAGG
1 CATATTAGTAAGG
1117739 CATATTAGTAAGG
1 CATATTAGTAAGG
*
1117752 CATATTAGTGAGG
1 CATATTAGTAAGG
1117765 CATA
1 CATA
1117769 CCAGGTGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.30
Consensus pattern (13 bp):
CATATTAGTAAGG
Found at i:1117755 original size:26 final size:26
Alignment explanation
Indices: 1117717--1117768 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1117707 TTGGATTTCG
*
1117717 TTAGTACGACATATTAGTAAGGCATA
1 TTAGTAAGACATATTAGTAAGGCATA
* *
1117743 TTAGTAAGGCATATTAGTGAGGCATA
1 TTAGTAAGACATATTAGTAAGGCATA
1117769 CCAGGTGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (26 bp):
TTAGTAAGACATATTAGTAAGGCATA
Found at i:1119899 original size:13 final size:13
Alignment explanation
Indices: 1119881--1119905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1119871 TTGAGATAAT
1119881 TCAAATATATATA
1 TCAAATATATATA
1119894 TCAAATATATAT
1 TCAAATATATAT
1119906 TAACTTTAAT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TCAAATATATATA
Found at i:1130599 original size:18 final size:18
Alignment explanation
Indices: 1130573--1130607 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1130563 TCGTTGTATT
*
1130573 TGGAATTACTGAGGCATG
1 TGGAATTACTCAGGCATG
*
1130591 TGGACTTACTCAGGCAT
1 TGGAATTACTCAGGCAT
1130608 CATTTGATTT
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:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (18 bp):
TGGAATTACTCAGGCATG
Found at i:1137925 original size:39 final size:39
Alignment explanation
Indices: 1137849--1137933 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 39
1137839 CGAGGTAAAA
* **
1137849 GTGAGGATGATGATTTCAGTAAAGGCGATAATACCTAAG
1 GTGAGGATGATGAGTTCAAAAAAGGCGATAATACCTAAG
* * * *
1137888 GTGAGGATGATGAGTTCAAAAAATGTGGTAATGCCTAAG
1 GTGAGGATGATGAGTTCAAAAAAGGCGATAATACCTAAG
1137927 GTTGAGG
1 G-TGAGG
1137934 TAAAATGAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 33 0.87
40 5 0.13
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (39 bp):
GTGAGGATGATGAGTTCAAAAAAGGCGATAATACCTAAG
Found at i:1139614 original size:74 final size:75
Alignment explanation
Indices: 1139512--1139805 Score: 398
Period size: 74 Copynumber: 3.9 Consensus size: 75
1139502 TTACCCGACC
* *
1139512 GATATGATGTTTTCAAATGAATTTTTAAAAAAGCCAAATTTGATTTTGAAAGGTTTCTTGATGAT
1 GATATGATGTTTTCAAATGAATTTTTAAAAAAGCCAAGTTTGATTTTCAAAGGTTTCTTGATGAT
1139577 TACCCCTACT
66 TACCCCTACT
* * * *
1139587 GATATGATGTTTTCAAA-GAATTTTTAAAGAATCCAAGTTTTATTTTCAAAGGATTCTTGATGAT
1 GATATGATGTTTTCAAATGAATTTTTAAAAAAGCCAAGTTTGATTTTCAAAGGTTTCTTGATGAT
1139651 TACCCCTA-T
66 TACCCCTACT
* * * *
1139660 CGATGTGAT-TTTTCAAATGAATTTTTACATAAGCCAAGTTTGATTTTTAAAGGTTTCTTGATGA
1 -GATATGATGTTTTCAAATGAATTTTTAAAAAAGCCAAGTTTGATTTTCAAAGGTTTCTTGATGA
*
1139724 TTACCCCTACC
65 TTACCCCTACT
* * * *
1139735 GATATAATGTTTTCAAATGAATTTTTTTAAGAAA-CCAAGTTTGATTTTCAAATGTATCTTGATG
1 GATATGATGTTTTCAAATGAA--TTTTTAAAAAAGCCAAGTTTGATTTTCAAAGGTTTCTTGATG
1139799 ATTACCC
64 ATTACCC
1139806 AACTGTTATT
Statistics
Matches: 191, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
73 9 0.05
74 111 0.58
75 29 0.15
76 34 0.18
77 8 0.04
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (75 bp):
GATATGATGTTTTCAAATGAATTTTTAAAAAAGCCAAGTTTGATTTTCAAAGGTTTCTTGATGAT
TACCCCTACT
Found at i:1139869 original size:26 final size:26
Alignment explanation
Indices: 1139830--1139895 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
1139820 ACACACGTCC
1139830 AATTAT-TTATTATTAACTT-TTTTATT
1 AATTATATTATTATT--CTTATTTTATT
1139856 -ATTATATTATTATTCTTATTTTATT
1 AATTATATTATTATTCTTATTTTATT
* *
1139881 AATAATATTTTTATT
1 AATTATATTATTATT
1139896 TTTTACAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 3 0.09
25 12 0.34
26 20 0.57
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (26 bp):
AATTATATTATTATTCTTATTTTATT
Found at i:1141673 original size:16 final size:16
Alignment explanation
Indices: 1141652--1141686 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1141642 ATCGTTTTTA
1141652 TATATTTATG-AAATTG
1 TATATTT-TGCAAATTG
1141668 TATATTTTGCAAATTG
1 TATATTTTGCAAATTG
1141684 TAT
1 TAT
1141687 TTATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (16 bp):
TATATTTTGCAAATTG
Found at i:1145358 original size:7 final size:7
Alignment explanation
Indices: 1145342--1145463 Score: 67
Period size: 7 Copynumber: 17.3 Consensus size: 7
1145332 AGATGAGAAC
1145342 AAAAAG-
1 AAAAAGA
1145348 AAAAAG-
1 AAAAAGA
1145354 AAAAAGA
1 AAAAAGA
1145361 ATAAAAGA
1 A-AAAAGA
**
1145369 TGAAAGA
1 AAAAAGA
1145376 ATAAAAG-
1 A-AAAAGA
1145383 -AAAAGTA
1 AAAAAG-A
1145390 AAAAAGA
1 AAAAAGA
*
1145397 AAGAAGA
1 AAAAAGA
*
1145404 GAAAAATA
1 -AAAAAGA
1145412 AGAAGAAGA
1 A-AA-AAGA
1145421 AAAAAG-
1 AAAAAGA
1145427 AAAAAGA
1 AAAAAGA
*
1145434 ATAGAA-A
1 A-AAAAGA
*
1145441 AATAAGA
1 AAAAAGA
*
1145448 AATAAGA
1 AAAAAGA
*
1145455 AATAAGA
1 AAAAAGA
1145462 AA
1 AA
1145464 GAGAACATGT
Statistics
Matches: 94, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
5 5 0.05
6 21 0.22
7 37 0.39
8 27 0.29
9 4 0.04
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.07
Consensus pattern (7 bp):
AAAAAGA
Found at i:1145366 original size:15 final size:15
Alignment explanation
Indices: 1145348--1145441 Score: 65
Period size: 13 Copynumber: 6.3 Consensus size: 15
1145338 GAACAAAAAG
1145348 AAAAAGAAAAAGAAT
1 AAAAAGAAAAAGAAT
*
1145363 -AAAAGATGAAAGAAT
1 AAAAAGA-AAAAGAAT
*
1145378 -AAAAG-AAAAGTA-
1 AAAAAGAAAAAGAAT
*
1145390 AAAAAGAAAGAAGAGAA
1 AAAAAGAAA-AAGA-AT
*
1145407 AAATAAGAAGAAG-A-
1 AAA-AAGAAAAAGAAT
1145421 AAAAAGAAAAAGAAT
1 AAAAAGAAAAAGAAT
1145436 AGAAAA
1 A-AAAA
1145442 ATAAGAAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
13 18 0.29
14 12 0.19
15 17 0.27
16 5 0.08
17 6 0.10
18 5 0.08
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
AAAAAGAAAAAGAAT
Found at i:1145395 original size:28 final size:26
Alignment explanation
Indices: 1145349--1145454 Score: 79
Period size: 28 Copynumber: 3.7 Consensus size: 26
1145339 AACAAAAAGA
1145349 AAAAGAAAAAGAATAAAAGATGAAAGAAT
1 AAAAG-AAAAGAA-AAAAGA-GAAAGAAT
*
1145378 AAAAGAAAAGTAAAAAAGAAAGAAGAGAAA
1 AAAAGAAAAG-AAAAAAG--AGAA-AGAAT
*
1145408 AATAAGAAGAAGAAAAAAGAAAAAGAAT
1 AA-AAGAA-AAGAAAAAAGAGAAAGAAT
*
1145436 AGAAA-AATAAGAAATAAGA
1 A-AAAGAA-AAGAAAAAAGA
1145455 AATAAGAAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
27 12 0.18
28 17 0.26
29 14 0.22
30 7 0.11
31 12 0.18
32 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.08
Consensus pattern (26 bp):
AAAAGAAAAGAAAAAAGAGAAAGAAT
Found at i:1145401 original size:17 final size:18
Alignment explanation
Indices: 1145379--1145449 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 18
1145369 TGAAAGAATA
*
1145379 AAAGAAAAGTAAAA-AAG
1 AAAGAAAAGAAAAATAAG
*
1145396 AAAGAAGAGAAAAATAAG
1 AAAGAAAAGAAAAATAAG
* *
1145414 -AAGAAGA-AAAAAGAA-
1 AAAGAAAAGAAAAATAAG
*
1145429 AAAGAATAGAAAAATAAG
1 AAAGAAAAGAAAAATAAG
1145447 AAA
1 AAA
1145450 TAAGAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
16 13 0.29
17 26 0.58
18 6 0.13
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (18 bp):
AAAGAAAAGAAAAATAAG
Found at i:1147982 original size:13 final size:13
Alignment explanation
Indices: 1147964--1147996 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1147954 CATCTTGACA
1147964 TCCATAAAATCAT
1 TCCATAAAATCAT
*
1147977 TCCATATAATCAT
1 TCCATAAAATCAT
1147990 T-CATAAA
1 TCCATAAA
1147997 TGCATCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (13 bp):
TCCATAAAATCAT
Found at i:1148299 original size:36 final size:36
Alignment explanation
Indices: 1148176--1148299 Score: 99
Period size: 36 Copynumber: 3.4 Consensus size: 36
1148166 CTTTGAGATT
* * *
1148176 GTTTCT-TTCGAAACGAAGTTTCGTCTCGTTTGAGACA
