Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 68 of 89
Found at i:16184817 original size:23 final size:23
Alignment explanation
Indices: 16184770--16184829 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
16184760 CCACTAGTTA
16184770 GTGCATCGATTCA--CCATGAAG
1 GTGCATCGATTCACTCCATGAAG
* * *
16184791 GTGCATCGATGCACTCCTTGAAT
1 GTGCATCGATTCACTCCATGAAG
16184814 GTGCATCGATTCACTC
1 GTGCATCGATTCACTC
16184830 TACTGTGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.36
23 21 0.64
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (23 bp):
GTGCATCGATTCACTCCATGAAG
Found at i:16187253 original size:64 final size:65
Alignment explanation
Indices: 16187167--16187319 Score: 166
Period size: 64 Copynumber: 2.4 Consensus size: 65
16187157 TGATATTTCT
* * * ** * * *
16187167 AATGCATTTTGTGTACCGATGCACAAGGCATGCATTGATGTACTCCTGAAT-ATTTTG-AACATC
1 AATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCCAGAATCA-TTTGAAACATC
16187230 G
65 G
* ** *
16187231 AATGCATTTTATGCATCAATGCACAAACCATGCATCGATGCACTCCAGGCTCATTTGAAACATTG
1 AATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCCAGAATCATTTGAAACATCG
*
16187296 AATGTATTTTATGCATCGATGCAC
1 AATGCATTTTATGCATCGATGCAC
16187320 CCCTATTGTA
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
64 44 0.60
65 29 0.40
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (65 bp):
AATGCATTTTATGCATCGATGCACAAACCATGCATCGATGCACTCCAGAATCATTTGAAACATCG
Found at i:16188463 original size:2 final size:2
Alignment explanation
Indices: 16188456--16188509 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
16188446 TTACTCTTAA
16188456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16188498 AT AT AT AT AT AT
1 AT AT AT AT AT AT
16188510 CAAAAGATAA
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):
AT
Found at i:16198036 original size:131 final size:131
Alignment explanation
Indices: 16197742--16198100 Score: 434
Period size: 131 Copynumber: 2.7 Consensus size: 131
16197732 GTTCTGGTCG
* * * *
16197742 TCTAAGGGTGACATGGCTCCTACTTGATGGGGAGATCT-AGTCGGTGGATGACACGGTTCCTACG
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGA-TCGGTGGATGACACGGTTCCTACG
* * * *
16197806 CGATGAAGACGACATGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACAAAT
65 CGATGAGGATGGCATGCCATCTTTA-G--GGATGATAACACGGTTCCTACGCGATGAGGACAAAT
16197871 GGTTA
127 GGTTA
* ** * * * *
16197876 TCTAGGGGTGACACAACTCTTACGTGATGAGGAGGTCTGATCGGTGGATGACATGGTTTCTACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGATCGGTGGATGACACGGTTCCTACGC
* ** *
16197941 GATGAGGATGGCATGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGACAGTTGTTT
66 GATGAGGATGGCATGCCATCTTTAGGGATGATAACACGGTTCCTACGCGATGAGGACAAATGGTT
16198006 A
131 A
* * * * *
16198007 TCTAAGGGTGACACGGCTCCTACGCGATGAAGAGGTATGGTCGATGGATGACACGGTTCCTACGC
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGATCGGTGGATGACACGGTTCCTACGC
*
16198072 GATGAGGATGG-AAGACCATCTTTAGGGAT
66 GATGAGGATGGCATG-CCATCTTTAGGGAT
16198101 TTGTTTCAAG
Statistics
Matches: 191, Mismatches: 32, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
130 2 0.01
131 114 0.60
133 1 0.01
134 73 0.38
135 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (131 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGATCGGTGGATGACACGGTTCCTACGC
GATGAGGATGGCATGCCATCTTTAGGGATGATAACACGGTTCCTACGCGATGAGGACAAATGGTT
A
Found at i:16198237 original size:66 final size:66
Alignment explanation
Indices: 16198102--16198248 Score: 179
Period size: 66 Copynumber: 2.2 Consensus size: 66
16198092 TTTAGGGATT
* * * * *
16198102 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATCCGTTTCAAGGGAAACGATCTTACATATTG
1 TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAATCCGTTTCAAGGGAAACAATCTCAAAGATTG
16198167 G
66 G
* * * *
16198168 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAA-CTTGTTTCAAGGGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAATC-CGTTTCAAGGGAAACAATCTCAAAGATT
*
16198232 TG
65 GG
*
16198234 TGTTTCAAGCGAAAT
1 TGTTTCAAGAGAAAT
16198249 AATATCAAAG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
65 1 0.01
66 68 0.99
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (66 bp):
TGTTTCAAGAGAAATTATCTCAAGAGAGACAAAATCCGTTTCAAGGGAAACAATCTCAAAGATTG
G
Found at i:16198238 original size:30 final size:30
Alignment explanation
Indices: 16198204--16198278 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
16198194 AGACAAAACT
*
16198204 TGTTTCAAGGGAAACAATCTCAAAGGTTTG
1 TGTTTCAAGGGAAACAATATCAAAGGTTTG
* *
16198234 TGTTTCAAGCGAAATAATATCAAAGGTTTG
1 TGTTTCAAGGGAAACAATATCAAAGGTTTG
16198264 TGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAAC
16198279 CGTCTTAAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (30 bp):
TGTTTCAAGGGAAACAATATCAAAGGTTTG
Found at i:16198510 original size:37 final size:37
Alignment explanation
Indices: 16198468--16198544 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
16198458 TGTGTTATGA
16198468 CTCAAGTAAGACGAA-ATTTG-TTTTAAGAGAAAACTGT
1 CTCAAGTAAGAC-AACATTTGTTTTTAAGA-AAAACTGT
* *
16198505 CTCAAGTGAGACAACATTTGTTTTTAAGAAAAATTGT
1 CTCAAGTAAGACAACATTTGTTTTTAAGAAAAACTGT
16198542 CTC
1 CTC
16198545 TAGCAAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 2 0.06
37 26 0.72
38 8 0.22
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (37 bp):
CTCAAGTAAGACAACATTTGTTTTTAAGAAAAACTGT
Found at i:16198917 original size:16 final size:15
Alignment explanation
Indices: 16198896--16198936 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
16198886 TTCATGTATC
*
16198896 ATGTATGTATGTGTTG
1 ATGTATGT-TGTATTG
16198912 ATGTATGCTTGTATTG
1 ATGTATG-TTGTATTG
16198928 ATGTATGTT
1 ATGTATGTT
16198937 TTCTCGATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.09
16 20 0.87
17 1 0.04
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.51
Consensus pattern (15 bp):
ATGTATGTTGTATTG
Found at i:16199976 original size:2 final size:2
Alignment explanation
Indices: 16199969--16199993 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16199959 CTTTATTGTG
16199969 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 T
16199994 TCTAGGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16206042 original size:3 final size:3
Alignment explanation
Indices: 16206034--16206067 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
16206024 TATGTAATTA
*
16206034 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16206068 TTTTTTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16209353 original size:21 final size:21
Alignment explanation
Indices: 16209327--16209368 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
16209317 AGAAAAGATT
16209327 TAGTCTAGCAATTAAGTTCAG
1 TAGTCTAGCAATTAAGTTCAG
16209348 TAGTCTAGCAATTAAGTTCAG
1 TAGTCTAGCAATTAAGTTCAG
16209369 GCATCAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TAGTCTAGCAATTAAGTTCAG
Found at i:16210944 original size:14 final size:14
Alignment explanation
Indices: 16210925--16210964 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
16210915 AACGAATATA
*
16210925 AACGAACACGAACG
1 AACGAACACAAACG
*
16210939 AACGAACATAAACG
1 AACGAACACAAACG
16210953 AAC-AACACAAAC
1 AACGAACACAAAC
16210965 ACACAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.57, C:0.28, G:0.12, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:16211239 original size:14 final size:14
Alignment explanation
Indices: 16211220--16211261 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
16211210 CCCTCTCTTG
16211220 GAACATAAATGAAC
1 GAACATAAATGAAC
16211234 GAACATAAATGAAC
1 GAACATAAATGAAC
* *
16211248 GAATATAAACGAAC
1 GAACATAAATGAAC
16211262 ATATAATCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:16212177 original size:20 final size:20
Alignment explanation
Indices: 16212152--16212202 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
16212142 ACTATTGTCA
16212152 AGGGTTTTAAGTTAGGCTTT
1 AGGGTTTTAAGTTAGGCTTT
16212172 AGGGTTTTAAGTTAGGCTTT
1 AGGGTTTTAAGTTAGGCTTT
16212192 AGGGTTTTAAG
1 AGGGTTTTAAG
16212203 GTTTATGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.04, G:0.31, T:0.43
Consensus pattern (20 bp):
AGGGTTTTAAGTTAGGCTTT
Found at i:16212205 original size:28 final size:28
Alignment explanation
Indices: 16212177--16212248 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
16212167 GCTTTAGGGT
16212177 TTTAAG-TTAGGCTTTAGGGTTTTAAGG
1 TTTAAGATTAGGCTTTAGGGTTTTAAGG
* * *
16212204 TTTATGATTATGATTTAGGGTTTTAA-G
1 TTTAAGATTAGGCTTTAGGGTTTTAAGG
*
16212231 -TTAAGTTTAGGCTTTAGG
1 TTTAAGATTAGGCTTTAGG
16212249 CTTTAGGGCT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 14 0.38
27 6 0.16
28 17 0.46
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (28 bp):
TTTAAGATTAGGCTTTAGGGTTTTAAGG
Found at i:16212659 original size:3 final size:3
Alignment explanation
Indices: 16212651--16212702 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
16212641 AATTCTAGCC
16212651 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16212699 AAT A
1 AAT A
16212703 TCCATGAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16217616 original size:20 final size:19
Alignment explanation
Indices: 16217580--16217629 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
16217570 AATGCAATCA
*
16217580 GTATCGATACCGAGAGGGAC
1 GTATCGATA-CGAGAGGAAC
* *
16217600 GTATCGATACTATGAGGAAG
1 GTATCGATACGA-GAGGAAC
16217620 GTATCGATAC
1 GTATCGATAC
16217630 CATTAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (19 bp):
GTATCGATACGAGAGGAAC
Found at i:16217792 original size:14 final size:14
Alignment explanation
Indices: 16217773--16217800 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16217763 TAGAAAAGTT
16217773 AATATTAGTTACTC
1 AATATTAGTTACTC
16217787 AATATTAGTTACTC
1 AATATTAGTTACTC
16217801 TTGAGTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
AATATTAGTTACTC
Found at i:16218133 original size:57 final size:57
Alignment explanation
Indices: 16218066--16218344 Score: 479
Period size: 57 Copynumber: 4.9 Consensus size: 57
16218056 TGGCACTAAA
*
16218066 TGTGTACAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTT
1 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTT
16218123 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTT
1 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTT
*
16218180 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTAT-AATTTTCCATATGGGCACTT
