Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 72 of 100
Found at i:12772760 original size:21 final size:20
Alignment explanation
Indices: 12772727--12772767 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
12772717 GAATTTGGTC
*
12772727 CAATTTTAGGCTAAATTTGTT
1 CAATTATAGGCT-AATTTGTT
*
12772748 CAATTATATGCTAATTTGTT
1 CAATTATAGGCTAATTTGTT
12772768 AGTTTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (20 bp):
CAATTATAGGCTAATTTGTT
Found at i:12778978 original size:23 final size:23
Alignment explanation
Indices: 12778947--12779086 Score: 94
Period size: 23 Copynumber: 6.0 Consensus size: 23
12778937 ACTTATAAAT
*
12778947 AATATTATATTAATTAATTAATA
1 AATAATATATTAATTAATTAATA
* *
12778970 AATAATATATTATAATAAATGAATA
1 AATAATATA-T-TAATTAATTAATA
*
12778995 AATAATATATT-ATTAATAAAT-
1 AATAATATATTAATTAATTAATA
*
12779016 AAT-ATACTATTAATATAA-TATATT
1 AATAATA-TATTAAT-TAATTA-ATA
*
12779040 AATAAATATTATTAA-TAAATAATA
1 AAT-AATA-TATTAATTAATTAATA
* *
12779064 TTATAATATATTAA-TAAATAATA
1 -AATAATATATTAATTAATTAATA
12779087 TAAAGAATAA
Statistics
Matches: 97, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.03
21 7 0.07
22 11 0.11
23 29 0.30
24 14 0.14
25 24 0.25
26 9 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
AATAATATATTAATTAATTAATA
Found at i:12778996 original size:8 final size:7
Alignment explanation
Indices: 12778965--12779102 Score: 59
Period size: 7 Copynumber: 18.3 Consensus size: 7
12778955 ATTAATTAAT
12778965 TAATAAA
1 TAATAAA
12778972 TAATATATTA
1 TAATA-A--A
12778982 TAATAAA
1 TAATAAA
12778989 TGAATAAA
1 T-AATAAA
12778997 TAATATATTA
1 TAATA-A--A
12779007 TTAATAAA
1 -TAATAAA
*
12779015 TAATATAC
1 TAATA-AA
*
12779023 TATTAATA
1 TAATAA-A
*
12779031 TAATATAT
1 TAATA-AA
12779039 TAATAAA
1 TAATAAA
* *
12779046 T-ATTAT
1 TAATAAA
12779052 TAATAAA
1 TAATAAA
*
12779059 TAATATTA
1 TAATA-AA
*
12779067 TAATATAT
1 TAATA-AA
12779075 TAATAAA
1 TAATAAA
12779082 TAAT--A
1 TAATAAA
12779087 TAA-AGAA
1 TAATA-AA
12779094 TAATAAA
1 TAATAAA
12779101 TA
1 TA
12779103 GTTTTATTTT
Statistics
Matches: 100, Mismatches: 14, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
5 4 0.04
6 4 0.04
7 40 0.40
8 37 0.37
9 2 0.02
10 8 0.08
11 5 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (7 bp):
TAATAAA
Found at i:12779074 original size:36 final size:34
Alignment explanation
Indices: 12778965--12779098 Score: 101
Period size: 36 Copynumber: 4.1 Consensus size: 34
12778955 ATTAATTAAT
* *
12778965 TAATAAATAATATATT-AT-AATA-AATGAATAAA
1 TAATATATAATATATTAATAAATATTAT-AATAAA
* *
12778997 T-A-ATATA-T-TATTAATAAATAATATACT--A
1 TAATATATAATATATTAATAAATATTATAATAAA
*
12779025 TTA-ATATAATATATTAATAAATATTATTAATAAA
1 TAATATATAATATATTAATAAATATTA-TAATAAA
*
12779059 TAATATTATAATATATTAATAAATAATATAA-AGAA
1 TAATA-TATAATATATTAATAAATATTATAATA-AA
12779094 TAATA
1 TAATA
12779099 AATAGTTTTA
Statistics
Matches: 83, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
28 6 0.07
29 9 0.11
30 11 0.13
31 17 0.20
32 4 0.05
34 4 0.05
35 11 0.13
36 21 0.25
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (34 bp):
TAATATATAATATATTAATAAATATTATAATAAA
Found at i:12779086 original size:26 final size:27
Alignment explanation
Indices: 12779013--12779086 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 27
12779003 ATTATTAATA
* *
12779013 AATAATATACTATTAATATAAT-ATATT
1 AATAATATATTAATAA-ATAATAATATT
*
12779040 AATAA-ATATT-ATTAATAAATAATATT
1 AATAATATATTAATAAAT-AATAATATT
12779066 -ATAATATATTAATAAATAATA
1 AATAATATATTAATAAATAATA
12779087 TAAAGAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 2 0.05
25 9 0.23
26 18 0.46
27 10 0.26
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAATATATTAATAAATAATAATATT
Found at i:12779102 original size:23 final size:23
Alignment explanation
Indices: 12779044--12779102 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
12779034 TATATTAATA
* * *
12779044 AATATTATTAATAAATAATATTAT
1 AATA-TATAAATAAATAATATAAG
*
12779068 AATATATTAATAAATAATATAAAG
1 AATATATAAATAAATAATAT-AAG
12779092 AATA-ATAAATA
1 AATATATAAATA
12779103 GTTTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 22 0.71
24 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
AATATATAAATAAATAATATAAG