1 GTTTCTCTT-GAAAC-AAATTTTGTCTCGCTTGAGACA
* * ** **
1148213 GTTTTTCTTGAAACAAA-ATTGATCTTACTTGAGATT
1 GTTTCTCTTGAAACAAATTTTG-TCTCGCTTGAGACA
* **
1148249 GTTTTTCTAAAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
1148285 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1148300 TAAACCTTTG
Statistics
Matches: 65, Mismatches: 19, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
35 2 0.03
36 48 0.74
37 13 0.20
38 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
Found at i:1148341 original size:66 final size:66
Alignment explanation
Indices: 1148164--1148420 Score: 282
Period size: 66 Copynumber: 3.8 Consensus size: 66
1148154 ACTGTCTGTC
* * * * * *
1148164 ACCTTTGAGATTGTTTCTTTCGAAACGAAGTTTCGTCTCGTTTGAGACAGTTTTTCTTGAAACAA
1 ACCTTTGAGATTGTTTCTCTCAAAAC-AAATTTCGTCTCGCTTGAGACAGTTTCTCTTGAAACAT
1148229 AA
65 AA
* * * *
1148231 TTGATCTTACTTGAGATTGTTTTTCTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGA
1 ---A-CCT--TTGAGATTGTTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAGTTTCTCTTGA
1148296 AACATAA
60 AACATAA
* * * *
1148303 ACCTTTGAGATT-TTTCTCTCCAAACAAAGTTCCATCTCGCTTGAGACAGTTTCTTTTGAAACAT
1 ACCTTTGAGATTGTTTCTCTCAAAACAAA-TTTCGTCTCGCTTGAGACAGTTTCTCTTGAAACAT
1148367 AA
65 AA
* * *
1148369 GCCTTTGAGATTGTTTCTCTCAAAATAAATTTCTTCTCGCTTGAGACAGTTT
1 ACCTTTGAGATTGTTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAGTTT
1148421 TTCCTCGAAA
Statistics
Matches: 159, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
65 13 0.08
66 73 0.46
67 14 0.09
68 2 0.01
69 1 0.01
70 1 0.01
71 2 0.01
72 35 0.22
73 18 0.11
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (66 bp):
ACCTTTGAGATTGTTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAGTTTCTCTTGAAACATA
A
Found at i:1148419 original size:132 final size:136
Alignment explanation
Indices: 1148164--1148420 Score: 328
Period size: 138 Copynumber: 1.9 Consensus size: 136
1148154 ACTGTCTGTC
* * * * * *
1148164 ACCTTTGAGATTGTTTCTTTCGAAACGAAGTTTCGTCTCGTTTGAGACAGTTTTTCTTGAAACAA
1 ACCTTTGAGATTGTTTCTCTCCAAACAAAGTTCCATCTCGCTTGAGACAGTTTTTCTTGAAACAA
* *
1148229 AATTGATCTTACTTGAGATTGTTTTTCTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTT
66 AA-TGA-CCTA-TTGAGATTGTTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTT
1148294 GAAACATAA
128 GAAACATAA
1148303 ACCTTTGAGATT-TTTCTCTCCAAACAAAGTTCCATCTCGCTTGAGACAGTTTCTT-TTGAAACA
1 ACCTTTGAGATTGTTTCTCTCCAAACAAAGTTCCATCTCGCTTGAGACAGTTT-TTCTTGAAACA
* * *
1148366 TAA-G-CCT-TTGAGATTGTTTCTCTCAAAATAAATTTCT-TCTCGCTTGAGACAGTTT
65 AAATGACCTATTGAGATTGTTTCTCTAAAAACAAATTT-TGTCTCGCTTGAGACAGTTT
1148421 TTCCTCGAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
132 43 0.41
133 1 0.01
134 2 0.02
136 1 0.01
138 44 0.42
139 14 0.13
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (136 bp):
ACCTTTGAGATTGTTTCTCTCCAAACAAAGTTCCATCTCGCTTGAGACAGTTTTTCTTGAAACAA
AATGACCTATTGAGATTGTTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
ACATAA
Found at i:1148442 original size:66 final size:65
Alignment explanation
Indices: 1148241--1148451 Score: 230
Period size: 66 Copynumber: 3.2 Consensus size: 65
1148231 TTGATCTTAC
* * *
1148241 TTGAGATTGTTTTTCTAAAAACAAATTT-TGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGAGATTGTTTCTCTCAAAACAAATTTCT-TCTCGCTTGAGACAGTTTTTCTTGAAACATAAA-
1148305 CT
64 CT
* * *
1148307 TTGAGATT-TTTCTCTCCAAACAAAGTTCCATCTCGCTTGAGACAGTTTCTT-TTGAAACATAAG
1 TTGAGATTGTTTCTCTCAAAACAAA-TTTCTTCTCGCTTGAGACAGTTT-TTCTTGAAACATAA-
*
1148370 CCT
63 ACT
* * * *
1148373 TTGAGATTGTTTCTCTCAAAATAAATTTCTTCTCGCTTGAGACAGTTTTTCCTCGAAACACAAAT
1 TTGAGATTGTTTCTCTCAAAACAAATTTCTTCTCGCTTGAGACAGTTTTT-CTTGAAACATAAAC
1148438 T
65 T
* *
1148439 TTGAAATTATTTC
1 TTGAGATTGTTTC
1148452 ACTTGAAACA
Statistics
Matches: 121, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
65 15 0.12
66 82 0.68
67 24 0.20
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (65 bp):
TTGAGATTGTTTCTCTCAAAACAAATTTCTTCTCGCTTGAGACAGTTTTTCTTGAAACATAAACT
Found at i:1148480 original size:132 final size:132
Alignment explanation
Indices: 1148241--1148480 Score: 288
Period size: 132 Copynumber: 1.8 Consensus size: 132
1148231 TTGATCTTAC
* * *
1148241 TTGAGATTGTTTTTCTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACC
1 TTGAGATTGTTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTCGAAACACAAACC
* * * * * *
1148306 TTTGAGATTTTTCTCTCCAAACAAAGTTCCATCTCGCTTGAGACAGTTTCTTTTGAAACATAAGC
66 TTTGAAATTTTTCACTCCAAACAAAATTCCACCTCACATGAGACAGTTTCTTTTGAAACATAAGC
1148371 CT
131 CT
* * *
1148373 TTGAGATTGTTTCTCTCAAAATAAATTTCT-TCTCGCTTGAGACAGTTTTTCCTCGAAACACAAA
1 TTGAGATTGTTTCTCTAAAAACAAATTT-TGTCTCGCTTGAGACAGTTTCT-CTCGAAACACAAA
* ** *
1148437 -TTTTGAAATTATTTCACTTGAAACAAAATT-GACCTCACATGAGA
64 CCTTTGAAATT-TTTCACTCCAAACAAAATTCCACCTCACATGAGA
1148481 TTGTTTTCCT
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
132 62 0.70
133 27 0.30
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (132 bp):
TTGAGATTGTTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTCGAAACACAAACC
TTTGAAATTTTTCACTCCAAACAAAATTCCACCTCACATGAGACAGTTTCTTTTGAAACATAAGC
CT
Found at i:1148503 original size:102 final size:102
Alignment explanation
Indices: 1148374--1148618 Score: 314
Period size: 102 Copynumber: 2.4 Consensus size: 102
1148364 CATAAGCCTT
* * * ** *
1148374 TGAGATTG-TTTCTCTCAAAATAAATTTCTTCTCGCTTGAGACAGTTTTTC-CTCGAAACACAAA
1 TGAGATTGTTTTC-CTAAAAACAAATTTCATCTCGCTTGAGACAG-AGTTCACTCGAAACAAAAA
*
1148437 TTTTGAAATTATTTCACTTGAAACAAAATTGACCTCACA
64 TTTTGAAATTATTTCACTTGAAACAAAATTAACCTCACA
*
1148476 TGAGATTGTTTTCCTAAAAACAAATTTCATCTCGCTTGAGACAGAGTTCATTCGAAACAAAAATT
1 TGAGATTGTTTTCCTAAAAACAAATTTCATCTCGCTTGAGACAGAGTTCACTCGAAACAAAAATT
* ** *
1148541 TTGAAATTGTTTCACTTGAAACAAAATTAATTTCACT
66 TTGAAATTATTTCACTTGAAACAAAATTAACCTCACA
* * * *
1148578 TCATATTATTTTCCTAAAAACAAATTTCGTCTCGCTTGAGA
1 TGAGATTGTTTTCCTAAAAACAAATTTCATCTCGCTTGAGA
1148619 TACTTTTCCC
Statistics
Matches: 125, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
101 3 0.02
102 118 0.94
103 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (102 bp):
TGAGATTGTTTTCCTAAAAACAAATTTCATCTCGCTTGAGACAGAGTTCACTCGAAACAAAAATT
TTGAAATTATTTCACTTGAAACAAAATTAACCTCACA
Found at i:1151340 original size:3 final size:3
Alignment explanation
Indices: 1151327--1151381 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
1151317 CCGTGTTTTA
1151327 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1151373 ATT -TT ATT A
1 ATT ATT ATT A
1151382 ATAAATATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1152196 original size:16 final size:16
Alignment explanation
Indices: 1152175--1152206 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1152165 TGGATTTTTT
1152175 GGGGCTTCAAGAAGAA
1 GGGGCTTCAAGAAGAA
1152191 GGGGCTTCAAGAAGAA
1 GGGGCTTCAAGAAGAA
1152207 AGTTTCGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (16 bp):
GGGGCTTCAAGAAGAA
Found at i:1159949 original size:21 final size:22
Alignment explanation
Indices: 1159919--1159964 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1159909 CAAGCTTAAC
1159919 TTTCAAATCAAAG-TTTTC-TT
1 TTTCAAATCAAAGATTTTCATT
*
1159939 TTTCTAAATCATAGATTTTCATT
1 TTTC-AAATCAAAGATTTTCATT
1159962 TTT
1 TTT
1159965 GAAAGCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 8 0.36
22 5 0.23
23 5 0.23
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTCAAATCAAAGATTTTCATT
Found at i:1163305 original size:21 final size:22
Alignment explanation
Indices: 1163275--1163320 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1163265 CAAGCTTAAC
1163275 TTTCAAATCAAAG-TTTTC-TT
1 TTTCAAATCAAAGATTTTCATT
*
1163295 TTTCTAAATCATAGATTTTCATT
1 TTTC-AAATCAAAGATTTTCATT
1163318 TTT
1 TTT