1 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAA-TTTCCGTATGGGCACTT
* *
16218237 TGTGTGCAAAAAGTTAAGGAATTCATACTAAGTGTATGAATTTCCATATGGGCACTT
1 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTT
* * *
16218294 TGTATGCAAAAAGTTAAGAGATTCATACTAAGTGTATGAATTTCTGTATGG
1 TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGG
16218345 AAACTATATG
Statistics
Matches: 212, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
56 2 0.01
57 208 0.98
58 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (57 bp):
TGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTT
Found at i:16218433 original size:57 final size:57
Alignment explanation
Indices: 16218366--16218573 Score: 362
Period size: 57 Copynumber: 3.6 Consensus size: 57
16218356 ATAGACATAA
16218366 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACG
1 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACG
* * * * * *
16218423 GAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAATTGCCCATATG
1 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACG
16218480 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACG
1 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACG
16218537 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTT
1 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTT
16218574 GCACACCAAG
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 139 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (57 bp):
GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACG
Found at i:16218512 original size:114 final size:114
Alignment explanation
Indices: 16218366--16218579 Score: 419
Period size: 114 Copynumber: 1.9 Consensus size: 114
16218356 ATAGACATAA
16218366 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACGGAAATTCA
1 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACGGAAATTCA
*
16218431 TACACTTAGTATGAATTTCTTAACTTTTTGCACACAAATTGCCCATATG
66 TACACTTAGTATAAATTTCTTAACTTTTTGCACACAAATTGCCCATATG
16218480 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACGGAAATTCA
1 GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACGGAAATTCA
16218545 TACACTTAGTATAAATTTCTTAACTTTTTGCACAC
66 TACACTTAGTATAAATTTCTTAACTTTTTGCACAC
16218580 CAAGTGCCAT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (114 bp):
GAAATTCATACACTTAGTATAAATTTCTTAACTTTTTTCGCACAAAGTGCTCATACGGAAATTCA
TACACTTAGTATAAATTTCTTAACTTTTTGCACACAAATTGCCCATATG
Found at i:16219043 original size:20 final size:19
Alignment explanation
Indices: 16218999--16219049 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
16218989 TGTTTTTAAT
16218999 GGTATCGATACCTTCCTCA
1 GGTATCGATACCTTCCTCA
*
16219018 TAGTATCGATACCTCTCTCTC-
1 -GGTATCGATACCT-TC-CTCA
16219039 GGTATCGATAC
1 GGTATCGATAC
16219050 TGATTGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 22 0.81
21 2 0.07
22 3 0.11
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (19 bp):
GGTATCGATACCTTCCTCA
Found at i:16219071 original size:21 final size:21
Alignment explanation
Indices: 16219044--16219092 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
16219034 CTCTCGGTAT
16219044 CGATACTGATTGCATTAGTAC
1 CGATACTGATTGCATTAGTAC
*
16219065 TGATACTGATTGCATTAGTAC
1 CGATACTGATTGCATTAGTAC
16219086 CGATACT
1 CGATACT
16219093 ACTCAACTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (21 bp):
CGATACTGATTGCATTAGTAC
Found at i:16225716 original size:21 final size:21
Alignment explanation
Indices: 16225690--16225758 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
16225680 TCAGTTGAGT
*
16225690 AGTATCGGTACTAATGCAATC
1 AGTATCAGTACTAATGCAATC
16225711 AGTATCAGTACTAATGCAATC
1 AGTATCAGTACTAATGCAATC
16225732 AGTATCAGTACTAATGCAATC
1 AGTATCAGTACTAATGCAATC
16225753 AGTATC
1 AGTATC
16225759 GATACCGAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (21 bp):
AGTATCAGTACTAATGCAATC
Found at i:16225779 original size:20 final size:21
Alignment explanation
Indices: 16225754--16225804 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
16225744 AATGCAATCA
16225754 GTATCGATACCGA-GA-GAGAG
1 GTATCGATACCGATGAGGA-AG
*
16225774 GTATCGATA-CTATGAGGAAG
1 GTATCGATACCGATGAGGAAG
16225794 GTATCGATACC
1 GTATCGATACC
16225805 ATTAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (21 bp):
GTATCGATACCGATGAGGAAG
Found at i:16226291 original size:57 final size:57
Alignment explanation
Indices: 16226217--16226443 Score: 355
Period size: 57 Copynumber: 4.0 Consensus size: 57
16226207 TTACCAAAAG
* *
16226217 GCACTTGGTGTGCAAAAAGTTAAGAAATTTATACTAAGTGTATGAATTTCCGTATGA
1 GCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGA
* * * * *
16226274 GCACTTTGTGCGAAAAAAGTTAAGAAATTTATACTAAGTGTATGAATTTCCATATGG
1 GCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGA
*
16226331 GCAATTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGA
1 GCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGA
* * *
16226388 GCACTTTGTGTGCAAAAAGTTAAGAGATCCATACTAATTGTATGAATTTCCGTATG
1 GCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
16226444 GGAACTATAT
Statistics
Matches: 155, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 155 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (57 bp):
GCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGA
Found at i:16241007 original size:23 final size:22
Alignment explanation
Indices: 16240957--16241007 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
16240947 AATAACAATC
16240957 TAATTTAAAATCCAATTACTTA
1 TAATTTAAAATCCAATTACTTA
* *
16240979 TTATTTAAAACTACCCA-TACTTA
1 TAATTTAAAA-T-CCAATTACTTA
16241002 TAATTT
1 TAATTT
16241008 GTAGTCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 9 0.38
23 12 0.50
24 3 0.12
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTTAAAATCCAATTACTTA
Found at i:16241589 original size:61 final size:61
Alignment explanation
Indices: 16241458--16241581 Score: 169
Period size: 61 Copynumber: 2.0 Consensus size: 61
16241448 GTAATGCTAA
* * * **
16241458 ACCTACACTATGCTTGCACTCTAGTACTGATCTGGATATACCACATAAGGTCGTGCCCACC
1 ACCTACACTAGGTTTACACTCTAGTACTGATCCAGATATACCACATAAGGTCGTGCCCACC
* *
16241519 ACCTACACTAGGTTTACACTCTAGTGCTGATCCAGATATGA-CACATAAGGTTGTGCCCACC
1 ACCTACACTAGGTTTACACTCTAGTACTGATCCAGATAT-ACCACATAAGGTCGTGCCCACC
16241580 AC
1 AC
16241582 TTGCACTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
61 54 0.98
62 1 0.02
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (61 bp):
ACCTACACTAGGTTTACACTCTAGTACTGATCCAGATATACCACATAAGGTCGTGCCCACC
Found at i:16244184 original size:55 final size:55
Alignment explanation
Indices: 16244117--16244741 Score: 829
Period size: 55 Copynumber: 11.4 Consensus size: 55
16244107 ATTTATTAAA
* * * * * *
16244117 TTGCATACATAGTTCCTATACGG-TAGTTCATCAACTCATGATGACTTTCATGGAT
1 TTGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGAT
* * * * *
16244172 TTGCACACATAGTGTCTGTACGGTTATTCATCAACTCATAACGAATTCTGTCGAT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
* * * ** *
16244227 TTGTACACATAGTGCCTGTATGATTATTCATCAACTCAAAATTAATTCCGTGGAT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
* * *
16244282 TTACACACATAGTGCTTGTACGGTTATTCATCAACTCCTGATGAATTCCGTGGAT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
**
16244337 TTGCACACATAGTGTTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
* * ** *
16244392 TTGAACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTATCGAT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
* *
16244447 TTGTACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGAT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
* * *
16244502 TTGCACACATAGTGCATGTACGGTTATTCATCAACTCAGGATGAATTCCATGGAT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
* * * * * *
16244557 TTGAACATATAGTGTCTGTACGATTATTCATCAACTTAAGATGAATTCCGTGGAT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
* * * * *
16244612 TTGTACACATAGTTCTTGTAGGGTTATTCATCAACTCATGATGAATTCCATGGAT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
*
16244667 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGGT
1 TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
*
16244722 TTGTACACATAGTGCCTGTA
1 TTGCACACATAGTGCCTGTA
16244742 GTACACATAG
Statistics
Matches: 497, Mismatches: 72, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
55 495 1.00
56 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (55 bp):
TTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAT
Found at i:16245109 original size:22 final size:21
Alignment explanation
Indices: 16245068--16245137 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 21
16245058 TGGCTAAATA
*
16245068 GTATCGATAC-C-ATACCATG
1 GTATCGATACTCTATACTATG
16245087 GTATCGATACTACTATACTATG
1 GTATCGATACT-CTATACTATG
* * *
16245109 GTACCGATATTCTA-A-TACG
1 GTATCGATACTCTATACTATG
16245128 GTATCGATAC
1 GTATCGATAC
16245138 CATTTTTGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 21 0.50
20 1 0.02
21 4 0.10
22 16 0.38
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (21 bp):
GTATCGATACTCTATACTATG
Found at i:16251404 original size:55 final size:55
Alignment explanation
Indices: 16251338--16251901 Score: 355
Period size: 55 Copynumber: 10.3 Consensus size: 55
16251328 ATTTATTAAA
* * *
16251338 TTGCACACATAGTGCCTATA-TGAAAGCTCATCAACTCATAATGATTTATGTTGAT
1 TTGCACACATAGTGCCTATACGGAAA-CTCATCAACTCATAATGAATTATGTGGAT
* * ** * * *
16251393 TTGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGAT
1 TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTATGTGGAT
* * ** * * * ** *
16251448 TTGCACACATAGTGCCTGTACTGTTATTCATCAACTCCTGATGAATTCCGTAGAT
1 TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTATGTGGAT
* * ** * * ***
16251503 TTGTACA-ATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGAT
1 TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTATGTGGAT
* * * * ** * * * *
16251557 TTGCACACATAATACGTGTACGGTTATTCATCAACTCATGATGAATTCTGTCGAT
1 TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTATGTGGAT
* * ** * * *
16251612 TTGCACACATAGTGTCTGTACGGTTATTCATCAACTCATGATGAATT-TCATGGAT
1 TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTAT-GTGGAT
* ** * ** *
16251667 TTGCACACATAGTGCCTATACAGTTATTCATCAACTCAGGATGAATTTTGTGGAT
1 TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTATGTGGAT
* * * * ** * ** *
16251722 TTGAACACATAGTGTCTGTACAGTTATTCATCAACTCAGGATGAATTTTGTGGAT
1 TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTATGTGGAT
* * ** * * **
16251777 TTGTACACATAGT-CCTATAGGGTTATTCATCAACTCATGATGAATTCCGTGGAT
1 TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTATGTGGAT
* ** * * **
16251831 TCGCACACATAGTGCCTATACGGTTA-TTATCAACTCATGATGAATTCCGTGGAT
1 TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTATGTGGAT
* *
16251885 TTGCATATATAGTGCCT
1 TTGCACACATAGTGCCT
16251902 GTAGTACACA
Statistics
Matches: 448, Mismatches: 56, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
54 136 0.30
55 309 0.69
56 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (55 bp):
TTGCACACATAGTGCCTATACGGAAACTCATCAACTCATAATGAATTATGTGGAT
Found at i:16251803 original size:219 final size:218
Alignment explanation
Indices: 16251365--16251901 Score: 729
Period size: 219 Copynumber: 2.5 Consensus size: 218
16251355 ATATGAAAGC
* * * *
16251365 TCATCAACTCATAATGATTTATGTTGATTTGCACACATAGTGCTTGTACGGTTATTCATCAACTC
1 TCATCAACTCATGATGAATTCTGTCGATTTGCACACATAGTGC-TGTACGGTTATTCATCAACTC
* * **
16251430 ATGATGAA-TTCTGTGGATTTGCACACATAGTGCCTGTACTGTTATTCATCAACTCCTGATGAAT
65 ATGATGAATTTC-GTGGATTTGCACACATAGTGCCTATACAGTTATTCATCAACTCAGGATGAAT
* * *
16251494 TCCGTAGATTTGTACAATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTT
129 TCCGTAGATTTGAACAATAGTGCCTGTACAGTTATTCATCAACTCAGGATGAATTCCATGGATTT
* *
16251559 GCACACATAATACGTGTACGGTTAT
194 GCACACATAATACCTATACGGTTAT
16251584 TCATCAACTCATGATGAATTCTGTCGATTTGCACACATAGTGTCTGTACGGTTATTCATCAACTC
1 TCATCAACTCATGATGAATTCTGTCGATTTGCACACATAGTG-CTGTACGGTTATTCATCAACTC
*
16251649 ATGATGAATTTCATGGATTTGCACACATAGTGCCTATACAGTTATTCATCAACTCAGGATGAATT
65 ATGATGAATTTCGTGGATTTGCACACATAGTGCCTATACAGTTATTCATCAACTCAGGATGAATT
** * * ***
16251714 TTGTGGATTTGAACACATAGTGTCTGTACAGTTATTCATCAACTCAGGATGAATTTTGTGGATTT
130 CCGTAGATTTGAACA-ATAGTGCCTGTACAGTTATTCATCAACTCAGGATGAATTCCATGGATTT
* * *
16251779 GTACACATAGT-CCTATAGGGTTAT
194 GCACACATAATACCTATACGGTTAT
* * * *
16251803 TCATCAACTCATGATGAATTCCGTGGATTCGCACACATAGTGCCTATACGGTTATT-ATCAACTC
1 TCATCAACTCATGATGAATTCTGTCGATTTGCACACATAGTG-CTGTACGGTTATTCATCAACTC
* * *
16251867 ATGATGAATTCCGTGGATTTGCATATATAGTGCCT
65 ATGATGAATTTCGTGGATTTGCACACATAGTGCCT
16251902 GTAGTACACA
Statistics
Matches: 282, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
218 39 0.14
219 187 0.66
220 56 0.20
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (218 bp):
TCATCAACTCATGATGAATTCTGTCGATTTGCACACATAGTGCTGTACGGTTATTCATCAACTCA
TGATGAATTTCGTGGATTTGCACACATAGTGCCTATACAGTTATTCATCAACTCAGGATGAATTC
CGTAGATTTGAACAATAGTGCCTGTACAGTTATTCATCAACTCAGGATGAATTCCATGGATTTGC
ACACATAATACCTATACGGTTAT
Found at i:16251839 original size:274 final size:272
Alignment explanation
Indices: 16251365--16251904 Score: 778
Period size: 274 Copynumber: 2.0 Consensus size: 272
16251355 ATATGAAAGC
* * *
16251365 TCATCAACTCATAATGATTTATGTTGATTTGCACACATAGTGCTTGTACGGTTATTCATCAACTC
1 TCATCAACTCATAATGATTTATG-TGATTTGCACACATAGTGCCTATACAGTTATTCATCAACTC
* * * **
16251430 ATGATGAATTCTGTGGATTTGCACACATAGTGCCTGTACTGTTATTCATCAACTCCTGATGAATT
65 AGGATGAATTCTGTGGATTTGAACACATAGTGCCTGTACAGTTATTCATCAACTCAGGATGAATT
* *
16251495 CCGTAGATTTGTACAATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTTG
130 CCGTAGATTTGTACAATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCATGGATTCG
* * *
16251560 CACACATAATACGTGTACGGTTATTCATCAACTCATGATGAATTCTGTCGATTTGCACACATAGT
195 CACACATAATACCTATACGGTTATT-ATCAACTCATGATGAATTCCGTCGATTTGCACACATAGT
*
16251625 GTCTGTACGGTTAT
259 GCCTGTACGGTTAT
*
16251639 TCATCAACTCATGATGAATTTCATG-GATTTGCACACATAGTGCCTATACAGTTATTCATCAACT
1 TCATCAACTCATAATG-ATTT-ATGTGATTTGCACACATAGTGCCTATACAGTTATTCATCAACT
* *
16251703 CAGGATGAATTTTGTGGATTTGAACACATAGTGTCTGTACAGTTATTCATCAACTCAGGATGAAT
64 CAGGATGAATTCTGTGGATTTGAACACATAGTGCCTGTACAGTTATTCATCAACTCAGGATGAAT
** * * *
16251768 TTTGTGGATTTGTACACATAGT-CCTATAGGGTTATTCATCAACTCATGATGAATTCCGTGGATT
129 TCCGTAGATTTGTACA-ATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * * * *
16251832 CGCACACATAGTGCCTATACGGTTATTATCAACTCATGATGAATTCCGTGGATTTGCATATATAG
193 CGCACACATAATACCTATACGGTTATTATCAACTCATGATGAATTCCGTCGATTTGCACACATAG
16251897 TGCCTGTA
258 TGCCTGTA
16251905 GTACACATAG
Statistics
Matches: 236, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
273 41 0.17
274 183 0.78
275 9 0.04
276 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (272 bp):
TCATCAACTCATAATGATTTATGTGATTTGCACACATAGTGCCTATACAGTTATTCATCAACTCA
GGATGAATTCTGTGGATTTGAACACATAGTGCCTGTACAGTTATTCATCAACTCAGGATGAATTC
CGTAGATTTGTACAATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCATGGATTCGC
ACACATAATACCTATACGGTTATTATCAACTCATGATGAATTCCGTCGATTTGCACACATAGTGC
CTGTACGGTTAT
Found at i:16252299 original size:19 final size:22
Alignment explanation
Indices: 16252248--16252301 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 22
16252238 TACCCCTACC
16252248 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACTACTATACT
*
16252270 ATGGT-TCCGATA-TTCTA-A-T
1 ATGGTAT-CGATACTACTATACT
16252289 ATGGTATCGATAC
1 ATGGTATCGATAC
16252302 CATTTTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 11 0.39
20 2 0.07
21 5 0.18
22 10 0.36
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (22 bp):
ATGGTATCGATACTACTATACT
Found at i:16253894 original size:30 final size:30
Alignment explanation
Indices: 16253838--16253894 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
16253828 GGAAATTATA
* *
16253838 CTTTTGGTCCTCAAACTTTTGAAAACTACC
1 CTTTTAGTCCTCAAACTTTTCAAAACTACC
* *
16253868 CTTTTAGTCCTTAAACTTTTCCAAACT
1 CTTTTAGTCCTCAAACTTTTCAAAACT
16253895 TTATACTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.40
Consensus pattern (30 bp):
CTTTTAGTCCTCAAACTTTTCAAAACTACC
Found at i:16254581 original size:2 final size:2
Alignment explanation
Indices: 16254574--16254606 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16254564 AAACCATTTA
16254574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16254607 CACTATTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16256026 original size:39 final size:39
Alignment explanation
Indices: 16255983--16256063 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
16255973 AGCAGTTTGC
*
16255983 ACTACCTTCAAAGAAGTATTATTCTGTATTAATCTACAT
1 ACTACCTTCAAAGAAGTATTATTATGTATTAATCTACAT
16256022 ACTACCTTCAAAGAAGTATTATTATGTATTAATCTACAT
1 ACTACCTTCAAAGAAGTATTATTATGTATTAATCTACAT
16256061 ACT
1 ACT
16256064 TAAAAATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (39 bp):
ACTACCTTCAAAGAAGTATTATTATGTATTAATCTACAT
Found at i:16256983 original size:24 final size:26
Alignment explanation
Indices: 16256937--16256991 Score: 87
Period size: 24 Copynumber: 2.2 Consensus size: 26
16256927 AAAAAAGTAA
16256937 AAATTTACAGTATTCATAAGTAAAAC
1 AAATTTACAGTATTCATAAGTAAAAC
*
16256963 AAATTT-CAG-ATTCATATGTAAAAC
1 AAATTTACAGTATTCATAAGTAAAAC
16256987 AAATT
1 AAATT
16256992 ACAACCTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 19 0.68
25 3 0.11
26 6 0.21
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (26 bp):
AAATTTACAGTATTCATAAGTAAAAC
Found at i:16257547 original size:32 final size:32
Alignment explanation
Indices: 16257501--16257569 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
16257491 GAGCCAACCA
*
16257501 AAGGGAATGCTTTGGGGCCTATAGGCCTACCT
1 AAGGGAATGCTTTGGGGCCTATAGGCCTACCC
*
16257533 AAGGGAATGTTTTGGGGCCTATAGGCCTACCC
1 AAGGGAATGCTTTGGGGCCTATAGGCCTACCC
16257565 AAGGG
1 AAGGG
16257570 TATCCTTAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.23
Consensus pattern (32 bp):
AAGGGAATGCTTTGGGGCCTATAGGCCTACCC
Found at i:16265437 original size:81 final size:81
Alignment explanation
Indices: 16265305--16265466 Score: 288
Period size: 81 Copynumber: 2.0 Consensus size: 81
16265295 AACTCTTCCA
* *
16265305 AATAATCCACTCGTCCAAGCCTTGGAAAAGAAGACCAGAACAACAACAGATTTGCGATGGCTTTT
1 AATAATCCACTCATCCAAGCCTTGGAAAAGAAGACCAGAACAACAACAGATTTGCGATGACTTTT
16265370 TGAATGGGAACCTAAT
66 TGAATGGGAACCTAAT
*
16265386 AATAATCCACTCATCCAAGCCTTGGAAAATAAGACCAGAACAACAACAGATTTGCGATGACTTTT
1 AATAATCCACTCATCCAAGCCTTGGAAAAGAAGACCAGAACAACAACAGATTTGCGATGACTTTT
*
16265451 TGAATGGGAGCCTAAT
66 TGAATGGGAACCTAAT
16265467 CTTATTTGGT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (81 bp):
AATAATCCACTCATCCAAGCCTTGGAAAAGAAGACCAGAACAACAACAGATTTGCGATGACTTTT
TGAATGGGAACCTAAT
Found at i:16266135 original size:59 final size:59
Alignment explanation
Indices: 16266042--16266162 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 59
16266032 GGAGGTTTGG
* ** * * * * *
16266042 TTAGAGCGATATTATCGTGTTTGCCTTTTTATTGCGATTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCAAGTTTACATTTTCATTGCAACTAGGAGGGTTCGATAGGACAC
*
16266101 TTAGAGCCATATTATCAAGTTTACATTTTCATTGCAACTAGGAGGGTTCGTTAGGACAC
1 TTAGAGCCATATTATCAAGTTTACATTTTCATTGCAACTAGGAGGGTTCGATAGGACAC
16266160 TTA
1 TTA
16266163 TCCATCTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATTATCAAGTTTACATTTTCATTGCAACTAGGAGGGTTCGATAGGACAC
Found at i:16270132 original size:19 final size:20
Alignment explanation
Indices: 16270108--16270151 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
16270098 TAATTTAATC
*
16270108 GAATATATAAT-TTAAAATT
1 GAATATAAAATCTTAAAATT
16270127 GAATATAAAATCTTAAAATT
1 GAATATAAAATCTTAAAATT
*
16270147 TAATA
1 GAATA
16270152 ATACTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (20 bp):
GAATATAAAATCTTAAAATT
Found at i:16270259 original size:13 final size:13
Alignment explanation
Indices: 16270243--16270278 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
16270233 TAAGATTTTC
16270243 TTTTTGAAAATCA
1 TTTTTGAAAATCA
16270256 TTTTTG-AAATCA
1 TTTTTGAAAATCA
*
16270268 ATTTTGAAAAT
1 TTTTTGAAAAT
16270279 TACTCCTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:16272599 original size:21 final size:23
Alignment explanation
Indices: 16272553--16272599 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
16272543 GGGTATTGAC
**
16272553 ACACATTCAAGGAATGTATCGGT
1 ACACATTCAAGGAATGTATCAAT
16272576 ACACATTCAA-G-ATGTATCAAT
1 ACACATTCAAGGAATGTATCAAT
16272597 ACA
1 ACA
16272600 TAGAAAGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 1 0.05
23 10 0.45
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (23 bp):
ACACATTCAAGGAATGTATCAAT
Found at i:16275299 original size:160 final size:161
Alignment explanation
Indices: 16275035--16275356 Score: 637
Period size: 160 Copynumber: 2.0 Consensus size: 161