Found at i:12779141 original size:18 final size:18
Alignment explanation
Indices: 12779119--12779206 Score: 69
Period size: 19 Copynumber: 4.9 Consensus size: 18
12779109 TTTTAAGTAT
*
12779119 TTTTTATATTAATATAATA
1 TTTTAATATTAA-ATAATA
12779138 TTTTAATATTAAATAATA
1 TTTTAATATTAAATAATA
* *
12779156 TTATTAA-AATATAATTAT-
1 TT-TTAATATTA-AATAATA
12779174 TTTTGAATATT-AAT-A-A
1 TTTT-AATATTAAATAATA
*
12779190 TTTTAATAATAAATAAT
1 TTTTAATATTAAATAAT
12779207 TTCAATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
15 5 0.09
16 8 0.14
17 6 0.11
18 15 0.27
19 22 0.39
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:12779204 original size:16 final size:16
Alignment explanation
Indices: 12779128--12779240 Score: 55
Period size: 16 Copynumber: 7.1 Consensus size: 16
12779118 TTTTTTATAT
12779128 TAATATAAT-ATTTTAA
1 TAATA-AATAATTTTAA
*
12779144 TATTAAATAATATTATTAA
1 TAATAAAT-A-ATT-TTAA
*
12779163 -AATATAATTATTTTTGAA
1 TAATA-AA-TAATTTT-AA
*
12779181 T-ATTAATAATTTTAA
1 TAATAAATAATTTTAA
12779196 TAATAAATAA-TTT--
1 TAATAAATAATTTTAA
*
12779209 CAAT--AT-ATTTTAA
1 TAATAAATAATTTTAA
12779222 TAATAAATAATTTTTAA
1 TAATAAATAA-TTTTAA
12779239 TA
1 TA
12779241 TTTTAATAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 31
0.65 0.07 0.28
Matches are distributed among these distances:
10 1 0.01
11 5 0.07
13 6 0.08
15 11 0.15
16 18 0.25
17 12 0.16
18 12 0.16
19 7 0.10
20 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
TAATAAATAATTTTAA
Found at i:12779218 original size:26 final size:26
Alignment explanation
Indices: 12779185--12779248 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
12779175 TTTGAATATT
12779185 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
*
12779210 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
12779236 TA-ATATTTTAATA
1 AATATATTTTAATA
12779249 GTTATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:12779240 original size:10 final size:9
Alignment explanation
Indices: 12779183--12779248 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
12779173 TTTTTGAATA
12779183 TTAATAATT
1 TTAATAATT
12779192 TTAATAA--
1 TTAATAATT
*
12779199 TAAATAATT
1 TTAATAATT
*
12779208 TCAATATATT
1 TTAATA-ATT
12779218 TTAATAA--
1 TTAATAATT
*
12779225 TAAATAATTT
1 TTAATAA-TT
12779235 TTAAT-ATT
1 TTAATAATT
12779243 TTAATA
1 TTAATA
12779249 GTTATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
7 12 0.27
8 7 0.16
9 14 0.31
10 12 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (9 bp):
TTAATAATT
Found at i:12779400 original size:15 final size:14
Alignment explanation
Indices: 12779364--12779396 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12779354 TAAAAAATAT
*
12779364 AAAT-ATTTTTCAG
1 AAATCATTTTTCAA
12779377 AAATCATTTTTCAA
1 AAATCATTTTTCAA
12779391 AAATCA
1 AAATCA
12779397 ATTTATGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (14 bp):
AAATCATTTTTCAA
Found at i:12782521 original size:6 final size:6
Alignment explanation
Indices: 12782510--12782543 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
12782500 AAATATTGTA
12782510 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA
12782544 GAATTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:12782681 original size:45 final size:45
Alignment explanation
Indices: 12782632--12782719 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
12782622 AGTTCAATTT
* *
12782632 TTTTTTTATTATAGTGCCAAAATTGAAAAGATATTCAAGTTAAAA
1 TTTTTTTATTATAGTGACAAAATTGAAAAGATATACAAGTTAAAA
12782677 TTTTTTTATTATAGTGACAAAATTGAAAAGATATACAAGTTAA
1 TTTTTTTATTATAGTGACAAAATTGAAAAGATATACAAGTTAA
12782720 CGGTTGTCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (45 bp):
TTTTTTTATTATAGTGACAAAATTGAAAAGATATACAAGTTAAAA
Found at i:12792169 original size:22 final size:22
Alignment explanation
Indices: 12792144--12792187 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12792134 TATATATTTA
**
12792144 TATTTGTATCTTTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
12792166 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
12792188 GATAGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:12796235 original size:22 final size:22
Alignment explanation