1163321 GAAAGCTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 8 0.36
22 5 0.23
23 5 0.23
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTCAAATCAAAGATTTTCATT
Found at i:1167288 original size:15 final size:16
Alignment explanation
Indices: 1167270--1167303 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1167260 TGAAAGTTAT
*
1167270 AAAAGTATATGAAA-G
1 AAAAGAATATGAAATG
1167285 AAAAGAATATGAAATG
1 AAAAGAATATGAAATG
1167301 AAA
1 AAA
1167304 GTTTTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (16 bp):
AAAAGAATATGAAATG
Found at i:1167321 original size:40 final size:40
Alignment explanation
Indices: 1167260--1167340 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
1167250 AAAGTAAATG
*
1167260 TGAAAGTTATAAAAGTATATGAA-AGAAAAGAATATGAAA
1 TGAAAGTTATAAAAGTATATGAATAAAAAAGAATATGAAA
* *
1167299 TGAAAGTTTTGAAATGTATATGAATAAAAAAGAATATGAAA
1 TGAAAGTTAT-AAAAGTATATGAATAAAAAAGAATATGAAA
1167340 T
1 T
1167341 AGTTATTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 9 0.24
40 12 0.32
41 16 0.43
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (40 bp):
TGAAAGTTATAAAAGTATATGAATAAAAAAGAATATGAAA
Found at i:1167863 original size:11 final size:11
Alignment explanation
Indices: 1167849--1167882 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1167839 AAGATAAGGG
1167849 ATAATAATAAT
1 ATAATAATAAT
1167860 ATAATAATAAT
1 ATAATAATAAT
* *
1167871 ATGATAAGAAT
1 ATAATAATAAT
1167882 A
1 A
1167883 ACTTAGCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:1170594 original size:15 final size:16
Alignment explanation
Indices: 1170555--1170595 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1170545 CAATTCAAAA
1170555 AAATAATATATTAAATT
1 AAATAAT-TATTAAATT
1170572 ATAA-AATT-TTAAATT
1 A-AATAATTATTAAATT
1170587 AAATAATTA
1 AAATAATTA
1170596 ATAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
14 2 0.10
15 12 0.57
16 1 0.05
17 4 0.19
18 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAATTATTAAATT
Found at i:1175412 original size:30 final size:30
Alignment explanation
Indices: 1175359--1175424 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1175349 AAAACCGGAA
* * **
1175359 GAACAGGCTGAAAATCGGTAAAACCGAGGT
1 GAACCGGCTGAAAACCGACAAAACCGAGGT
**
1175389 GAACCGGCTGAAAACCGACAAAACCGATTT
1 GAACCGGCTGAAAACCGACAAAACCGAGGT
1175419 GAACCG
1 GAACCG
1175425 TCGGTTCACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGACAAAACCGAGGT
Found at i:1176608 original size:204 final size:205
Alignment explanation
Indices: 1176258--1176668 Score: 815
Period size: 204 Copynumber: 2.0 Consensus size: 205
1176248 TTTACCCTTT
1176258 TTTTCGATTTATTGATCGATTGATTTAAATAAAATTTTACAGAATCTACTATAAGAATAATTCTC
1 TTTTCGATTTATTGATCGATTGATTTAAATAAAATTTTACAGAATCTACTATAAGAATAATTCTC
1176323 CCAGCCTAATTTAATATATTTATAAATATAGAAATAAAAACTCTTGATTTTACATAAAAAATTTT
66 CCAGCCTAATTTAATATATTTATAAATATAGAAATAAAAACTCTTGATTTTACATAAAAAATTTT
1176388 AATAGTTTATCCCATTAGACCAACTAATTATTGATTTTCTACGTTA-TTCATTAATATGGTCTGA
131 AATAGTTTATCCCATTAGACCAACTAATTATTGATTTTCTACGTTATTTCATTAATATGGTCTGA
1176452 TTAAAGGATG
196 TTAAAGGATG
1176462 TTTTCGATTTATTGATCGATTGATTTAAATAAAATTTTACAGAATCTACTATAAGAATAATTCTC
1 TTTTCGATTTATTGATCGATTGATTTAAATAAAATTTTACAGAATCTACTATAAGAATAATTCTC
1176527 CCAGCCTAATTTAATATATTTATAAATATAGAAATAAAAACTCTTGATTTTACATAAAAAATTTT
66 CCAGCCTAATTTAATATATTTATAAATATAGAAATAAAAACTCTTGATTTTACATAAAAAATTTT
1176592 AATAGTTTATCCCATTAGACCAACTAATTATTGATTTTCTACGTTATTTCATTAATATGGTCTGA
131 AATAGTTTATCCCATTAGACCAACTAATTATTGATTTTCTACGTTATTTCATTAATATGGTCTGA
1176657 TTAAAGGATG
196 TTAAAGGATG
1176667 TT
1 TT
1176669 ACTATTCTCG
Statistics
Matches: 206, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
204 176 0.85
205 30 0.15
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (205 bp):
TTTTCGATTTATTGATCGATTGATTTAAATAAAATTTTACAGAATCTACTATAAGAATAATTCTC
CCAGCCTAATTTAATATATTTATAAATATAGAAATAAAAACTCTTGATTTTACATAAAAAATTTT
AATAGTTTATCCCATTAGACCAACTAATTATTGATTTTCTACGTTATTTCATTAATATGGTCTGA
TTAAAGGATG
Found at i:1178644 original size:130 final size:127
Alignment explanation
Indices: 1178443--1178952 Score: 440
Period size: 130 Copynumber: 3.9 Consensus size: 127
1178433 AATCCCATCT
* * * * * *
1178443 TTTATATTTATAATTGAGGCCCCTACTTTTT-AATCCCAC-TTTTTATATTTATAATTGAGGCCC
1 TTTATCTTTATAATTGAGGTCTCTAATTTTTCAAT-TCACTTTTTTACATTTATAATTGAGGCCC
* * * **
1178506 CTAATTTTTCCAATCTTTCTTTCTACCTTTATAATTGAAGCCCCTAAATTTTTTAATCTCACAG
65 TTATTTTTTTCAATCTCACTTTCTACCTTTATAATTGAAGCCCCT-AATTTTTTAATCTCACAG
1178570 TTTATCTTTATAATTGAGGTCTCTAATTTCTTCAATTCAACTTTTTTACATTTATAATTGAGGCC
1 TTTATCTTTATAATTGAGGTCTCTAATTT-TTCAATTC-ACTTTTTTACATTTATAATTGAGGCC
* * * * ***
1178635 CTTATTTTTTTTCAATCTCACTTTCAACCTTTATAATTGAACCCCCGAATTTTATAATCTCATTT
64 CTTA-TTTTTTTCAATCTCACTTTCTACCTTTATAATTGAAGCCCCTAATTTTTTAATCTCACAG
* *
1178700 TTTATCTTTATAATTGAGGTCTCTAATTGTTTCAATCTCA-TTTTTTACCTTTATAATTGAAGCC
1 TTTATCTTTATAATTGAGGTCTCTAATT-TTTCAAT-TCACTTTTTTACATTTATAATTGAGGCC
* * * ** * *
1178764 CATGATTTTTTTTAATCTCACTTTTTATATTTATAATTG-AGACCCCTAATTTTTTCAATCTGAT
64 C-TTATTTTTTTCAATCTCACTTTCTACCTTTATAATTGAAG-CCCCTAATTTTTT-AATCTCAC
**
1178828 TT
126 AG
* * * * * * * * *
1178830 TTTAATTTTTTTAATT-ATGGCCACTAATTTTTTAGTCTCAC-TTTCTACCTTTATAATTGAAGC
1 TTT-ATCTTTATAATTGA-GGTCTCTAATTTTTCAAT-TCACTTTTTTACATTTATAATTG-AGG
* * * * *
1178893 CCCCTAGTTTTTT-AATCTCATTATTTTACCTTTATAATTGAGGCCCCTAATTTTTCTAAT
62 CCCTTATTTTTTTCAATCTCACT-TTCTACCTTTATAATTGAAGCCCCTAATTTTT-TAAT
1178953 ACAACTTTTT
Statistics
Matches: 320, Mismatches: 46, Indels: 31
0.81 0.12 0.08
Matches are distributed among these distances:
127 25 0.08
128 4 0.01
129 76 0.24
130 152 0.47
131 63 0.20
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (127 bp):
TTTATCTTTATAATTGAGGTCTCTAATTTTTCAATTCACTTTTTTACATTTATAATTGAGGCCCT
TATTTTTTTCAATCTCACTTTCTACCTTTATAATTGAAGCCCCTAATTTTTTAATCTCACAG
Found at i:1178750 original size:85 final size:87
Alignment explanation
Indices: 1178612--1178938 Score: 277
Period size: 87 Copynumber: 3.8 Consensus size: 87
1178602 CAATTCAACT
* * * * * * **
1178612 TTTTTACATTTATAATTGAGGCCCTTATTTTTTTTCAATCTCACTTTCAACCTTTATAATTGAA-
1 TTTTTATATTTATAATTGAGACCCCTA-ATTGTTTCAATCTCATTTTTTACCTTTATAATTGAAG
* *
1178676 CCCCCGA-ATTTTATAATCTCAT
65 CCCACGATATTTTATAATCTCAC
* ** *
1178698 TTTTTATCTTTATAATTGAGGTCTCTAATTGTTTCAATCTCATTTTTTACCTTTATAATTGAAGC
1 TTTTTATATTTATAATTGAGACCCCTAATTGTTTCAATCTCATTTTTTACCTTTATAATTGAAGC
* * *
1178763 CCATGATTTTTTTTAATCTCAC
66 CCACGATATTTTATAATCTCAC
* * ** * *
1178785 TTTTTATATTTATAATTGAGACCCCTAATTTTTTCAATCTGATTTTTTAATTTTTTTAATT-ATG
1 TTTTTATATTTATAATTGAGACCCCTAATTGTTTCAATCTCATTTTTT-ACCTTTATAATTGAAG
* * * *
1178849 GCCACTA-ATTTTTTAGTCTCAC
65 CCCACGATATTTTATAATCTCAC
* ** * * * *
1178871 TTTCTACCTTTATAATTGAAGCCCCCTAGTT-TTTTAATCTCATTATTTTACCTTTATAATTGAG
1 TTTTTATATTTATAATTG-AGACCCCTAATTGTTTCAATCTCATT-TTTTACCTTTATAATTGAA
1178935 GCCC
64 GCCC
1178939 CTAATTTTTC
Statistics
Matches: 193, Mismatches: 42, Indels: 11
0.78 0.17 0.04
Matches are distributed among these distances:
85 31 0.16
86 75 0.39
87 78 0.40
88 9 0.05
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (87 bp):
TTTTTATATTTATAATTGAGACCCCTAATTGTTTCAATCTCATTTTTTACCTTTATAATTGAAGC
CCACGATATTTTATAATCTCAC
Found at i:1178962 original size:173 final size:170
Alignment explanation
Indices: 1178442--1178988 Score: 516
Period size: 173 Copynumber: 3.2 Consensus size: 170
1178432 TAATCCCATC
* *
1178442 TTTTATATTTATAATTGAGGCCCCT-ACTTTTT-AATCCCACTTTTT-ATATTTATAATTGAGGC
1 TTTTATATTTATAATTGAGGCCCCTAATTTTTTCAATCTCA-TTTTTAATATTTATAATTGAGGC
* ** *
1178504 CCCTAATTTTTCCAATCTTTCTTTCTACCTTTATAATTGAAGCCCCTAAATTTTTTAATCTCA-C
65 CCCTAATTTTT-TAATCTCACTTTCTACCTTTATAATTGAAGCCCCT-AATTTTTTAATCTCATT
* * * *