16275025 AAAGCATGAT
16275035 TTTAGCCATTTCTTCTAAAGTTCGATTTTTCCTATCAACAACTCTATTTTGTTGAGGGGTTCTAG
1 TTTAGCCATTTCTTCTAAAGTTCGATTTTTCCTATCAACAACTCTATTTTGTTGAGGGGTTCTAG
16275100 GTTCTGAAAAATTATGGCTAATCCCATTTGAATTACAAAAATCAGTAAATCCAAGATTTTAAAAT
66 GTTCTGAAAAATTATGGCTAATCCCATTTGAATTACAAAAATCAGTAAATCCAAGATTTTAAAAT
16275165 TCAGTACCATGATCACTCC-AACACTAGAAA
131 TCAGTACCATGATCACTCCTAACACTAGAAA
16275195 TTTAGCCATTTCTTCTAAAGTTCGATTTTTCCTATCAACAACTCTATTTTGTTGAGGGGTTCTAG
1 TTTAGCCATTTCTTCTAAAGTTCGATTTTTCCTATCAACAACTCTATTTTGTTGAGGGGTTCTAG
16275260 GTTCTGAAAAATTATGGCTAATCCCATTTGAATTACAAAAATCAGTAAATCCAAGATTTTAAAAT
66 GTTCTGAAAAATTATGGCTAATCCCATTTGAATTACAAAAATCAGTAAATCCAAGATTTTAAAAT
16275325 TCAGTACCATGATCACTCCTAACACTAGAAA
131 TCAGTACCATGATCACTCCTAACACTAGAAA
16275356 T
1 T
16275357 GGAGTAACCT
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 149 0.93
161 12 0.07
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (161 bp):
TTTAGCCATTTCTTCTAAAGTTCGATTTTTCCTATCAACAACTCTATTTTGTTGAGGGGTTCTAG
GTTCTGAAAAATTATGGCTAATCCCATTTGAATTACAAAAATCAGTAAATCCAAGATTTTAAAAT
TCAGTACCATGATCACTCCTAACACTAGAAA
Found at i:16278773 original size:19 final size:20
Alignment explanation
Indices: 16278749--16278792 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
16278739 TAATTTAATC
*
16278749 GAATATATAAT-TTAAAATT
1 GAATATAAAATCTTAAAATT
16278768 GAATATAAAATCTTAAAATT
1 GAATATAAAATCTTAAAATT
*
16278788 TAATA
1 GAATA
16278793 ATACTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (20 bp):
GAATATAAAATCTTAAAATT
Found at i:16283821 original size:24 final size:23
Alignment explanation
Indices: 16283766--16283810 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
16283756 TTTTTTATTT
*
16283766 AAAAAAAACAAAAAAGAGAAAGA
1 AAAAAAAACAAAAAAGACAAAGA
*
16283789 AAAACAAAACCAAAAAGACAAA
1 AAAA-AAAACAAAAAAGACAAA
16283811 ATATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (23 bp):
AAAAAAAACAAAAAAGACAAAGA
Found at i:16295090 original size:29 final size:31
Alignment explanation
Indices: 16295000--16295091 Score: 86
Period size: 29 Copynumber: 3.1 Consensus size: 31
16294990 TGGTAATATA
* * *
16295000 TAAAATTTTA-AAAAC-TACATTTTGGTCCC
1 TAAACTTTTACAAAACTTATATTTTGGTCAC
* * *
16295029 TCAACTTTTACAAAATTTATACTTTGG-CAAC
1 TAAACTTTTACAAAACTTATATTTTGGTC-AC
16295060 TAAAC-TTT-CAAAACTTATATTTTGGTCAC
1 TAAACTTTTACAAAACTTATATTTTGGTCAC
16295089 TAA
1 TAA
16295092 TCAAAACTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
29 28 0.56
30 9 0.18
31 13 0.26
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (31 bp):
TAAACTTTTACAAAACTTATATTTTGGTCAC
Found at i:16299940 original size:35 final size:33
Alignment explanation
Indices: 16299887--16299956 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 33
16299877 AATGGAATTG
*
16299887 TTTTAATATATAAATATTTATTATTTGTTTATTTA
1 TTTTAATATATAAATATTTA-T-TTAGTTTATTTA
* * *
16299922 TTTTAGTATCTAATTATTTATTTAGTTTATTTA
1 TTTTAATATATAAATATTTATTTAGTTTATTTA
16299955 TT
1 TT
16299957 CATTTGTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 13 0.42
34 1 0.03
35 17 0.55
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (33 bp):
TTTTAATATATAAATATTTATTTAGTTTATTTA
Found at i:16301074 original size:12 final size:12
Alignment explanation
Indices: 16301057--16301103 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
16301047 TTAGGTGCTG
16301057 GAAACAAGATAA
1 GAAACAAGATAA
16301069 GAAACAAGATAA
1 GAAACAAGATAA
* *
16301081 GAAACAAGTTTA
1 GAAACAAGATAA
16301093 -AAACAAGATAA
1 GAAACAAGATAA
16301104 ATAAAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.64, C:0.09, G:0.15, T:0.13
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:16305420 original size:10 final size:10
Alignment explanation
Indices: 16305406--16305455 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
16305396 AATTTTGGCT
*
16305406 TTTTTGTTTTT
1 TTTTT-TTTTG
16305417 TTTTTTTTTG
1 TTTTTTTTTG
**
16305427 CCTTTTTTTG
1 TTTTTTTTTG
*
16305437 TCTTTTTTTG
1 TTTTTTTTTG
16305447 TTTTTTTTT
1 TTTTTTTTT
16305456 TTTGTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 29 0.85
11 5 0.15
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:16305807 original size:12 final size:12
Alignment explanation
Indices: 16305790--16305836 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
16305780 TTAGGTGCTG
16305790 GAAACAAGATAA
1 GAAACAAGATAA
16305802 GAAACAAGATAA
1 GAAACAAGATAA
*
16305814 GAAACAAGATTA
1 GAAACAAGATAA
16305826 -AAACAAGATAA
1 GAAACAAGATAA
16305837 ATTAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
11 10 0.30
12 23 0.70
ACGTcount: A:0.66, C:0.09, G:0.15, T:0.11
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:16305833 original size:23 final size:24
Alignment explanation
Indices: 16305790--16305836 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
16305780 TTAGGTGCTG
16305790 GAAACAAGATAAGAAACAAGATAA
1 GAAACAAGATAAGAAACAAGATAA
*
16305814 GAAACAAGATTA-AAACAAGATAA
1 GAAACAAGATAAGAAACAAGATAA
16305837 ATTAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.66, C:0.09, G:0.15, T:0.11
Consensus pattern (24 bp):
GAAACAAGATAAGAAACAAGATAA
Found at i:16309565 original size:24 final size:24
Alignment explanation
Indices: 16309533--16309580 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16309523 TAAAGATGTC
*
16309533 ACACTGACTCTTTCTAACATTCTA
1 ACACTGACTCTTTATAACATTCTA
* *
16309557 ACACTGACTTTTTATAATATTCTA
1 ACACTGACTCTTTATAACATTCTA
16309581 CACAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (24 bp):
ACACTGACTCTTTATAACATTCTA
Found at i:16314307 original size:122 final size:121
Alignment explanation
Indices: 16314161--16314698 Score: 415
Period size: 122 Copynumber: 4.4 Consensus size: 121
16314151 GCAAGTGGCT
* * * *
16314161 ATATCTCTTCAATGTGGATGAGTAGTGTTATCTTCAACACCAAATTATCTCCATATT-ACCCCGA
1 ATATCTCTTCAATGTGGATGAGTAGTGTCATCTTCAACACCAAATTATCTCTAAATTGA-CCCAA
* * * *
16314225 CTTCCTTAATGAGAAGGAACATCGTGATATTCAACAAACAATTTATCCGAAAGAGACC
65 CTTCCTCAATGAGAAGGAACAT-GTAATATTCAACAAACAATTTACCCAAAAGAGACC
* * * *
16314283 ATATCTCTTCAATATGGATAAGTAGTGTCATCTTCAACACAAAATTATCTCTAGATTGACCCAAC
1 ATATCTCTTCAATGTGGATGAGTAGTGTCATCTTCAACACCAAATTATCTCTAAATTGACCCAAC
* * * * ** * * *
16314348 TTTCTCAATGAGAAGAAATAATGTAATCTTCAACAAATTATTTACCCAAAAGTGGCT
66 TTCCTCAATGAGAAGGAA-CATGTAATATTCAACAAACAATTTACCCAAAAGAGACC
* * * * *
16314405 AAATCTCTTCAATGTGGATGAGCAATGTCATCTTCAGCACCAAATTAACTCTAAATTGACCCAAC
1 ATATCTCTTCAATGTGGATGAGTAGTGTCATCTTCAACACCAAATTATCTCTAAATTGACCCAAC
* * * * * * * *
16314470 TTCCTCATTGAGAAGGAACAATATCATCTTTAACAAATAATTTA-CCGAAAGTA-TCC
66 TTCCTCAATGAGAAGGAAC-ATGTAATATTCAACAAACAATTTACCCAAAAG-AGACC
* * * ** * * * * * ***
16314526 AAATATCTTCAATGTGGATGAGGAAAGTCGTCTTCAACACCTAATTATCTCCAGATTAACTTGAC
1 ATATCTCTTCAATGTGGATGAGTAGTGTCATCTTCAACACCAAATTATCTCTAAATTGACCCAAC
** * * * * * *
16314591 TTCAACAATGAGAAGGATGGAC-T-TCATCTTCAACAAACAATTTACCCGAGAGTGGCC
66 TTCCTCAATGAGAAGGA---ACATGTAATATTCAACAAACAATTTACCCAAAAGAGACC
* * *
16314648 GA-ATCTCTTCAGTGTGGATGAGCAGTGTCAT-TTCCAACATCAAATTATCTC
1 -ATATCTCTTCAATGTGGATGAGTAGTGTCATCTT-CAACACCAAATTATCTC
16314699 CATGCAATCA
Statistics
Matches: 335, Mismatches: 70, Indels: 22
0.78 0.16 0.05
Matches are distributed among these distances:
121 94 0.28
122 235 0.70
123 4 0.01
124 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (121 bp):
ATATCTCTTCAATGTGGATGAGTAGTGTCATCTTCAACACCAAATTATCTCTAAATTGACCCAAC
TTCCTCAATGAGAAGGAACATGTAATATTCAACAAACAATTTACCCAAAAGAGACC
Found at i:16314655 original size:243 final size:244
Alignment explanation
Indices: 16314153--16314700 Score: 563
Period size: 243 Copynumber: 2.2 Consensus size: 244
16314143 AACAGCAAGC
* * * * * *
16314153 AAGTGGCTATATCTCTTCAATGTGGATGAGTAGTGTTATCTTCAACACCAAATTATCTCCATATT
1 AAGTGGCCAAATCTCTTCAATGTGGATGAGCAGTGTCATCTTCAACACCAAATTAACTCCAAATT
* * * *
16314218 ACCCCGACTTCCTTAATGAGAAGGAACATCGTGATATTCAACAAACAATTTATCCGAAAGAGACC
66 ACCCCAACTTCCTCAATGAGAAGGAACATCATCATATTCAACAAACAATTTATCCGAAAGAGACC
* * * ** * *
16314283 ATATCTCTTCAATATGGATAAGTAGTGTCATCTTCAACACAAAATTATCTCTAGATTGACCCAAC
131 AAATATCTTCAATATGGATAAGGAAAGTCATCTTCAACACAAAATTATCTCCAGATTAACCCAAC
* **
16314348 TTTCTCAATGAGAAGAAATAATGTAATCTTCAACAAATTATTTACCCAA
196 TTTCACAATGAGAAGAAATAATGTAATCTTCAACAAACAATTTACCCAA
* * * *
16314397 AAGTGGCTAAATCTCTTCAATGTGGATGAGCAATGTCATCTTCAGCACCAAATTAACTCTAAATT
1 AAGTGGCCAAATCTCTTCAATGTGGATGAGCAGTGTCATCTTCAACACCAAATTAACTCCAAATT
* * * *
16314462 GA-CCCAACTTCCTCATTGAGAAGGAACAAT-ATCATCTTTAACAAATAATTTA-CCGAAAGTA-
66 -ACCCCAACTTCCTCAATGAGAAGGAAC-ATCATCATATTCAACAAACAATTTATCCGAAAG-AG
* * * * ** **
16314523 TCCAAATATCTTCAATGTGGATGAGGAAAGTCGTCTTCAACACCTAATTATCTCCAGATTAACTT
128 ACCAAATATCTTCAATATGGATAAGGAAAGTCATCTTCAACACAAAATTATCTCCAGATTAACCC
* * * * *
16314588 GAC-TTCAACAATGAGAAG-GATGGACT-TCATCTTCAACAAACAATTTACCCGA
193 AACTTTC-ACAATGAGAAGAAAT--AATGTAATCTTCAACAAACAATTTACCCAA
* * * * *
16314640 GAGTGGCCGAATCTCTTCAGTGTGGATGAGCAGTGTCAT-TTCCAACATCAAATTATCTCCA
1 AAGTGGCCAAATCTCTTCAATGTGGATGAGCAGTGTCATCTT-CAACACCAAATTAACTCCA
16314701 TGCAATCAAA
Statistics
Matches: 249, Mismatches: 48, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
242 7 0.03
243 140 0.56
244 99 0.40
245 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (244 bp):
AAGTGGCCAAATCTCTTCAATGTGGATGAGCAGTGTCATCTTCAACACCAAATTAACTCCAAATT
ACCCCAACTTCCTCAATGAGAAGGAACATCATCATATTCAACAAACAATTTATCCGAAAGAGACC
AAATATCTTCAATATGGATAAGGAAAGTCATCTTCAACACAAAATTATCTCCAGATTAACCCAAC
TTTCACAATGAGAAGAAATAATGTAATCTTCAACAAACAATTTACCCAA
Found at i:16323063 original size:2 final size:2
Alignment explanation
Indices: 16323056--16323083 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16323046 TCAATCTACA
16323056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16323084 TTACGACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16323261 original size:13 final size:13
Alignment explanation
Indices: 16323238--16323275 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
16323228 AATGACGCGC
*
16323238 AATGAGCGTCATA
1 AATGCGCGTCATA
*
16323251 AATGCGTGTCATA
1 AATGCGCGTCATA
16323264 AATGCGCGTCAT
1 AATGCGCGTCAT
16323276 GAATTCATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:16325733 original size:22 final size:22
Alignment explanation
Indices: 16325706--16325750 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
16325696 GATTTAAATT
16325706 ATTATTCATTTAAAGAGTTACA
1 ATTATTCATTTAAAGAGTTACA
16325728 ATTATTCATTTAAAGAGTTACA
1 ATTATTCATTTAAAGAGTTACA
16325750 A
1 A
16325751 GATGCTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
ATTATTCATTTAAAGAGTTACA
Found at i:16325842 original size:22 final size:23
Alignment explanation
Indices: 16325817--16325860 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
16325807 TATTTCTAAA
16325817 TTTTAAAAATAAAAT-GATTTTC
1 TTTTAAAAATAAAATAGATTTTC
* *
16325839 TTTTGAAAGTAAAATAGATTTT
1 TTTTAAAAATAAAATAGATTTT
16325861 GAAAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (23 bp):
TTTTAAAAATAAAATAGATTTTC
Found at i:16328479 original size:162 final size:162
Alignment explanation
Indices: 16328232--16328570 Score: 527
Period size: 162 Copynumber: 2.1 Consensus size: 162
16328222 CGGTATTGAA
* * * *
16328232 ATGATAAAACTGGTAAAGCGCTACCAGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGA
1 ATGATAAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGA
*
16328297 CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTAAAAAAAT
66 CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATAC-TTTAAAAAAAT
* *
16328362 GTATCGATCCAAAACGATATACCAGGTAAAAAT
130 ATATCGATCCAAAACGATATAACAGGTAAAAAT
* * *
16328395 ATGATAAAACCGGTAAAACGTTACCAGATATATTGATAGTGTCGATACTTT-ATATAAGGATCGA
1 ATGATAAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGA
* ** *
16328459 CACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAAAAAAATA
66 CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAATA
*
16328524 TATCGATCCACAACGATATAACAGGTAAAAAT
131 TATCGATCCAAAACGATATAACAGGTAAAAAT
16328556 ATGATAAAACCGGTA
1 ATGATAAAACCGGTA
16328571 TCAAAATGAT
Statistics
Matches: 161, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
161 56 0.35
162 61 0.38
163 44 0.27
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (162 bp):
ATGATAAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGA
CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAATA
TATCGATCCAAAACGATATAACAGGTAAAAAT
Found at i:16328570 original size:20 final size:19
Alignment explanation
Indices: 16328547--16328592 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
16328537 CGATATAACA
16328547 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
16328567 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
16328587 -GTAAAA
1 GGTAAAA
16328593 CGATACCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 3 0.13
20 15 0.65
21 3 0.13
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:16330829 original size:21 final size:21
Alignment explanation
Indices: 16330803--16330867 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
16330793 AAGACAATCA
* *
16330803 AGAGTCGAAGAGAAATTTGAT
1 AGAGTCGAAGAGAAACTTGAG
16330824 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
16330845 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
16330866 AG
1 AG
16330868 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.09, G:0.31, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:16330943 original size:33 final size:33
Alignment explanation
Indices: 16330901--16330966 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
16330891 AAATAGATGG
*
16330901 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
16330934 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
16330967 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:16332738 original size:19 final size:19
Alignment explanation
Indices: 16332714--16332762 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
16332704 AATGTAGGGT
16332714 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
16332733 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTTA
16332752 TAATTTTGTAT
1 TAATTTTGTAT
16332763 GTAAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:16332773 original size:18 final size:19
Alignment explanation
Indices: 16332714--16332774 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
16332704 AATGTAGGGT
* **
16332714 TAATTTTGTATAAGATTTA
1 TAATTTTGTATATGAAATA
**
16332733 TAATTTTGTATATGATTTA
1 TAATTTTGTATATGAAATA
*
16332752 TAATTTTGTATGT-AAATA
1 TAATTTTGTATATGAAATA
16332770 TAATT
1 TAATT
16332775 ATGAGTGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 8 0.21
19 30 0.79
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATATGAAATA
Found at i:16334173 original size:200 final size:200
Alignment explanation
Indices: 16332996--16334154 Score: 1927
Period size: 200 Copynumber: 5.8 Consensus size: 200
16332986 AATTTACAAT
*
16332996 ATGGCAAACAGGGTGCAACCATAAAGTGTCGAT-C-TATATAAAAA-TGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
16333058 CGAAACCCAAAAGTATAATGTAATAGGTAA-TTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
16333122 ATGAGAGAATAGGTCT-AATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
16333186 AATGA
196 AATGA
*
16333191 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
16333256 CGAAACCCATAAGTATAACGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
16333321 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCAATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
*
16333386 AAAGA
196 AATGA
* * *
16333391 ATGGCAAACAGGGTGCAACAATAAAGTATCGATCCATATATAAAAAATGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
16333456 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
16333521 ATGAGATG-ATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
131 ATGAGA-GAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
16333585 GAATGA
195 GAATGA
* *
16333591 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCTATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
16333656 CGAAACCCAAAAGTATAATGTAATAGGTAGTTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
16333721 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
16333786 AATGA
196 AATGA
* *
16333791 ATGGCAAACATGGTGCAATAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * * *
16333856 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAGTATATCGATTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
16333921 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
16333986 AATGA
196 AATGA
* * *
16333991 ATGACAAACAGGGTGCAACCATAAAGTGTCGATACATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * * *
16334056 CAAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACTGGTATAAGTATACCTGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
16334121 ATGGGAGAATTGGTATATAAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTATCGACACT
16334155 GTTTAATGTT
Statistics
Matches: 908, Mismatches: 48, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
195 32 0.04
196 1 0.00
197 10 0.01
198 45 0.05
199 51 0.06
200 765 0.84
201 4 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:16335669 original size:12 final size:12
Alignment explanation
Indices: 16335647--16335698 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
16335637 CAAGCGGTCA
*
16335647 ATGAAGATGAAG
1 ATGACGATGAAG
*
16335659 CTGACGATGAAG
1 ATGACGATGAAG
16335671 ATGACGATGAAG
1 ATGACGATGAAG
*
16335683 ATGACGATGATG
1 ATGACGATGAAG
16335695 ATGA
1 ATGA
16335699 TGATCCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.40, C:0.08, G:0.33, T:0.19
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:16335702 original size:6 final size:6
Alignment explanation
Indices: 16335647--16335698 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
16335637 CAAGCGGTCA
* * * * *
16335647 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
16335695 ATGA
1 ATGA
16335699 TGATCCAAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.40, C:0.08, G:0.33, T:0.19
Consensus pattern (6 bp):
ATGAAG
Found at i:16346460 original size:183 final size:183
Alignment explanation
Indices: 16346118--16346869 Score: 1364
Period size: 183 Copynumber: 4.1 Consensus size: 183
16346108 AAGTTTTCAT
* *
16346118 ACTTTTTAATATTGTGTCGGTACTTTATATCCAGAATGGAAGAAAAATGTGTCGATACCTTTTCA
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
* *
16346183 AAAAGTGTCG--ATTGTAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATA
66 AAAAGTGTCGACATT-T--ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
*
16346246 TAATCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
128 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
*
16346302 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTTTCGATACCTTGTCA
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
16346367 AAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
66 AAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
*
16346432 CCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
131 CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
16346485 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
*
16346550 AAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAA
66 AAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
*
16346615 CCGGTATAAATATACCGGTTTTATGAGCAAATAGGTCTACAACCTATATCGAC
131 CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
16346668 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
* *
16346733 AAAAGTGTCGAAATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTGGTAATATAA
66 AAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
16346798 CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
131 CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
16346851 ACTTTTTAATATTGTGTCG
1 ACTTTTTAATATTGTGTCG
16346870 CTAATTTTAA
Statistics
Matches: 551, Mismatches: 15, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
183 475 0.86
184 72 0.13
185 1 0.00
186 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (183 bp):
ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
AAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
Found at i:16350323 original size:87 final size:87
Alignment explanation
Indices: 16350219--16350381 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
16350209 AAATAGGTCA
16350219 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
16350284 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
* * *
16350306 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
**
16350371 CTGGTTAAATA
66 CCCGTTAAATA
16350382 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACCTATTTTATT
Found at i:16350353 original size:23 final size:23
Alignment explanation
Indices: 16350303--16350347 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16350293 TACCTATTTT