1178568 AGTTTATCTTTATAATTGAGGTCTCTAATTTCTTC-AATTCAACTT
128 ATTTTACCTTTATAATTGAGGCCCCTAATTT-TTCTAA-TCAAC-T
* * * * * ** **
1178613 TTTTACATTTATAATTGAGGCCCTTATTTTTTTTCAATCTCACTTTCAACCTTTATAATTGAACC
1 TTTTATATTTATAATTGAGGCCCCTA-ATTTTTTCAATCTCATTTTTAATATTTATAATTGAGGC
* * * * * * * * *
1178678 CCCGAATTTTATAATCTCATTTTTTATCTTTATAATTGAGGTCTCTAATTGTTTCAATCTCATT-
65 CCCTAATTTTTTAATCTCACTTTCTACCTTTATAATTGAAGCCCCTAATT-TTTTAATCTCATTA
* * * * *
1178742 TTTTACCTTTATAATTGAAGCCCATGATTTTTTTTAATCTCACT
129 TTTTACCTTTATAATTGAGGCCCCT-AATTTTTCTAATC-AACT
* * * *
1178786 TTTTATATTTATAATTGAGACCCCTAATTTTTTCAATCTGATTTTTTAATTTTTTTAATT-ATGG
1 TTTTATATTTATAATTGAGGCCCCTAATTTTTTCAATCTCA-TTTTTAATATTTATAATTGA-GG
* * *
1178850 CCACTAATTTTTTAGTCTCACTTTCTACCTTTATAATTGAAGCCCCCTAGTTTTTTAATCTCATT
64 CCCCTAATTTTTTAATCTCACTTTCTACCTTTATAATTGAAG-CCCCTAATTTTTTAATCTCATT
1178915 ATTTTACCTTTATAATTGAGGCCCCTAATTTTTCTAATACAACT
128 ATTTTACCTTTATAATTGAGGCCCCTAATTTTTCTAAT-CAACT
* **
1178959 TTTTAGT-TTTATAATTTAGGTACCTAATTT
1 TTTTA-TATTTATAATTGAGGCCCCTAATTT
1178989 AATTATTTTC
Statistics
Matches: 295, Mismatches: 66, Indels: 28
0.76 0.17 0.07
Matches are distributed among these distances:
171 23 0.08
172 18 0.06
173 187 0.63
174 67 0.23
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (170 bp):
TTTTATATTTATAATTGAGGCCCCTAATTTTTTCAATCTCATTTTTAATATTTATAATTGAGGCC
CCTAATTTTTTAATCTCACTTTCTACCTTTATAATTGAAGCCCCTAATTTTTTAATCTCATTATT
TTACCTTTATAATTGAGGCCCCTAATTTTTCTAATCAACT
Found at i:1178963 original size:43 final size:42
Alignment explanation
Indices: 1178364--1178988 Score: 434
Period size: 43 Copynumber: 14.5 Consensus size: 42
1178354 CAAATGTTTT
*** * * *
1178364 TTTATAATTGACATCCCTGAATTTTGTAATCTTACTTTTCACC
1 TTTATAATTGAGGCCCCT-AATTTTTTAATCTCACTTTTTACC
** * * ** *
1178407 TTTATAATTGATTCTCTTACGTTTTTAATCCCATCTTTTATA--
1 TTTATAATTGAGGCCCCTAATTTTTTAATCTCA-CTTTT-TACC
* * **
1178449 TTTATAATTGAGGCCCCT-ACTTTTTAATCCCACTTTTTATA
1 TTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTTTACC
* ** *
1178490 TTTATAATTGAGGCCCCTAATTTTTCCAATCTTTCTTTCTACC
1 TTTATAATTGAGGCCCCTAATTTTT-TAATCTCACTTTTTACC
* ** *
1178533 TTTATAATTGAAGCCCCTAAATTTTTTAATCTCACAGTTTATC
1 TTTATAATTGAGGCCCCT-AATTTTTTAATCTCACTTTTTACC
* * * *
1178576 TTTATAATTGAGGTCTCTAATTTCTTCAAT-TCAACTTTTTTACA
1 TTTATAATTGAGGCCCCTAATTT-TTTAATCTC-AC-TTTTTACC
* * **
1178620 TTTATAATTGAGGCCCTTATTTTTTTTCAATCTCACTTTCAACC
1 TTTATAATTGAGGCCCCTA-ATTTTTT-AATCTCACTTTTTACC
** * * * *
1178664 TTTATAATTGAACCCCCGAATTTTATAATCTCATTTTTTATC
1 TTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTTTACC
* * * *
1178706 TTTATAATTGAGGTCTCTAATTGTTTCAATCTCATTTTTTACC
1 TTTATAATTGAGGCCCCTAATT-TTTTAATCTCACTTTTTACC
* * * **
1178749 TTTATAATTGAAGCCCATGATTTTTTTTAATCTCACTTTTTATA
1 TTTATAATTGAGGCCCCT-A-ATTTTTTAATCTCACTTTTTACC
* * * **
1178793 TTTATAATTGAGACCCCTAATTTTTTCAATCTGATTTTTTAATT
1 TTTATAATTGAGGCCCCTAATTTTTT-AATCTCACTTTTT-ACC
* * * *
1178837 TTTTTAATT-ATGGCCACTAATTTTTTAGTCTCACTTTCTACC
1 TTTATAATTGA-GGCCCCTAATTTTTTAATCTCACTTTTTACC
* * *
1178879 TTTATAATTGAAGCCCCCTAGTTTTTTAATCTCATTATTTTACC
1 TTTATAATTG-AGGCCCCTAATTTTTTAATCTCACT-TTTTACC
* **
1178923 TTTATAATTGAGGCCCCTAATTTTTCTAATAC-AACTTTTTAGT
1 TTTATAATTGAGGCCCCTAATTTTT-TAAT-CTCACTTTTTACC
* **
1178966 TTTATAATTTAGGTACCTAATTT
1 TTTATAATTGAGGCCCCTAATTT
1178989 AATTATTTTC
Statistics
Matches: 450, Mismatches: 108, Indels: 48
0.74 0.18 0.08
Matches are distributed among these distances:
39 2 0.00
40 5 0.01
41 30 0.07
42 80 0.18
43 192 0.43
44 128 0.28
45 11 0.02
46 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (42 bp):
TTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTTTACC
Found at i:1179751 original size:43 final size:43
Alignment explanation
Indices: 1179577--1180197 Score: 435
Period size: 43 Copynumber: 14.5 Consensus size: 43
1179567 ATTTTTTCTT
* * * * *
1179577 TTTATAATCGATGTCCCTAATTTTTGT-AATCTTACTTTTCACC
1 TTTATAATTGAGGCCCCTAATTTTT-TCAATCTCACTTTTTACC
** * * * *
1179620 TTTATAATTGATTCTCTTAAGTTTTT-AATCCCATCTTTTATA--
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCA-CTTTT-TACC
* * * * *
1179662 TTTATAGTTGAGGCCCCT-A-CTTTTGAATCCCACTTTTTACA
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACC
*
1179703 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTCTACC
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACC
* * *
1179746 TTTATAATTAAAGCCCCTAATTTTTT-AATCTC-GTTGTTTACC
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTT-TTTACC
* * ** * * *
1179788 TTTATAATTTAGGTCTTTAATTTCTTCAAT-TCCACCTTTTACA
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCT-CACTTTTTACC
* * **
1179831 TTTATAATTGAGGGCCTTAATTTTTTTTTCAATCTCACTTTCAACC
1 TTTATAATTGAGGCCCCTAA---TTTTTTCAATCTCACTTTTTACC
* * * *
1179877 TTTATAATTGA-ACCCC-AATTTTTTTAATCTCATTTTTTATC
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACC
** ** * * *
1179918 TTTATAATTGAATCCTTTAATTGTTTCAATATCATTTTTTACC
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACC
* ** * * * *
1179961 GTTATAATTGAAACCCATGATTTTTTTAATCTCACTTTTTACA
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACC
* * * *
1180004 TTTATAATTGAGACCCCTAATTTTTTCAATCTCATTTTTTTCT
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACC
* * *
1180047 TTTTTAATT-ATGGCCCCTAATTTTTT-AGTCTCACTTTCTACC
1 TTTATAATTGA-GGCCCCTAATTTTTTCAATCTCACTTTTTACC
* * * *
1180089 TTTATAATTGAAGCCCCTAGTTTTTT-AATCTCATTATTTTACA
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACT-TTTTACC
* * **
1180132 TTTATAATTTAGGCCCCTAATTTTTCCAATC-CAACTTTTTAGT
1 TTTATAATTGAGGCCCCTAATTTTTTCAATCTC-ACTTTTTACC
* **
1180175 TTTATAATTTAGGTACCTAATTT
1 TTTATAATTGAGGCCCCTAATTT
1180198 AATTATTTTC
Statistics
Matches: 458, Mismatches: 98, Indels: 44
0.76 0.16 0.07
Matches are distributed among these distances:
39 2 0.00
40 9 0.02
41 56 0.12
42 94 0.21
43 257 0.56
44 10 0.02
45 2 0.00
46 27 0.06
47 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (43 bp):
TTTATAATTGAGGCCCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:1179796 original size:85 final size:85
Alignment explanation
Indices: 1179577--1180162 Score: 427
Period size: 85 Copynumber: 6.9 Consensus size: 85
1179567 ATTTTTTCTT
* * * * * * ** * * *
1179577 TTTATAATCGATGTCCCTAATTTTTGTAATCTTACTTTTCACCTTTATAATTGATTCTCTTAAGT
1 TTTATAATTGAAGCCCCTAATTTTT-TAATCTCATTTTTTACCTTTATAATTGAGGCCCCTAATT
* **
1179642 TTTT-AATCCCATCTTT-TATA
65 TTTTCAATCTCA-CTTTCTACC
* * * * * * *
1179662 TTTATAGTTGAGGCCCCT-ACTTTTGAATCCCACTTTTTACATTTATAATTGAGGCCCCTAATTT
1 TTTATAATTGAAGCCCCTAATTTTTTAATCTCATTTTTTACCTTTATAATTGAGGCCCCTAATTT
1179726 TTTCAATCTCACTTTCTACC
66 TTTCAATCTCACTTTCTACC
* * * * * **
1179746 TTTATAATTAAAGCCCCTAATTTTTTAATCTCGTTGTTTACCTTTATAATTTAGGTCTTTAATTT
1 TTTATAATTGAAGCCCCTAATTTTTTAATCTCATTTTTTACCTTTATAATTGAGGCCCCTAATTT
* *
1179811 CTTCAAT-TCCACCTTT-TACA
66 TTTCAATCT-CA-CTTTCTACC
* * * * ** *
1179831 TTTATAATTGAGGGCCTTAATTTTTTTTTCAATCTCACTTTCAACCTTTATAATTGA-ACCCC-A
1 TTTATAATTGAAGCCCCTAA---TTTTTT-AATCTCATTTTTTACCTTTATAATTGAGGCCCCTA
* * * *
1179894 ATTTTTTTAATCTCATTTTTTATC
62 ATTTTTTCAATCTCACTTTCTACC
* ** * * * ** * *
1179918 TTTATAATTGAATCCTTTAATTGTTTCAATATCATTTTTTACCGTTATAATTGAAACCCATGATT
1 TTTATAATTGAAGCCCCTAATT-TTTTAATCTCATTTTTTACCTTTATAATTGAGGCCCCTAATT
* * *
1179983 TTTTTAATCTCACTTTTTACA
65 TTTTCAATCTCACTTTCTACC
* * *
1180004 TTTATAATTG-AGACCCCTAATTTTTTCAATCTCATTTTTTTCTTTTTTAATT-ATGGCCCCTAA
1 TTTATAATTGAAG-CCCCTAATTTTTT-AATCTCATTTTTTACCTTTATAATTGA-GGCCCCTAA
*
1180067 TTTTTT-AGTCTCACTTTCTACC
63 TTTTTTCAATCTCACTTTCTACC
* * *
1180089 TTTATAATTGAAGCCCCTAGTTTTTTAATCTCATTATTTTACATTTATAATTTAGGCCCCTAATT
1 TTTATAATTGAAGCCCCTAATTTTTTAATCTCATT-TTTTACCTTTATAATTGAGGCCCCTAATT
*
1180154 TTTCCAATC
65 TTTTCAATC
1180163 CAACTTTTTA
Statistics
Matches: 390, Mismatches: 90, Indels: 41
0.75 0.17 0.08
Matches are distributed among these distances:
83 37 0.09
84 62 0.16
85 150 0.38
86 82 0.21
87 30 0.08
88 8 0.02
89 21 0.05
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.49
Consensus pattern (85 bp):
TTTATAATTGAAGCCCCTAATTTTTTAATCTCATTTTTTACCTTTATAATTGAGGCCCCTAATTT
TTTCAATCTCACTTTCTACC
Found at i:1179939 original size:130 final size:130
Alignment explanation
Indices: 1179691--1180048 Score: 419
Period size: 130 Copynumber: 2.8 Consensus size: 130
1179681 CTTTTGAATC
*
1179691 CCACTTTTTACATTTATAATTGAGGCCCCTAA-TTTTTTCAATCTCACTTTCTACCTTTATAATT
1 CCACTTTTTACATTTATAATTGAGGCCCATAATTTTTTTCAATCTCACTTTCTACCTTTATAATT
* * * * * *
1179755 AAAGCCCCTAA-TTTTTTAATCTCGTTGTTTACCTTTATAATTTAGGTCTTTAATT-TCTTCAAT
66 GAA-CCCCTAATTTTTTTAATCTCATTTTTTATCTTTATAATTGAGATCTTTAATTGT-TTCAAT
1179818 -T
129 AT
* * * *
1179819 CCACCTTTTACATTTATAATTGAGGGCCTTAATTTTTTTTTCAATCTCACTTTCAACCTTTATAA
1 CCACTTTTTACATTTATAATTGAGGCCCATAA--TTTTTTTCAATCTCACTTTCTACCTTTATAA
1179884 TTGAACCCC-AATTTTTTTAATCTCATTTTTTATCTTTATAATTGA-ATCCTTTAATTGTTTCAA
64 TTGAACCCCTAATTTTTTTAATCTCATTTTTTATCTTTATAATTGAGAT-CTTTAATTGTTTCAA
1179947 TAT
128 TAT
* ** ** * * *
1179950 -CATTTTTTACCGTTATAATTGAAACCCATGATTTTTTT-AATCTCACTTTTTACATTTATAATT
1 CCACTTTTTACATTTATAATTGAGGCCCATAATTTTTTTCAATCTCACTTTCTACCTTTATAATT
*
1180013 GAGACCCCTAATTTTTTCAATCTCATTTTTT-TCTTT
66 GA-ACCCCTAATTTTTTTAATCTCATTTTTTATCTTT
1180049 TTTAATTATG
Statistics
Matches: 198, Mismatches: 23, Indels: 18
0.83 0.10 0.08
Matches are distributed among these distances:
127 24 0.12
128 46 0.23
129 24 0.12
130 69 0.35
131 35 0.18
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.50
Consensus pattern (130 bp):
CCACTTTTTACATTTATAATTGAGGCCCATAATTTTTTTCAATCTCACTTTCTACCTTTATAATT
GAACCCCTAATTTTTTTAATCTCATTTTTTATCTTTATAATTGAGATCTTTAATTGTTTCAATAT
Found at i:1180099 original size:128 final size:127
Alignment explanation
Indices: 1179853--1180183 Score: 343
Period size: 128 Copynumber: 2.6 Consensus size: 127
1179843 GGCCTTAATT
** * *
1179853 TTTTTTTCAATCTCACTTTCAACCTTTATAATTGA-ACCCC-AATTTTTTTAATCTCATTTTTTA
1 TTTTTTT-AATCTCACTTTTTACATTTATAATTGAGACCCCTAATTTTTTCAATCTCATTTTTTA
** * *
1179916 TCTTTATAATTGAATCCTTTAATTGTTTCAATATCATTTTTTACCGTTATAATTGAAACCCATGA
65 TCTTTATAATT-AATCCCCTAATTGTTTCAATATCACTTTCTACCGTTATAATTGAAACCCAT-A
1179981 TTTTTTTAATCTCACTTTTTACATTTATAATTGAGACCCCTAATTTTTTCAATCTCATTTTTT-T
1 TTTTTTTAATCTCACTTTTTACATTTATAATTGAGACCCCTAATTTTTTCAATCTCATTTTTTAT
* * * * * * *
1180045 CTTTTTTAATT-ATGGCCCCTAATT-TTTTAGTCTCACTTTCTACCTTTATAATTGAAGCCCCTA
66 C-TTTATAATTAAT--CCCCTAATTGTTTCAATATCACTTTCTACCGTTATAATTGAAACCCATA
* * * * * *
1180108 GTTTTTTAATCTCATTATTTTACATTTATAATTTAGGCCCCTAATTTTTCCAATC-CAACTTTTT
1 TTTTTTTAATCTCACT-TTTTACATTTATAATTGAGACCCCTAATTTTTTCAATCTC-ATTTTTT
1180172 AGT-TTTATAATT
64 A-TCTTTATAATT
1180184 TAGGTACCTA
Statistics
Matches: 172, Mismatches: 22, Indels: 18
0.81 0.10 0.08
Matches are distributed among these distances:
127 42 0.24
128 93 0.54
129 36 0.21
130 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (127 bp):
TTTTTTTAATCTCACTTTTTACATTTATAATTGAGACCCCTAATTTTTTCAATCTCATTTTTTAT
CTTTATAATTAATCCCCTAATTGTTTCAATATCACTTTCTACCGTTATAATTGAAACCCATA
Found at i:1182712 original size:18 final size:18
Alignment explanation
Indices: 1182691--1182730 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1182681 ATATACGTGG
* *
1182691 TGGAAATTATATGTTTGT
1 TGGAAAGTATATGTTGGT
*
1182709 TGGATAGTATATGTTGGT
1 TGGAAAGTATATGTTGGT
1182727 TGGA
1 TGGA
1182731 TATTCATGTG
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:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (18 bp):
TGGAAAGTATATGTTGGT
Found at i:1182731 original size:18 final size:18
Alignment explanation
Indices: 1182698--1182732 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1182688 TGGTGGAAAT
*
1182698 TATATGTTTGTTGGATAG
1 TATATGTTGGTTGGATAG
1182716 TATATGTTGGTTGGATA
1 TATATGTTGGTTGGATA
1182733 TTCATGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (18 bp):
TATATGTTGGTTGGATAG
Found at i:1186654 original size:13 final size:13
Alignment explanation
Indices: 1186638--1186710 Score: 146
Period size: 13 Copynumber: 5.6 Consensus size: 13
1186628 GAACACATCT
1186638 CTTGAACCTTTCC
1 CTTGAACCTTTCC
1186651 CTTGAACCTTTCC
1 CTTGAACCTTTCC
1186664 CTTGAACCTTTCC
1 CTTGAACCTTTCC
1186677 CTTGAACCTTTCC
1 CTTGAACCTTTCC
1186690 CTTGAACCTTTCC
1 CTTGAACCTTTCC
1186703 CTTGAACC
1 CTTGAACC
1186711 ATCATGTTCC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 60 1.00
ACGTcount: A:0.16, C:0.38, G:0.08, T:0.37
Consensus pattern (13 bp):
CTTGAACCTTTCC
Found at i:1192835 original size:20 final size:19
Alignment explanation
Indices: 1192760--1192836 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 19
1192750 ACTGGAATCC
*
1192760 AAGGGATCGTTCCTTTT-T
1 AAGGGATCGATCCTTTTCT
* *
1192778 CAAGGGGAACGATTCTTTGGTCT
1 -AA-GGGATCGATCCTTT--TCT
* *
1192801 AAGGGATCAAACCTTTTACT
1 AAGGGATCGATCCTTTT-CT
1192821 AAGGGATCGATCCTTT
1 AAGGGATCGATCCTTT
1192837 GAGCCAAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
19 3 0.07
20 27 0.61
21 10 0.23
22 3 0.07
23 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (19 bp):
AAGGGATCGATCCTTTTCT
Found at i:1199423 original size:56 final size:56
Alignment explanation
Indices: 1199337--1199449 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
1199327 TGGGGATCAA
*
1199337 TTTTCGTGCAAAATAAAGTTGCCCAGTCCAAGGGGTATCGGTACTCCTAGAGTGAG
1 TTTTCGTGCAAAATAAAGTTGCCCAGTCCAAGGGGTATCGATACTCCTAGAGTGAG
1199393 TTTTCGTGCAAAATAAAGTTGCCCAGTCCAAGGGGTATCGATACTCCTAGAGTGAG
1 TTTTCGTGCAAAATAAAGTTGCCCAGTCCAAGGGGTATCGATACTCCTAGAGTGAG
1199449 T
1 T
1199450 ATCAGTACTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (56 bp):
TTTTCGTGCAAAATAAAGTTGCCCAGTCCAAGGGGTATCGATACTCCTAGAGTGAG
Found at i:1201105 original size:19 final size:20
Alignment explanation
Indices: 1201066--1201106 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1201056 TCAAAATTTC
*
1201066 ATTTTGATTTTCAAAATCAA
1 ATTTTGATTTTCAAAAGCAA
*
1201086 ATTTTGCTTTT-AAAAGCAA
1 ATTTTGATTTTCAAAAGCAA
1201105 AT
1 AT
1201107 CATTTTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATTTTGATTTTCAAAAGCAA
Found at i:1203477 original size:14 final size:14
Alignment explanation
Indices: 1203458--1203487 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1203448 AATTCATTGT
1203458 AAATGATGAATGGA
1 AAATGATGAATGGA
1203472 AAATGATGAATGGA
1 AAATGATGAATGGA
1203486 AA
1 AA
1203488 CAAGTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (14 bp):
AAATGATGAATGGA
Found at i:1212703 original size:21 final size:21
Alignment explanation
Indices: 1212679--1212730 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
1212669 AAAGGATAGA
*
1212679 CCCTTTTGAAAAA-TGACCCAT
1 CCCTTTTGAAAAAGT-ACCAAT
*
1212700 CCC-TTTGAAAAAGTATCAAT
1 CCCTTTTGAAAAAGTACCAAT
1212720 CCCTTTTGAAA
1 CCCTTTTGAAA
1212731 GTTTAGCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.31
Consensus pattern (21 bp):
CCCTTTTGAAAAAGTACCAAT
Found at i:1213485 original size:55 final size:55
Alignment explanation
Indices: 1213380--1213546 Score: 205
Period size: 55 Copynumber: 3.0 Consensus size: 55
1213370 CCCACTACCA
* * ** * *
1213380 ATACGAAAATTCAC-CTACTTATTATGAATTTCTT-ATGTTT-CTTCGTATAGTTCTC
1 ATACGAAAATTCACAC-ACTTAGTATGAATTTCTTAAT-TTTGC-ACACATAGTGCCC
*
1213435 ATACGGAAATTCACACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCC
* *
1213490 ATACGAAAATTCATACACTTAGTATGCATTTCTTAATTTTGCACACATAGTGCCC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCC
1213545 AT
1 AT
1213547 TCGGTAATCA
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
55 95 0.96