* *
16350303 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
16350326 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
16350348 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:16352520 original size:136 final size:135
Alignment explanation
Indices: 16352290--16352560 Score: 481
Period size: 136 Copynumber: 2.0 Consensus size: 135
16352280 ACTATTAGTG
* *
16352290 AAAAATTAAAATAAGAGCATAAAATTCTTATCAGGCTACTGCATACTGAAAACTAAAATAAAAGC
1 AAAAAATAAAATAAGAGCATAAAATTCTTATCAGACTACTGCATACTGAAAACTAAAATAAAAGC
16352355 ATTAAACTAAGAGCAATAAACTAATTCGGGCATACTGCATTGAATGAGAATGGAACTATAAAGTT
66 ATTAAACTAAGAGCAATAAACTAATTCGGGCATACTGCATTGAATGAGAATGGAACTATAAAGTT
16352420 TATAA
131 TATAA
* *
16352425 AAAAAATAAAATAAGAGCATAAATATTCTTAT-ACGACTGCTGCATACTGAAAATTAAAATAAAA
1 AAAAAATAAAATAAGAGCATAAA-ATTCTTATCA-GACTACTGCATACTGAAAACTAAAATAAAA
16352489 GCATTAAACTAAGAGCAATAAACTAATTCGGGCATACTGCATTGAATGAGAATGGAACTATAAAG
64 GCATTAAACTAAGAGCAATAAACTAATTCGGGCATACTGCATTGAATGAGAATGGAACTATAAAG
16352554 TTTATAA
129 TTTATAA
16352561 TCAGACTGTT
Statistics
Matches: 130, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
135 23 0.18
136 107 0.82
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.25
Consensus pattern (135 bp):
AAAAAATAAAATAAGAGCATAAAATTCTTATCAGACTACTGCATACTGAAAACTAAAATAAAAGC
ATTAAACTAAGAGCAATAAACTAATTCGGGCATACTGCATTGAATGAGAATGGAACTATAAAGTT
TATAA
Found at i:16355882 original size:3 final size:3
Alignment explanation
Indices: 16355874--16355900 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16355864 GTGGTTTTTC
16355874 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
16355901 TTAATTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:16357035 original size:18 final size:18
Alignment explanation
Indices: 16357009--16357045 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16356999 ATTAACTTGT
*
16357009 TTCCTTTTTTCTTTTTTA
1 TTCCCTTTTTCTTTTTTA
16357027 TTCCCTTTTTCTTTTTTA
1 TTCCCTTTTTCTTTTTTA
16357045 T
1 T
16357046 CTATTGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (18 bp):
TTCCCTTTTTCTTTTTTA
Found at i:16360562 original size:39 final size:38
Alignment explanation
Indices: 16360461--16360598 Score: 108
Period size: 37 Copynumber: 3.7 Consensus size: 38
16360451 TTTGTCTTCA
* *
16360461 AATTTTTGTCTCACTCAAGACAGTTTCTTTCAAAATAG
1 AATTTTTGTCTCACTCGAGACAGTTTCTTTCAAAATAC
* * * * *
16360499 AA-TTCTATCTCACTGGAAATAGTTT-TTCCTCAAAA-AC
1 AATTTTTGTCTCACTCGAGACAGTTTCTT--TCAAAATAC
*
16360536 AATTTTTTGTCTCACTCGAGACAGTTTCTTTC-AGA-A-
1 AA-TTTTTGTCTCACTCGAGACAGTTTCTTTCAAAATAC
* * *
16360572 AATTTTTATCTCACTCGAAATAGTTTC
1 AATTTTTGTCTCACTCGAGACAGTTTC
16360599 CCTTGATTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
35 22 0.28
36 4 0.05
37 23 0.29
38 10 0.13
39 18 0.23
40 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (38 bp):
AATTTTTGTCTCACTCGAGACAGTTTCTTTCAAAATAC
Found at i:16360585 original size:35 final size:36
Alignment explanation
Indices: 16360461--16360598 Score: 111
Period size: 39 Copynumber: 3.8 Consensus size: 36
16360451 TTTGTCTTCA
* *
16360461 AATTTTTGTCTCACTC-AAGACAGTTTCTTTCAAAAT
1 AATTTTTATCTCACTCGAA-ACAGTTTCTTTCAAAAC
* * * *
16360497 AGAATTCTATCTCACTGGAAATAGTTT-TTCCTCAAAAAC
1 A-ATTTTTATCTCACTCGAAACAGTTTCTT--TC-AAAAC
* * *
16360536 AATTTTTTGTCTCACTCGAGACAGTTTCTTTCAGAA-
1 AA-TTTTTATCTCACTCGAAACAGTTTCTTTCAAAAC
*
16360572 AATTTTTATCTCACTCGAAATAGTTTC
1 AATTTTTATCTCACTCGAAACAGTTTC
16360599 CCTTGATTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 15
0.72 0.15 0.14
Matches are distributed among these distances:
35 22 0.28
36 5 0.06
37 20 0.25
38 7 0.09
39 23 0.29
40 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (36 bp):
AATTTTTATCTCACTCGAAACAGTTTCTTTCAAAAC
Found at i:16360722 original size:35 final size:36
Alignment explanation
Indices: 16360683--16360772 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
16360673 AAGCTTCCCG
* *
16360683 TCTCACTCGAGACAATTTCACTCGAA-TTTTTTTTA
1 TCTCACTCGAGACAATTTCACTCGAACTCTTTTATA
* * * * * *
16360718 TCTCACTTGAGATATTTTCCCTTGAACTCTTTTATG
1 TCTCACTCGAGACAATTTCACTCGAACTCTTTTATA
16360754 TCTCACTCGAGACAATTTC
1 TCTCACTCGAGACAATTTC
16360773 TCTTGAAACG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
35 21 0.49
36 22 0.51
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.42
Consensus pattern (36 bp):
TCTCACTCGAGACAATTTCACTCGAACTCTTTTATA
Found at i:16360915 original size:72 final size:70
Alignment explanation
Indices: 16360839--16360993 Score: 186
Period size: 71 Copynumber: 2.2 Consensus size: 70
16360829 CACTTGAGGC
* ** *
16360839 AAAATTTAATATCCCTTGAGATATTTTCCCTTCAAAATTTTTTGTCTCAC-TAGAGACAGTTTCT
1 AAAATTT-ATATCCCTTGAGATATTTT-CCTTCAAAAGTTTTCATCTCACTTA-AGACAGTTTCC
16360903 CTCGAAAA
63 CTCGAAAA
* * *
16360911 AAAATTGTATATCCCTTGAGATATTTTCGTTGAAAAGTTTTCATCTTACTTAAGACAGTTTCCCT
1 AAAATT-TATATCCCTTGAGATATTTTCCTTCAAAAGTTTTCATCTCACTTAAGACAGTTTCCCT
16360976 CGAAAA
65 CGAAAA
* *
16360982 CAAATTTTTATC
1 AAAATTTATATC
16360994 TAACTTGAGT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
70 5 0.07
71 39 0.54
72 27 0.38
73 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (70 bp):
AAAATTTATATCCCTTGAGATATTTTCCTTCAAAAGTTTTCATCTCACTTAAGACAGTTTCCCTC
GAAAA
Found at i:16361024 original size:71 final size:71
Alignment explanation
Indices: 16360892--16361026 Score: 159
Period size: 71 Copynumber: 1.9 Consensus size: 71
16360882 GTCTCACTAG
* * * *
16360892 AGACAGTTTCTCTCGAAAAAAAATTGTATATCCCTTGAGATATTTTCGTTGAAAAGTTTTCATCT
1 AGACAGTTTCCCTCGAAAAAAAATTGTATATCACTTGAGATATTTTCATTGAAAAGATTTCATCT
16360957 TACTTA
66 TACTTA
* * *
16360963 AGACAGTTTCCCTCGAAAACAAATT-TTTATCTAACTTGAG-TATTTTATATTGAAAA-ATTTCA
1 AGACAGTTTCCCTCGAAAAAAAATTGTATATC--ACTTGAGATATTTT-CATTGAAAAGATTTCA
16361025 TC
63 TC
16361027 CCACTCGAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
70 5 0.09
71 36 0.67
72 13 0.24
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (71 bp):
AGACAGTTTCCCTCGAAAAAAAATTGTATATCACTTGAGATATTTTCATTGAAAAGATTTCATCT
TACTTA
Found at i:16371831 original size:21 final size:21
Alignment explanation
Indices: 16371805--16371859 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
16371795 AATTTTATGA
16371805 AGGAGTATCGATATTCATTAC
1 AGGAGTATCGATATTCATTAC
16371826 AGGAGTATCGATATTCATTAC
1 AGGAGTATCGATATTCATTAC
16371847 AGGAGTATCGATA
1 AGGAGTATCGATA
16371860 CTTGGGACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (21 bp):
AGGAGTATCGATATTCATTAC
Found at i:16377050 original size:11 final size:11
Alignment explanation
Indices: 16377034--16377058 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16377024 CCAGACCGTA
16377034 CATAATTTTCC
1 CATAATTTTCC
16377045 CATAATTTTCC
1 CATAATTTTCC
16377056 CAT
1 CAT
16377059 CATCTATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (11 bp):
CATAATTTTCC
Found at i:16377981 original size:17 final size:17
Alignment explanation
Indices: 16377959--16378003 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
16377949 TTTACCTGAC
16377959 TTTAACACAATCTAGTT
1 TTTAACACAATCTAGTT
**
16377976 TTTAACATGATCTAGTT
1 TTTAACACAATCTAGTT
16377993 TTTAACACAAT
1 TTTAACACAAT
16378004 TTCCAGATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.42
Consensus pattern (17 bp):
TTTAACACAATCTAGTT
Found at i:16383733 original size:22 final size:22
Alignment explanation
Indices: 16383673--16383734 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
16383663 GATTCTATTT
* * *
16383673 TCAGTGTTATGACACTTTTGTA
1 TCAGTGTTAAGGCACTTTTATA
** * *
16383695 TCAGTGCGAATGTACTTTTATA
1 TCAGTGTTAAGGCACTTTTATA
16383717 TCAGTGTTAAGGCACTTT
1 TCAGTGTTAAGGCACTTT
16383735 AGTATTAGTA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (22 bp):
TCAGTGTTAAGGCACTTTTATA
Found at i:16385948 original size:17 final size:17
Alignment explanation
Indices: 16385926--16385989 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
16385916 ATTGGAGTAC
16385926 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
16385943 ACAAAAAG-AAGAAAA-
1 ACAAAAAGAAAGAAAAG
*
16385958 ATTCAAAAAAAGAAGAAAAG
1 A--CAAAAAGA-AAGAAAAG
*
16385978 AAAAAGAAGAAA
1 ACAAA-AAGAAA
16385990 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
15 1 0.03
16 7 0.18
17 14 0.37
18 5 0.13
19 10 0.26
20 1 0.03
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.03
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:16388858 original size:2 final size:2
Alignment explanation
Indices: 16388851--16388893 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
16388841 AGTTATTTTC
*
16388851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16388893 A
1 A
16388894 GTTATTATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16393684 original size:30 final size:30
Alignment explanation
Indices: 16393650--16393716 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
16393640 TGTTAATTTG
*
16393650 TCATTTATAAAGCTTAAATGAATTTATAAT
1 TCATTTATAAAGCTTAAATAAATTTATAAT
*
16393680 TCATTTATTAAGCTTAAATAAATTTATAAT
1 TCATTTATAAAGCTTAAATAAATTTATAAT
16393710 TCATTTA
1 TCATTTA
16393717 ATGGGAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (30 bp):
TCATTTATAAAGCTTAAATAAATTTATAAT
Found at i:16397693 original size:82 final size:82
Alignment explanation
Indices: 16397567--16398022 Score: 594
Period size: 82 Copynumber: 5.6 Consensus size: 82
16397557 GGCATCATGA
* * *
16397567 AATAGCTT-ATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTGGATTCAGT
1 AATAG-TTCATCATTCAATTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAAT
* **
16397631 TCAATCATGGCAGCATGC
65 TCAATCAAGGCAGCATAT
* *
16397649 AATAGTTTATCATT-AATCTTGATTCGATCATGGTATCATGCAATAATTCACCATTCGATTCAAT
1 AATAGTTCATCATTCAAT-TTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAAT
* *
16397713 TTAATCAAGGCAGCCTAT
65 TCAATCAAGGCAGCATAT
* * * * * *
16397731 AATAGATCATCATTCAATTTTATTTGATCGTGGTAGCATACAATAATTCATCATTCGATTCAATT
1 AATAGTTCATCATTCAATTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATT
* *
16397796 CAATC-ATGCTAGCATAC
66 CAATCAAGGC-AGCATAT
* *
16397813 AATAGTTCATCAGTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATT
1 AATAGTTCATCATTCAATTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATT
*
16397878 CAATCAAGGCATCATAT
66 CAATCAAGGCAGCATAT
* * * *
16397895 ATTAGTTCGTCATTCAATTTGATTCGATCATGGTAGCATGTAATAATTCACTATTCGATTCAATT
1 AATAGTTCATCATTCAATTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATT
*
16397960 CAATCAAGGTAGCATAT
66 CAATCAAGGCAGCATAT
* ** *
16397977 AATAGTTTATCATTCAATTTGATTTTATCATGGTAGCATGAAATAA
1 AATAGTTCATCATTCAATTTGATTCGATCATGGTAGCATGCAATAA
16398023 CCAATTTATC
Statistics
Matches: 323, Mismatches: 46, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
81 7 0.02
82 310 0.96
83 6 0.02
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36
Consensus pattern (82 bp):
AATAGTTCATCATTCAATTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATT
CAATCAAGGCAGCATAT
Found at i:16398012 original size:41 final size:41
Alignment explanation
Indices: 16397567--16398015 Score: 283
Period size: 41 Copynumber: 11.0 Consensus size: 41
16397557 GGCATCATGA
* * * *
16397567 AATAGCTT-ATCATTCAACTTGATTCGATCATGGTAGCATGC
1 AATAG-TTCATCATTCAATTTAATTCAATCATGGTAGCATAC
* * ** * * * *
16397608 AATAATTCACCATTGGATTCAGTTCAATCATGGCAGCATGC
1 AATAGTTCATCATTCAATTTAATTCAATCATGGTAGCATAC
* * * * *
16397649 AATAGTTTATCATT-AATCTTGATTCGATCATGGTATCATGC
1 AATAGTTCATCATTCAAT-TTAATTCAATCATGGTAGCATAC
* * * * * * * * *
16397690 AATAATTCACCATTCGATTCAATTTAATCAAGGCAGCCTAT
1 AATAGTTCATCATTCAATTTAATTCAATCATGGTAGCATAC
* * ** *
16397731 AATAGATCATCATTCAATTTTATTTGATCGTGGTAGCATAC
1 AATAGTTCATCATTCAATTTAATTCAATCATGGTAGCATAC
* * * *
16397772 AATAATTCATCATTCGATTCAATTCAATCATGCTAGCATAC
1 AATAGTTCATCATTCAATTTAATTCAATCATGGTAGCATAC
* * * * *
16397813 AATAGTTCATCAGTCAACTTGATTCGATCATGGTAGCATGC
1 AATAGTTCATCATTCAATTTAATTCAATCATGGTAGCATAC
* * * * * * * *
16397854 AATAATTCACCATTCGATTCAATTCAATCAAGGCATCATAT
1 AATAGTTCATCATTCAATTTAATTCAATCATGGTAGCATAC
* * * * **
16397895 ATTAGTTCGTCATTCAATTTGATTCGATCATGGTAGCATGT
1 AATAGTTCATCATTCAATTTAATTCAATCATGGTAGCATAC
* * * * *
16397936 AATAATTCA-CTATTCGATTCAATTCAATCAAGGTAGCATAT
1 AATAGTTCATC-ATTCAATTTAATTCAATCATGGTAGCATAC
* * **
16397977 AATAGTTTATCATTCAATTTGATTTTATCATGGTAGCAT
1 AATAGTTCATCATTCAATTTAATTCAATCATGGTAGCAT
16398016 GAAATAACCA
Statistics
Matches: 297, Mismatches: 106, Indels: 10
0.72 0.26 0.02
Matches are distributed among these distances:
40 5 0.02
41 289 0.97
42 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36
Consensus pattern (41 bp):
AATAGTTCATCATTCAATTTAATTCAATCATGGTAGCATAC
Found at i:16399749 original size:17 final size:17
Alignment explanation
Indices: 16399727--16399759 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16399717 CTTTTCCCAA
16399727 TTCAATT-AATTTAGATT
1 TTCAATTCAA-TTAGATT
16399744 TTCAATTCAATTAGAT
1 TTCAATTCAATTAGAT
16399760 CTTTATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (17 bp):
TTCAATTCAATTAGATT
Found at i:16405506 original size:16 final size:17
Alignment explanation
Indices: 16405482--16405515 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
16405472 TTGTACACAT
*
16405482 CTAATTTAA-CAATTAA
1 CTAAATTAACCAATTAA
16405498 CTAAATTAACCAATTAA
1 CTAAATTAACCAATTAA
16405515 C
1 C
16405516 ATTTCAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (17 bp):
CTAAATTAACCAATTAA
Found at i:16406085 original size:41 final size:41
Alignment explanation
Indices: 16405999--16406470 Score: 274
Period size: 41 Copynumber: 11.6 Consensus size: 41
16405989 TTCAATCATT
* * * * * ***
16405999 TTCAATCTTGGTAGAATGCAATACTTCATCATTTAACTCGG
1 TTCAATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
*
16406040 TTCAATCATGGTAGCATGCAATATTTCACCATTCAATTTAA
1 TTCAATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
*
16406081 TTCAATCATGGTAACATG-AAGTAGTTT-ATCATTCAACTTT--
1 TTCAATCATGGTAGCATGCAA-TA-TTTCATCATTCAA-TTTAA
** * * *
16406121 TTTGATCATGGTAGCATGCAATAATTCAACATTCAATTCAA
1 TTCAATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
* * * ** *
16406162 TTCAATCAAGGCAACATATAATATTTCATCATTCAATTTGA
1 TTCAATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
** * * *
16406203 TTTGATCATGGTAGCATGCAATA-ATCACCATTCAATTCAA
1 TTCAATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
* ** * *** * *
16406243 TTCAATCATGGCAATATACAATAGCACATCATTCAACTTGA
1 TTCAATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
* * * ** *
16406284 TT-ATATCATTGTAGCATGCAATAATTCACCATTTGATTCAA
1 TTCA-ATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
* ** * * *
16406325 TTCAATCAAGGTAGCATATAATAGTTCATTATTCAATTTGA
1 TTCAATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
* * * * * ** *
16406366 TTCGATCATGGTAGCAAGTAAGAATTT-ACCATTTGATTCAA
1 TTCAATCATGGTAGCATGCAA-TATTTCATCATTCAATTTAA
* * * ** * *
16406407 TTCAATCAGGGCAACATATAATAGTTCATCATTCAATTTGA
1 TTCAATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
* *
16406448 TTCGATCATGGGAGCATGCAATA
1 TTCAATCATGGTAGCATGCAATA
16406471 ACCATCAGCA
Statistics
Matches: 312, Mismatches: 107, Indels: 24
0.70 0.24 0.05
Matches are distributed among these distances:
39 4 0.01
40 61 0.20
41 237 0.76
42 10 0.03
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (41 bp):
TTCAATCATGGTAGCATGCAATATTTCATCATTCAATTTAA
Found at i:16406359 original size:82 final size:82
Alignment explanation
Indices: 16406044--16406471 Score: 499
Period size: 82 Copynumber: 5.2 Consensus size: 82
16406034 ACTCGGTTCA
* * * * * *
16406044 ATCATGGTAGCATGCAATATTTCACCATTCAATTTAATTCAATCATGGTAACATGA-AGTAGTTT
1 ATCATGGTAGCATGCAATAATTCACCATTCAATTCAATTCAATCAAGGCAACAT-ATAATAGTTC
16406108 ATCATTCAACTTT--TT-T
65 ATCATTCAA-TTTGATTCT
* *
16406124 GATCATGGTAGCATGCAATAATTCAACATTCAATTCAATTCAATCAAGGCAACATATAATATTTC
1 -ATCATGGTAGCATGCAATAATTCACCATTCAATTCAATTCAATCAAGGCAACATATAATAGTTC
16406189 ATCATTCAATTTGATT-T
65 ATCATTCAATTTGATTCT
* * * **
16406206 GATCATGGTAGCATGCAATAA-TCACCATTCAATTCAATTCAATCATGGCAATATACAATAGCAC
1 -ATCATGGTAGCATGCAATAATTCACCATTCAATTCAATTCAATCAAGGCAACATATAATAGTTC
* *
16406270 ATCATTCAACTTGATTAT
65 ATCATTCAATTTGATTCT
* ** * *
16406288 ATCATTGTAGCATGCAATAATTCACCATTTGATTCAATTCAATCAAGGTAGCATATAATAGTTCA
1 ATCATGGTAGCATGCAATAATTCACCATTCAATTCAATTCAATCAAGGCAACATATAATAGTTCA
* *
16406353 TTATTCAATTTGATTCG
66 TCATTCAATTTGATTCT
* * * * ** *
16406370 ATCATGGTAGCAAGTAAGAATTTACCATTTGATTCAATTCAATCAGGGCAACATATAATAGTTCA
1 ATCATGGTAGCATGCAATAATTCACCATTCAATTCAATTCAATCAAGGCAACATATAATAGTTCA
*
16406435 TCATTCAATTTGATTCG
66 TCATTCAATTTGATTCT
*
16406452 ATCATGGGAGCATGCAATAA
1 ATCATGGTAGCATGCAATAA
16406472 CCATCAGCAT
Statistics
Matches: 299, Mismatches: 43, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
80 4 0.01
81 133 0.44
82 162 0.54
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (82 bp):
ATCATGGTAGCATGCAATAATTCACCATTCAATTCAATTCAATCAAGGCAACATATAATAGTTCA
TCATTCAATTTGATTCT
Found at i:16413625 original size:18 final size:17
Alignment explanation
Indices: 16413604--16413641 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
16413594 AATTATAAAG
*
16413604 TTATCCTAATATATATAA
1 TTATACTAATAT-TATAA
16413622 TTATACTAATATTATAA
1 TTATACTAATATTATAA
16413639 TTA
1 TTA
16413642 GTCTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATACTAATATTATAA
Found at i:16413669 original size:19 final size:17
Alignment explanation
Indices: 16413645--16413683 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
16413635 ATAATTAGTC
*
16413645 TTATAATAATAATTAATAA
1 TTATAAAAAT-ATTAA-AA
16413664 TTATAAAAATATTAAAA
1 TTATAAAAATATTAAAA
16413681 TTA
1 TTA
16413684 CTTAACATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTATAAAAATATTAAAA
Found at i:16414789 original size:3 final size:3
Alignment explanation
Indices: 16414772--16414827 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
16414762 TGTAAAATTG
16414772 TAA TAA TTAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TATA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
16414817 TAA TAA TAA TA
1 TAA TAA TAA TA
16414828 TTATAACAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:16415915 original size:66 final size:66
Alignment explanation
Indices: 16415838--16415962 Score: 223
Period size: 66 Copynumber: 1.9 Consensus size: 66
16415828 ACAAAACCAC
16415838 TAATAAATGAGGTTAGAAAAATCAACTCAGCCACTTTCATAGTTCATGTCACACCTTAATTACAA
1 TAATAAATGAGGTTAGAAAAATCAACTCAGCCACTTTCATAGTTCATGTCACACCTTAATTACAA
16415903 T
66 T
* **
16415904 TAATAAGTGAGGTTAGAAAAATCAACTCAGCCTTTTTCATAGTTCATGTCACACCTTAA
1 TAATAAATGAGGTTAGAAAAATCAACTCAGCCACTTTCATAGTTCATGTCACACCTTAA
16415963 CTTTCCCCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (66 bp):
TAATAAATGAGGTTAGAAAAATCAACTCAGCCACTTTCATAGTTCATGTCACACCTTAATTACAA
T
Found at i:16421728 original size:22 final size:22
Alignment explanation
Indices: 16421703--16421747 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16421693 CCAAAATAAC
*
16421703 ATTCGCAATAAACATCATATAT
1 ATTCACAATAAACATCATATAT
**
16421725 ATTCATGATAAACATCATATAT
1 ATTCACAATAAACATCATATAT
16421747 A
1 A
16421748 ATAACCAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (22 bp):
ATTCACAATAAACATCATATAT
Found at i:16422005 original size:26 final size:26
Alignment explanation
Indices: 16421955--16422005 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
16421945 GATCTGATGT
* * **
16421955 GGCAGTTTCTAGATGGTCTGGTCAGC
1 GGCAGTTTCTAGAAGATCTACTCAGC
16421981 GGCAGTTTCTAGAAGATCTACTCAG
1 GGCAGTTTCTAGAAGATCTACTCAG
16422006 TGCGTCTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (26 bp):
GGCAGTTTCTAGAAGATCTACTCAGC
Found at i:16422267 original size:26 final size:26
Alignment explanation
Indices: 16422224--16422274 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
16422214 GTTCTCCCAT
*
16422224 TTTATTTTTCAAGTTTTTGATTTTTAC
1 TTTATTTTTAAAGTTTTTG-TTTTTAC
16422251 TTTATTTTTAAAG-TTTTGTTTTTA
1 TTTATTTTTAAAGTTTTTGTTTTTA
16422275 AATATACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 5 0.22
27 12 0.52
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.69
Consensus pattern (26 bp):
TTTATTTTTAAAGTTTTTGTTTTTAC
Found at i:16431418 original size:24 final size:23
Alignment explanation
Indices: 16431373--16431419 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
16431363 AAGAAAAAAA
* *
16431373 TGAAAAACAAAACAACATAAATG
1 TGAAAAACAAAAAAAAATAAATG
*
16431396 TGAAAAAGAAAAAAAAATCAAATG
1 TGAAAAACAAAAAAAAAT-AAATG
16431420 CATTCCGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.68, C:0.09, G:0.11, T:0.13
Consensus pattern (23 bp):
TGAAAAACAAAAAAAAATAAATG
Found at i:16435138 original size:6 final size:7
Alignment explanation
Indices: 16435113--16435137 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16435103 GATATTGCTC