56 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (55 bp):
ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTGCACACATAGTGCCC
Found at i:1213547 original size:28 final size:28
Alignment explanation
Indices: 1213462--1213547 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 28
1213452 CTTAGTATGA
1213462 ATTTCTTAATTTTGCACACATAGTGCCC
1 ATTTCTTAATTTTGCACACATAGTGCCC
* ** * *** * ***
1213490 A-TACGAAAATTCATACACTTAGTATGC
1 ATTTCTTAATTTTGCACACATAGTGCCC
1213517 ATTTCTTAATTTTGCACACATAGTGCCC
1 ATTTCTTAATTTTGCACACATAGTGCCC
1213545 ATT
1 ATT
1213548 CGGTAATCAC
Statistics
Matches: 35, Mismatches: 22, Indels: 2
0.59 0.37 0.03
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (28 bp):
ATTTCTTAATTTTGCACACATAGTGCCC
Found at i:1215302 original size:72 final size:70
Alignment explanation
Indices: 1215211--1215342 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 70
1215201 AATGTTTTGG
* ****
1215211 TGCTTTGTTAATCTATATTAGAATCGATGTTTTGTTGCCATGTGTTGTTAATGTATGTTTTTAAT
1 TGCTTTGTAAATCTATATTAGAATCGATGTTCCACTGCCATGTGTTGTTAATGTATGTTTTTAAT
1215276 TTCTA
66 TTCTA
*
1215281 TGCTTTGTAAATTGCTATATTAGAATTGATGTTCCACTGCCATGTGTTGTTAATGTATGTTT
1 TGCTTTGTAAA-T-CTATATTAGAATCGATGTTCCACTGCCATGTGTTGTTAATGTATGTTT
1215343 CACTGCCATG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 10 0.19
71 1 0.02
72 43 0.80
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.50
Consensus pattern (70 bp):
TGCTTTGTAAATCTATATTAGAATCGATGTTCCACTGCCATGTGTTGTTAATGTATGTTTTTAAT
TTCTA
Found at i:1220079 original size:23 final size:23
Alignment explanation
Indices: 1220035--1220081 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1220025 TTCAGTTTAA
* *
1220035 AATTTCAATTTATCCATTAAAAC
1 AATTTCAATTAATCCATAAAAAC
1220058 AATTT-AATTAATCACATAAAAAC
1 AATTTCAATTAATC-CATAAAAAC
1220081 A
1 A
1220082 TAAAATAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (23 bp):
AATTTCAATTAATCCATAAAAAC
Found at i:1220763 original size:19 final size:20
Alignment explanation
Indices: 1220732--1220784 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1220722 ACTTTCTTTA
*
1220732 TTTTCAGACTCATAACTCAT
1 TTTTCAGATTCATAACTCAT
* *
1220752 TTTT-TGATTCATAGCTCAT
1 TTTTCAGATTCATAACTCAT
1220771 TTTTCAGATTCATA
1 TTTTCAGATTCATA
1220785 GACCAATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (20 bp):
TTTTCAGATTCATAACTCAT
Found at i:1223564 original size:11 final size:11
Alignment explanation
Indices: 1223548--1223579 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1223538 AATGTGAATA
1223548 CATAAATACTT
1 CATAAATACTT
1223559 CATAAATACTT
1 CATAAATACTT
1223570 CATAAATACT
1 CATAAATACT
1223580 CGTTCCTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (11 bp):
CATAAATACTT
Found at i:1227617 original size:19 final size:19
Alignment explanation
Indices: 1227564--1227618 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
1227554 TCCTTTCTTT
* *
1227564 ATTTTCAGATTCATAACTA
1 ATTTTCAAATTCATAGCTA
** *
1227583 ATTTTCTTATTCATAGCTC
1 ATTTTCAAATTCATAGCTA
1227602 ATTTTCAAATTCATAGC
1 ATTTTCAAATTCATAGC
1227619 CCAATATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTCAAATTCATAGCTA
Found at i:1235332 original size:26 final size:26
Alignment explanation
Indices: 1235280--1235339 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
1235270 ATGTATTTAA
* *
1235280 AAAAAATAGGGACTAAAATCATATAAT
1 AAAAAA-AGGGACTAAAATAAAATAAT
1235307 AAAAAAA-GGACTAAAATAAAAGTAAT
1 AAAAAAAGGGACTAAAATAAAA-TAAT
*
1235333 TAAAAAA
1 AAAAAAA
1235340 CAAGTATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 12 0.41
26 11 0.38
27 6 0.21
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (26 bp):
AAAAAAAGGGACTAAAATAAAATAAT
Found at i:1237909 original size:130 final size:129
Alignment explanation
Indices: 1237622--1238011 Score: 430
Period size: 130 Copynumber: 3.0 Consensus size: 129
1237612 GTTAGATATA
* * **
1237622 GGAAA-TTTGATTCACTTCA-ATGCTCTCCAGGGAAGATTGATTCGGGGTTGACTTGCTTCACTA
1 GGAAACTTTGATTCACTTCACA-GCTCTTCAGGGAAGATTGAATCGATGTTGA-TTGCTTCACTA
** * * * * ** *
1237685 TTCTTCAGGGAAAATAAAATCTAGAAAAAAGGATATGCTCTAGTACT-TTTCAGGGTTGATCAAT
64 TTCTT-AAAGAATATCAAATATAGAAAAAAGGATATGCTCTACTACTCTTT-AGGGAAGATCAAA
1237749 TCT
127 TCT
* * * ** *
1237752 AGAAACTTTGATTCAGTTAACTA-CTCTTGGGGGAATATTGAATCGATGTTGATGTGCTTCACTA
1 GGAAACTTTGATTCACTTCAC-AGCTCTTCAGGGAAGATTGAATCGATGTTGAT-TGCTTCACTA
* *
1237816 TTCTTAAAGAATATCAAATATGGAAAAAAGGATATGTTCTACTACTCTTTAGGGAAGATCAAATC
64 TTCTTAAAGAATATCAAATATAGAAAAAAGGATATGCTCTACTACTCTTTAGGGAAGATCAAATC
1237881 T
129 T
* *
1237882 GGAAACTTTGATTCACTTCACAGCTCTTCAAGGAAGATTGAATCAATGTTGATTTGCTTCACTA-
1 GGAAACTTTGATTCACTTCACAGCTCTTCAGGGAAGATTGAATCGATGTTGA-TTGCTTCACTAT
* * * *
1237946 TCGTTTAAGAATATCAAATATAGAAAAAGGGATATGCTCCACTACTCTTTAGGGAAGATCAGATC
65 TC-TTAAAGAATATCAAATATAGAAAAAAGGATATGCTCTACTACTCTTTAGGGAAGATCAAATC
1238011 T
129 T
1238012 ATTAATCAAA
Statistics
Matches: 217, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
129 3 0.01
130 160 0.74
131 53 0.24
133 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (129 bp):
GGAAACTTTGATTCACTTCACAGCTCTTCAGGGAAGATTGAATCGATGTTGATTGCTTCACTATT
CTTAAAGAATATCAAATATAGAAAAAAGGATATGCTCTACTACTCTTTAGGGAAGATCAAATCT
Found at i:1239647 original size:18 final size:18
Alignment explanation
Indices: 1239599--1239640 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1239589 TCTTCGTTTC
1239599 TCTTGCATCGCCTATTCT
1 TCTTGCATCGCCTATTCT
1239617 TCTTGCATCGCCTATTCT
1 TCTTGCATCGCCTATTCT
1239635 TCTTGC
1 TCTTGC
1239641 TTTGCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.12, T:0.45
Consensus pattern (18 bp):
TCTTGCATCGCCTATTCT
Found at i:1240499 original size:113 final size:113
Alignment explanation
Indices: 1240287--1240499 Score: 250
Period size: 113 Copynumber: 1.9 Consensus size: 113
1240277 TTAGTTTTGC
* * * * *
1240287 ATTGTTTGGCTAGCTGAAGGAATTTATCCATAAAGCTAGGGCTTTTAACCAATTATTTTAGTGAA
1 ATTGTTTGGCTAGCTGAAGGAATATATCAATAAAGCTAAGGCTTTTAACCAATTACTTTAGAGAA
* * * * **
1240352 ATAGCTCAACTTTATTTTTTGTGTATATATATATTTATATATATATAT
66 ATAACTCAACTTTATTGTATATACATATATATATTTATATATATATAT
* *
1240400 ATTGTTTGGCTAGCTGAAGGAATATATCAATAGAATC-AAGGCTTTTAACCAATTACTTTAGAGG
1 ATTGTTTGGCTAGCTGAAGGAATATATCAATA-AAGCTAAGGCTTTTAACCAATTACTTTAGAGA
***
1240464 AATAACTCTGTTTTATTGTATATACATA-ATAATATT
65 AATAACTCAACTTTATTGTATATACATATAT-ATATT
1240500 AACTTCTTGG
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
112 2 0.02
113 77 0.94
114 3 0.04
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (113 bp):
ATTGTTTGGCTAGCTGAAGGAATATATCAATAAAGCTAAGGCTTTTAACCAATTACTTTAGAGAA
ATAACTCAACTTTATTGTATATACATATATATATTTATATATATATAT
Found at i:1242353 original size:194 final size:196
Alignment explanation
Indices: 1242024--1242414 Score: 768
Period size: 194 Copynumber: 2.0 Consensus size: 196
1242014 AGACTAAAAC
1242024 TATGGCTTGCAGATGTTTGCTCTCGATTCTCTCTCTCTGCAGGTTCATCAATAAATTTTGAACTT
1 TATGGCTTGCAGATGTTTGCTCTCGATTCTCTCTCTCTGCAGGTTCATCAATAAATTTTGAACTT
1242089 CTAGAAAATTTAGGTTTTCTGTCTTCAAAACATAGTAACCCTTTTGTGATGAGGTTTTGAACTTT
66 CTAGAAAATTTAGGTTTTCTGTCTTCAAAACATAGTAACCCTTTTGTGATGAGGTTTTGAACTTT
1242154 TAATCTTAAGG-CCCAGAATTCTCTATCGAGTGGTTGAAATCACCGT-ATGATATACACATGAAT
131 TAATCTTAAGGTCCCAGAATTCTCTATCGAGTGGTTGAAATCACCGTAATGATATACACATGAAT
1242217 T
196 T
1242218 TATGGCTTGCAGATGTTTGCTCTCGATTCTCTCTCTCTGCAGGTTCATCAATAAATTTTGAACTT
1 TATGGCTTGCAGATGTTTGCTCTCGATTCTCTCTCTCTGCAGGTTCATCAATAAATTTTGAACTT
1242283 CTAGAAAATTTAGGTTTTCTGTCTTCAAAACATAGTAACCCTTTTGTGATGAGGTTTTGAACTTT
66 CTAGAAAATTTAGGTTTTCTGTCTTCAAAACATAGTAACCCTTTTGTGATGAGGTTTTGAACTTT
1242348 TAATCTTAAGGTCCCAGAATTCTCTATCGAGTGGTTGAAATCACCGTAATGATATACACATGAAT
131 TAATCTTAAGGTCCCAGAATTCTCTATCGAGTGGTTGAAATCACCGTAATGATATACACATGAAT
1242413 T
196 T
1242414 T