16435113 AAAAATA
1 AAAAATA
16435120 AAAAATA
1 AAAAATA
16435127 AAAAATA
1 AAAAATA
16435134 AAAA
1 AAAA
16435138 TTATCTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:16436441 original size:19 final size:20
Alignment explanation
Indices: 16436414--16436451 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
16436404 TGATTTTTTA
*
16436414 TTGAATTTT-AAAGGTATAT
1 TTGAATTTTCAAAGATATAT
*
16436433 TTGACTTTTCAAAGATATA
1 TTGAATTTTCAAAGATATA
16436452 ACTAAGAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (20 bp):
TTGAATTTTCAAAGATATAT
Found at i:16437367 original size:49 final size:49
Alignment explanation
Indices: 16437310--16437594 Score: 428
Period size: 49 Copynumber: 5.8 Consensus size: 49
16437300 GGTGCTAAAA
*
16437310 TAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCCATTAATGAAAGT
1 TAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCCACTAATGAAAGT
*
16437359 TAAATGCATAACGGTGCATTTAGGCATAATAGGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCCACTAATGAAAGT
* * *
16437408 TAAATGGATACCGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCCACTAATGAAAGT
* * *
16437457 TAAATGCATAATGGTGCATTTCGGCATAAAAAGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCCACTAATGAAAGT
* * * *
16437506 TAAATGCATAACGGGGTATTTCGGCATAAAAGGTGTCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCCACTAATGAAAGT
* *
16437555 TAAATGCATAATGGTGCATTTCA-GCATAAAAGGTGTCACT
1 TAAATGCATAACGGTGCATTT-AGGCATAAAAGGTGCCACT
16437595 CATGGTAGTC
Statistics
Matches: 216, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
49 216 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (49 bp):
TAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCCACTAATGAAAGT
Found at i:16455787 original size:5 final size:5
Alignment explanation
Indices: 16455777--16455976 Score: 330
Period size: 5 Copynumber: 39.8 Consensus size: 5
16455767 CTATATGTGT
16455777 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * * *
16455827 ATATA ATATA ATATA ATATA ATATA ATATG ATATG ATATG ATATG ATATG
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
16455877 ATAT- ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
16455926 ATATA ATATA ATATA ATATA ATATA ATATA ATATAA TATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATAT
16455977 TTTTTTGTAT
Statistics
Matches: 191, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
4 4 0.02
5 181 0.95
6 2 0.01
7 4 0.02
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:16458287 original size:2 final size:2
Alignment explanation
Indices: 16458282--16458308 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16458272 TACATTTTAT
16458282 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16458309 GAATCCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16458406 original size:16 final size:16
Alignment explanation
Indices: 16458385--16458417 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16458375 TACGTATATG
*
16458385 TATATTTTATTTGTTA
1 TATATTTTATTTATTA
16458401 TATATTTTATTTATTA
1 TATATTTTATTTATTA
16458417 T
1 T
16458418 TTTTGGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TATATTTTATTTATTA
Found at i:16458737 original size:17 final size:18
Alignment explanation
Indices: 16458707--16458744 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
16458697 TCATTTTTAG
16458707 TTTTTCATATTTTATTATT
1 TTTTTCATATTTTATT-TT
16458726 TTTTTC-TA-TTTATTTT
1 TTTTTCATATTTTATTTT
16458742 TTT
1 TTT
16458745 ATATTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 2 0.11
19 6 0.32
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCATATTTTATTTT
Found at i:16458740 original size:14 final size:14
Alignment explanation
Indices: 16458721--16458777 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
16458711 TCATATTTTA
*
16458721 TTATTTTTTTCTAT
1 TTATTTTTTTATAT
16458735 TTATTTTTTTATATT
1 TTATTTTTTTATA-T
*
16458750 TGTATTTTCATTT-TTT
1 T-TATTTT--TTTATAT
16458766 TTATTTTTTTAT
1 TTATTTTTTTAT
16458778 TTTCGCTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 3 0.08
14 13 0.36
15 8 0.22
16 8 0.22
17 1 0.03
18 3 0.08
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (14 bp):
TTATTTTTTTATAT
Found at i:16458746 original size:22 final size:21
Alignment explanation
Indices: 16458714--16458780 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 21
16458704 TAGTTTTTCA
* *
16458714 TATTTTATTATTTTTTTCTATT
1 TATTTTTTTATTTTTTTAT-TT
* *
16458736 TATTTTTTTATATTTGTATTT
1 TATTTTTTTATTTTTTTATTT
16458757 TCATTTTTTTTATTTTTTTATTT
1 T-A-TTTTTTTATTTTTTTATTT
16458780 T
1 T
16458781 CGCTTGTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.08
22 16 0.43
23 18 0.49
ACGTcount: A:0.16, C:0.03, G:0.01, T:0.79
Consensus pattern (21 bp):
TATTTTTTTATTTTTTTATTT
Found at i:16460616 original size:4 final size:4
Alignment explanation
Indices: 16460603--16460664 Score: 56
Period size: 4 Copynumber: 15.0 Consensus size: 4
16460593 GGTTTTTCTA
* *
16460603 ATTT ATTTT ATTT ATTT ATTT ATTCT -TTT ATTTT ATTC GTTT A-TT ATCTT
1 ATTT A-TTT ATTT ATTT ATTT ATT-T ATTT A-TTT ATTT ATTT ATTT AT-TT
16460653 ATTT ATTT ATTT
1 ATTT ATTT ATTT
16460665 TTTTGTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
3 4 0.08
4 31 0.65
5 13 0.27
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:16460657 original size:25 final size:26
Alignment explanation
Indices: 16460598--16460660 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
16460588 AACTTGGTTT
*
16460598 TTCTAATTTATTTTATTTATTTATTTA
1 TTCT-ATTTATTTTATTCATTTATTTA
*
16460625 TTCT-TTTATTTTATTCGTTTA-TTA
1 TTCTATTTATTTTATTCATTTATTTA
16460649 -TCTTATTTATTT
1 TTC-TATTTATTT
16460661 ATTTTTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.06
24 4 0.12
25 22 0.69
27 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (26 bp):
TTCTATTTATTTTATTCATTTATTTA
Found at i:16470709 original size:17 final size:17
Alignment explanation
Indices: 16470678--16470711 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16470668 AAAAAAACAA
*
16470678 AAAAAAAAATAAAAAAT
1 AAAAAAAAACAAAAAAT
16470695 AAAAAAAAACCAAAAAA
1 AAAAAAAAA-CAAAAAA
16470712 GGGAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAT
Found at i:16470709 original size:18 final size:18
Alignment explanation
Indices: 16470677--16470711 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16470667 AAAAAAAACA
*
16470677 AAAAAAAAAATAAAAAAT
1 AAAAAAAAAACAAAAAAT
*
16470695 AAAAAAAAACCAAAAAA
1 AAAAAAAAAACAAAAAA
16470712 GGGAAAAATG
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:0.89, C:0.06, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAAAAACAAAAAAT
Found at i:16472106 original size:110 final size:110
Alignment explanation
Indices: 16471908--16472272 Score: 506
Period size: 110 Copynumber: 3.4 Consensus size: 110
16471898 TCCCAATTTG
* * **
16471908 AGAGCCAATTTCAACTGCACAGTGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
*
16471973 CGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCATTT
66 CGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCATTC
16472018 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
* *
16472083 TGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCATTC
66 CGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCATTC
* * * *
16472128 AGAGTTAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
* ** * * *
16472193 CGAAGGGGTGGCTGGCTGTTAATAAACAA-TTTCCCAG-TTC---C
66 CGAAGGGGTGACTGATTGTCAACAAACAACTTT-TCAGTTTCATTC
** *
16472234 AGAGTCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
16472273 GGAGCAATAC
Statistics
Matches: 230, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
106 35 0.15
109 6 0.03
110 189 0.82
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (110 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
CGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCATTC
Found at i:16474644 original size:8 final size:8
Alignment explanation
Indices: 16474633--16474680 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
16474623 ATTGTTTCTT
16474633 TTATTTTA
1 TTATTTTA
16474641 TTATTTTA
1 TTATTTTA
*
16474649 TTATCTTA
1 TTATTTTA
16474657 TT-TATTTA
1 TTAT-TTTA
*
16474665 TTTTTTTA
1 TTATTTTA
*
16474673 TTTTTTTA
1 TTATTTTA
16474681 CTTCATGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
7 1 0.03
8 34 0.94
9 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTTTA
Found at i:16474649 original size:13 final size:13
Alignment explanation
Indices: 16474631--16474676 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
16474621 TTATTGTTTC
16474631 TTTTATTTTATTA
1 TTTTATTTTATTA
* *
16474644 TTTTATTATCTTA
1 TTTTATTTTATTA
*
16474657 -TTTA-TTTATTT
1 TTTTATTTTATTA
16474668 TTTTATTTT
1 TTTTATTTT
16474677 TTTACTTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
11 4 0.15
12 8 0.31
13 14 0.54
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:16474680 original size:16 final size:16
Alignment explanation
Indices: 16474633--16474680 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
16474623 ATTGTTTCTT
*
16474633 TTATTTTATTATTTTA
1 TTATTTTATTTTTTTA
* *
16474649 TTATCTTATTTATTTA
1 TTATTTTATTTTTTTA
*
16474665 TTTTTTTATTTTTTTA
1 TTATTTTATTTTTTTA
16474681 CTTCATGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTATTTTTTTA
Found at i:16478848 original size:2 final size:2
Alignment explanation
Indices: 16478841--16478910 Score: 65
Period size: 2 Copynumber: 36.0 Consensus size: 2
16478831 ACGTATCCAT
* * * * *
16478841 TA TA TA TA TA TA T- TA TA AA TA TG TA AA TA TA TT TT TA CTA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
16478882 TA TA T- 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
16478911 ACTTTTACGA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
1 3 0.05
2 51 0.91
3 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16487529 original size:31 final size:30
Alignment explanation
Indices: 16487472--16487532 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
16487462 CTAAATTAGC
*
16487472 AATTTACCCTTAAAATTAAAATATATTTACT
1 AATTTACCCTT-AAATGAAAATATATTTACT
16487503 AATTTACCCTT-AATGAAAATTGATATTTAC
1 AATTTACCCTTAAATGAAAA-T-ATATTTAC
16487533 CTTAATACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 7 0.26
30 1 0.04
31 19 0.70
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.41
Consensus pattern (30 bp):
AATTTACCCTTAAATGAAAATATATTTACT
Done.