1 T
1242415 TTAACACCCT
Statistics
Matches: 195, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
194 141 0.72
195 35 0.18
196 19 0.10
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (196 bp):
TATGGCTTGCAGATGTTTGCTCTCGATTCTCTCTCTCTGCAGGTTCATCAATAAATTTTGAACTT
CTAGAAAATTTAGGTTTTCTGTCTTCAAAACATAGTAACCCTTTTGTGATGAGGTTTTGAACTTT
TAATCTTAAGGTCCCAGAATTCTCTATCGAGTGGTTGAAATCACCGTAATGATATACACATGAAT
T
Found at i:1244312 original size:19 final size:19
Alignment explanation
Indices: 1244288--1244330 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1244278 TTTTTCAAAA
1244288 AGTTTCGATACTTTTTAAG
1 AGTTTCGATACTTTTTAAG
1244307 AGTTTCGATACTTTTTAAG
1 AGTTTCGATACTTTTTAAG
1244326 AGTTT
1 AGTTT
1244331 TGAAACTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (19 bp):
AGTTTCGATACTTTTTAAG
Found at i:1244809 original size:54 final size:54
Alignment explanation
Indices: 1244727--1244834 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
1244717 TGATTCTTGC
1244727 TAAACCTTTGAAAATCTAGGGAGTTTGTAAAGGTTATCTCTTTATCCTTGAAAA
1 TAAACCTTTGAAAATCTAGGGAGTTTGTAAAGGTTATCTCTTTATCCTTGAAAA
1244781 TAAACCTTTGAAAATCTAGGGAGTTTGTAAAGGTTATCTCTTTATCCTTGAAAA
1 TAAACCTTTGAAAATCTAGGGAGTTTGTAAAGGTTATCTCTTTATCCTTGAAAA
1244835 AGAAAGAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (54 bp):
TAAACCTTTGAAAATCTAGGGAGTTTGTAAAGGTTATCTCTTTATCCTTGAAAA
Found at i:1245694 original size:20 final size:20
Alignment explanation
Indices: 1245665--1245711 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1245655 ACAATTTTAT
1245665 TTTG-AAATCAAAAATGG-AC
1 TTTGAAAATC-AAAATGGAAC
*
1245684 TTTGAAAATCAAAATGGAAT
1 TTTGAAAATCAAAATGGAAC
1245704 TTTGAAAA
1 TTTGAAAA
1245712 AGTATTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30
Consensus pattern (20 bp):
TTTGAAAATCAAAATGGAAC
Found at i:1247964 original size:17 final size:16
Alignment explanation
Indices: 1247923--1247964 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
1247913 AAATAGCTTT
1247923 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
1247939 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
1247956 TAAAA-AATT
1 TAAAATAATT
1247965 GATATTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:1250277 original size:42 final size:41
Alignment explanation
Indices: 1250186--1250391 Score: 229
Period size: 42 Copynumber: 4.9 Consensus size: 41
1250176 CTATGCACCA
* *
1250186 GTAAGGCTTAACCTGTGCACA-AA-GAAGAGGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAACAAAG-GGA-CCT-GGGAAACT
* *
1250230 GTAAGGTTTATCCTTGCACACAACAAAGGGACCAGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAACAAAGGGACCTGGGAAACT
* *
1250272 GTAAGGCTTACCCTTTCACACAACAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAACAAAGGGACCTGGGAAACT
*
1250314 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAACAAAGGGACCTGGGAAACT
*
1250356 GTAAGGTTTACCTT-CACACACAGCAAAGGGACCTGG
1 GTAAGGCTTACCTTGCACACA-A-CAAAGGGACCTGG
1250392 TAATACTTCC
Statistics
Matches: 142, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
40 6 0.04
41 4 0.03
42 104 0.73
43 9 0.06
44 16 0.11
45 3 0.02
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.18
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAACAAAGGGACCTGGGAAACT
Found at i:1250333 original size:84 final size:84
Alignment explanation
Indices: 1250225--1250394 Score: 256
Period size: 84 Copynumber: 2.0 Consensus size: 84
1250215 GAGCCTAGGA
*
1250225 AAACTGTAAGGTTTATCCTTGCACACAACAAAGGGACCAGGGAAACTGTAAGGCTTACCCTTTCA
1 AAACTGTAAGGCTTATCCTTGCACACAACAAAGGGACCAGGGAAACTGTAAGGCTTA-CC-TTCA
1250290 CACA-A-CAAAGGGACCTGGT
64 CACACAGCAAAGGGACCTGGT
* * *
1250309 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGTTTACCTTCAC
1 AAACTGTAAGGCTTATCCTT-GCACACAACAAAGGGACCAGGGAAACTGTAAGGCTTACCTTCAC
1250373 ACACAGCAAAGGGACCTGGT
65 ACACAGCAAAGGGACCTGGT
1250393 AA
1 AA
1250395 TACTTCCTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
82 8 0.10
83 7 0.09
84 64 0.81
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (84 bp):
AAACTGTAAGGCTTATCCTTGCACACAACAAAGGGACCAGGGAAACTGTAAGGCTTACCTTCACA
CACAGCAAAGGGACCTGGT
Found at i:1251355 original size:29 final size:30
Alignment explanation
Indices: 1251322--1251385 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
1251312 CATTTTATAG
* *
1251322 AAATAGGAC-CCT-TTTTAAATTAATTTCTA
1 AAATA-GACACCTATTTCAAATTAATTACTA
*
1251351 AAATA-ACACCTATTTCGAATTAATTACTA
1 AAATAGACACCTATTTCAAATTAATTACTA
1251380 AAATAG
1 AAATAG
1251386 CACTTGTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 2 0.07
28 3 0.10
29 24 0.83
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (30 bp):
AAATAGACACCTATTTCAAATTAATTACTA
Found at i:1257644 original size:42 final size:41
Alignment explanation
Indices: 1257582--1257748 Score: 185
Period size: 42 Copynumber: 4.0 Consensus size: 41
1257572 GAGCCTAGGA
* * * *
1257582 AAACTATAAGGTTTATCCTTGCACACAACAAATGGACATGGG
1 AAACTGTAAGGCTTA-CCTTGCACACAACAAAAGGACCTGGG
*
1257624 AAACTGTAAGGCTTACCCTTGCACACAGA-AAAAGGACCTGGT
1 AAACTGTAAGGCTTA-CCTTGCACACA-ACAAAAGGACCTGGG
* *
1257666 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTT-GCACACAACAAAAGGACCTGGG
* *
1257708 AAACTGTAAGGTTTACCTT-CACACACAGCAAAGGGACCTGG
1 AAACTGTAAGGCTTACCTTGCACACA-A-CAAAAGGACCTGG
1257749 TAATACTTCT
Statistics
Matches: 109, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
40 6 0.06
41 4 0.04
42 98 0.90
43 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (41 bp):
AAACTGTAAGGCTTACCTTGCACACAACAAAAGGACCTGGG
Found at i:1257690 original size:84 final size:84
Alignment explanation
Indices: 1257582--1257751 Score: 227
Period size: 84 Copynumber: 2.0 Consensus size: 84
1257572 GAGCCTAGGA
* * *
1257582 AAACTATAAGGTTTATCCTTGCACACAACAAATGGACATGGGAAACTGTAAGGCTTACCCTT-GC
1 AAACTATAAGGCTTATCCTTGCACACAACAAAGGGACATGGGAAACTGTAAGGCTTA-CCTTCAC
1257646 ACACAGAAAAAGGACCTGGT
65 ACACAGAAAAAGGACCTGGT
* * * *
1257666 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGTTTACCTTCAC
1 AAACTATAAGGCTTATCCTT-GCACACAACAAAGGGACATGGGAAACTGTAAGGCTTACCTTCAC
* *
1257730 ACACAGCAAAGGGACCTGGT
65 ACACAGAAAAAGGACCTGGT
1257750 AA
1 AA
1257752 TACTTCTTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
83 8 0.11
84 67 0.89
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (84 bp):
AAACTATAAGGCTTATCCTTGCACACAACAAAGGGACATGGGAAACTGTAAGGCTTACCTTCACA
CACAGAAAAAGGACCTGGT
Found at i:1260323 original size:71 final size:72
Alignment explanation
Indices: 1260239--1260382 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
1260229 TATGAAAAAC
* *
1260239 TACATGCTAATAGAAAACTAACATACTAACATA-TTTTTTTAACAAAATAATTAGAATTTGTGAA
1 TACATGCTAATAGAAAACTAACATACTAACACATTTTTTTTAACAAAACAATTAGAATTTGTGAA
1260303 ACGAACA
66 ACGAACA
*
1260310 TACATGCTAATAGAAAACTAACATACTAACACATTTTTTTTAACAAAACAATTTGAATTTGTGAA
1 TACATGCTAATAGAAAACTAACATACTAACACATTTTTTTTAACAAAACAATTAGAATTTGTGAA
1260375 ACGAACA
66 ACGAACA
1260382 T
1 T
1260383 TATGAGTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 32 0.46
72 37 0.54
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (72 bp):
TACATGCTAATAGAAAACTAACATACTAACACATTTTTTTTAACAAAACAATTAGAATTTGTGAA
ACGAACA
Found at i:1261777 original size:29 final size:29
Alignment explanation
Indices: 1261744--1261834 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
1261734 AAATTTTGGC
1261744 TAGTGACCAAAATGAATAAA-TT-AAAAGTT
1 TAGTGACCAAAAT--ATAAACTTAAAAAGTT
* *
1261773 TAGTGGCTAAAATATAAACTTAAAAAGTT
1 TAGTGACCAAAATATAAACTTAAAAAGTT
* *
1261802 TAGTGGCTAAAATATAAACTTATGAAAAGTT
1 TAGTGACCAAAATATAAACTTA--AAAAGTT
1261833 TA
1 TA
1261835 ATGGCTAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.09
28 2 0.04
29 40 0.71
31 9 0.16
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (29 bp):
TAGTGACCAAAATATAAACTTAAAAAGTT
Found at i:1261833 original size:31 final size:29
Alignment explanation
Indices: 1261759--1261849 Score: 132
Period size: 29 Copynumber: 3.1 Consensus size: 29
1261749 ACCAAAATGA
1261759 ATAAA-TT-AAAAGTTTAGTGGCTAAAAT
1 ATAAACTTAAAAAGTTTAGTGGCTAAAAT
1261786 ATAAACTTAAAAAGTTTAGTGGCTAAAAT
1 ATAAACTTAAAAAGTTTAGTGGCTAAAAT
* *
1261815 ATAAACTTATGAAAAGTTTAATGGCTAAATT
1 ATAAACTTA--AAAAGTTTAGTGGCTAAAAT
1261846 ATAA
1 ATAA
1261850 TTTTCAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
27 5 0.09
28 2 0.03
29 29 0.50
31 22 0.38
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.33
Consensus pattern (29 bp):
ATAAACTTAAAAAGTTTAGTGGCTAAAAT
Found at i:1268223 original size:6 final size:6
Alignment explanation
Indices: 1268212--1268236 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1268202 ACGGCACGGT
1268212 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
1268237 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:1275938 original size:19 final size:19
Alignment explanation
Indices: 1275914--1275962 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1275904 GAATATCAAT
1275914 TTAAAATTAA-GCATCAAAA
1 TTAAAATTAATG-ATCAAAA
* *
1275933 TTAAAATTAATGATGAATA
1 TTAAAATTAATGATCAAAA
1275952 TTAAAATTAAT
1 TTAAAATTAAT
1275963 ATTATCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (19 bp):
TTAAAATTAATGATCAAAA
Found at i:1286069 original size:29 final size:30
Alignment explanation
Indices: 1286027--1286090 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
1286017 ACAAGCCTTA
* * *
1286027 GAAAAATTGGGGATCATTTCGTAAGTTTT-
1 GAAAAATTGGGGATAAATTCGTAAATTTTG
* *
1286056 GAAAAGTTTGGGATAAATTCGTAAATTTTG
1 GAAAAATTGGGGATAAATTCGTAAATTTTG
1286086 GAAAA
1 GAAAA
1286091 TGATGAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (30 bp):
GAAAAATTGGGGATAAATTCGTAAATTTTG
Found at i:1287317 original size:40 final size:40
Alignment explanation
Indices: 1287262--1287343 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1287252 TGCAGGTTTA
1287262 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1287302 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1287342 TA
1 TA
1287344 GCACTACGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1297840 original size:29 final size:30
Alignment explanation
Indices: 1297790--1297855 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
1297780 CCAAAATACA
1297790 TAAA-TTTTAAAAATTAAACTTTTAGTCCC
1 TAAACTTTTAAAAATTAAACTTTTAGTCCC
** *
1297819 T-AACTTTTAAAAATTACCCTTTTGGTCCC
1 TAAACTTTTAAAAATTAAACTTTTAGTCCC
1297848 TAAACTTT
1 TAAACTTT
1297856 CCAAACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 24 0.75
30 6 0.19
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (30 bp):
TAAACTTTTAAAAATTAAACTTTTAGTCCC
Found at i:1297908 original size:29 final size:30
Alignment explanation
Indices: 1297838--1297909 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
1297828 AAAATTACCC
*
1297838 TTTTGGTCCCTAAACTTTCCAAACTTTATA
1 TTTTGGTCACTAAACTTTCCAAACTTTATA
* *
1297868 ATTTAG-CTACTAAACTTT-CACAA-TTTATA
1 TTTTGGTC-ACTAAACTTTCCA-AACTTTATA
1297897 TTTTGGTCACTAA
1 TTTTGGTCACTAA
1297910 CCAAAATTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTTGGTCACTAAACTTTCCAAACTTTATA
Found at i:1300531 original size:61 final size:61
Alignment explanation
Indices: 1300429--1300550 Score: 174
Period size: 61 Copynumber: 2.0 Consensus size: 61
1300419 CATATTCAGT
* * * * *
1300429 TTAGCTCTATATTGTATATAAATGACACTTAGTACATATGGTGGGCACGACCTTATGTGTA
1 TTAGCACTATAGTGTATATAAAGGACACTTAGTACACATGGTGGGAACGACCTTATGTGTA
*
1300490 TTAGCACTATAGTGTATATAGAGGACACTTAGTGA-ACATGGTGGGAACGACCTTATGTGTA
1 TTAGCACTATAGTGTATATAAAGGACACTTAGT-ACACATGGTGGGAACGACCTTATGTGTA
1300551 ACGCTCTGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 53 0.98
62 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (61 bp):
TTAGCACTATAGTGTATATAAAGGACACTTAGTACACATGGTGGGAACGACCTTATGTGTA
Found at i:1306586 original size:23 final size:23
Alignment explanation
Indices: 1306551--1306596 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1306541 TATACCAATA
1306551 TGGGTATCTATACCAGC-AGGTGG
1 TGGGTATCTATACCA-CTAGGTGG
1306574 TGGGTAT-TGATACCACTAGGTGG
1 TGGGTATCT-ATACCACTAGGTGG
1306597 GTATCGATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.22, C:0.15, G:0.35, T:0.28
Consensus pattern (23 bp):
TGGGTATCTATACCACTAGGTGG
Found at i:1314953 original size:20 final size:21
Alignment explanation
Indices: 1314908--1314968 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
1314898 TTCCCCTGTG
1314908 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1314931 GGGGGAATCGGTTCCCT-AAA
1 GGGGGAATCGGTTCCCTCAAA
*
1314951 GGGGGAATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1314969 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 19 0.53
21 1 0.03
22 3 0.08
23 13 0.36
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1328268 original size:59 final size:59
Alignment explanation
Indices: 1328189--1328414 Score: 382
Period size: 59 Copynumber: 3.8 Consensus size: 59
1328179 CTAATCCGAG
*
1328189 TATGACACATAAGGTCGTGCCCACCATCTGCACTAGTTATACTTTAGTGTAGTCCCTAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGTAGTCCCTAA
*
1328248 TATGACACATAAGGTTGTGCCCACCATATGCACTAGTTATACTTTAGTGTAGTCCCTAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGTAGTCCCTAA
* * *
1328307 TATGACACATAAGGTTGTGCCCACCATATGCACTAGTTATACTTTAGTGCAAT-CCTGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGTAGTCCCT-AA
*
1328366 TATGACACATAAGGTCATGCCCACCATATGCACTAGTTATACTTTAGTG
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTG
1328415 AAATCCCGAA
Statistics
Matches: 160, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
58 3 0.02
59 157 0.98
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGTAGTCCCTAA
Found at i:1328420 original size:59 final size:59
Alignment explanation
Indices: 1328174--1328427 Score: 370
Period size: 59 Copynumber: 4.3 Consensus size: 59
1328164 ATATTCACCG
* *
1328174 TAGTGCTAATCC-GAGTATGACACATAAGGTCGTGCCCACCATCTGCACTAGTTATACTT
1 TAGTG-TAATCCTGAATATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTT
* *
1328233 TAGTGTAGTCCCT-AATATGACACATAAGGTTGTGCCCACCATATGCACTAGTTATACTT
1 TAGTGTAAT-CCTGAATATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTT
* *
1328292 TAGTGTAGTCCCT-AATATGACACATAAGGTTGTGCCCACCATATGCACTAGTTATACTT
1 TAGTGTAAT-CCTGAATATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTT
* *
1328351 TAGTGCAATCCTGAATATGACACATAAGGTCATGCCCACCATATGCACTAGTTATACTT
1 TAGTGTAATCCTGAATATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTT
* *
1328410 TAGTGAAATCCCGAATAT
1 TAGTGTAATCCTGAATAT
1328428 CCAACATGAT
Statistics
Matches: 182, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
58 6 0.03
59 176 0.97
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (59 bp):
TAGTGTAATCCTGAATATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTT
Found at i:1333512 original size:64 final size:65
Alignment explanation
Indices: 1333440--1333573 Score: 155
Period size: 65 Copynumber: 2.1 Consensus size: 65
1333430 ACCCTATTTT
* * * * * * * *
1333440 GAATGCATTTTGTGTACCGATGCACAG-CGATGCATCGTTGCACTCTTGA-TTTTATTGAAACAT
1 GAATGCATTCTATATACCGATGCACAGACCATACATCGATACACTCTTGACTCTT-TTGAAACAT
1333503 C
65 C
* *
1333504 GAATGCATTCTATATATCGATGCACAGACCATACATCGATATACTCTTGACTCTTTTGAAACATC
1 GAATGCATTCTATATACCGATGCACAGACCATACATCGATACACTCTTGACTCTTTTGAAACATC
1333569 GAATG
1 GAATG
1333574 TAATTAGTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
64 23 0.40
65 32 0.55
66 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (65 bp):
GAATGCATTCTATATACCGATGCACAGACCATACATCGATACACTCTTGACTCTTTTGAAACATC
Done.