Indices: 12796194--12796238 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12796184 CTATATATTT
** *
12796194 GTATTTGTATCTTTAGAATTAA
1 GTATTTGTATCAATAAAATTAA
12796216 GTATTTGTATCAATAAAATTAA
1 GTATTTGTATCAATAAAATTAA
12796238 G
1 G
12796239 GAAAAAAATT
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:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (22 bp):
GTATTTGTATCAATAAAATTAA
Found at i:12797286 original size:22 final size:22
Alignment explanation
Indices: 12797260--12797303 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12797250 CTGTATATTT
12797260 ATATTTGTATCCCTAGAATTAA
1 ATATTTGTATCCCTAGAATTAA
12797282 ATATTTGTATCCCTAGAATTAA
1 ATATTTGTATCCCTAGAATTAA
12797304 GGACAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
ATATTTGTATCCCTAGAATTAA
Found at i:12807193 original size:22 final size:22
Alignment explanation
Indices: 12807167--12807210 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
12807157 TGTGTATTTA
12807167 TATTTGTAT-CTCTAGAATTAAG
1 TATTTGTATCCT-TAGAATTAAG
12807189 TATTTGTATCCTTAGAATTAAG
1 TATTTGTATCCTTAGAATTAAG
12807211 GATAGACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCTTAGAATTAAG
Found at i:12807368 original size:24 final size:26
Alignment explanation
Indices: 12807341--12807390 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
12807331 ATATGCATTC
12807341 AGTTTTACTT-TTAG-TTTTTCACAT
1 AGTTTTACTTCTTAGTTTTTTCACAT
*
12807365 AGTTTTATTTCTTAGTTTTTTCACAT
1 AGTTTTACTTCTTAGTTTTTTCACAT
12807391 GGTATCAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.39
25 4 0.17
26 10 0.43
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (26 bp):
AGTTTTACTTCTTAGTTTTTTCACAT
Found at i:12807482 original size:25 final size:25
Alignment explanation
Indices: 12807454--12807516 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
12807444 TGACTTTTAT
12807454 TTTAGGCCTTCATTGCCGAACCCTG
1 TTTAGGCCTTCATTGCCGAACCCTG
* * * *
12807479 TTTAGACCTTCATTGTCGAATCTTG
1 TTTAGGCCTTCATTGCCGAACCCTG
*
12807504 TTAAGGCCTTCAT
1 TTTAGGCCTTCAT
12807517 AGCCATTCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (25 bp):
TTTAGGCCTTCATTGCCGAACCCTG
Found at i:12811260 original size:22 final size:22
Alignment explanation
Indices: 12811223--12811266 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12811213 TATGTATTTT
*
12811223 TATTTGTATCTCTAGATTTAAG
1 TATTTGTATCTCTAGAATTAAG
12811245 TATTTGTATC-CTTAGAATTAAG
1 TATTTGTATCTC-TAGAATTAAG
12811267 GACAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.48
Consensus pattern (22 bp):
TATTTGTATCTCTAGAATTAAG
Found at i:12812746 original size:15 final size:16
Alignment explanation
Indices: 12812728--12812767 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
12812718 AATATTGTTC
*
12812728 TTTTAAATTGATG-CA
1 TTTTAAATTGACGTCA
*
12812743 TTTTAAAATGACGTCA
1 TTTTAAATTGACGTCA
12812759 TTTTAAATT
1 TTTTAAATT
12812768 TCTCCTTTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (16 bp):
TTTTAAATTGACGTCA
Found at i:12819221 original size:30 final size:30
Alignment explanation
Indices: 12819166--12819222 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
12819156 ACAGACAGGA
**
12819166 CCATTGTTTGTTTAATATGTCAATAAAACT
1 CCATTGTTTGTTTAATATGAAAATAAAACT
12819196 CCATTGTTTGTTTAATATGAAAATAAA
1 CCATTGTTTGTTTAATATGAAAATAAA
12819223 GTTCATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (30 bp):
CCATTGTTTGTTTAATATGAAAATAAAACT
Found at i:12820944 original size:5 final size:5
Alignment explanation
Indices: 12820934--12820958 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12820924 ATAATTTTAA
12820934 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
12820959 TCTAACTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:12822008 original size:9 final size:9
Alignment explanation
Indices: 12821996--12822044 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
12821986 AATCATCTAA
*
12821996 ATTAAAATT
1 ATTAATATT
*
12822005 ATTATTATT
1 ATTAATATT
*
12822014 ATTATTATT
1 ATTAATATT
12822023 ATT-ATATT
1 ATTAATATT
*
12822031 ATTATTATT
1 ATTAATATT
12822040 ATTAA
1 ATTAA
12822045 CAATAATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
8 7 0.21
9 27 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTAATATT
Found at i:12822010 original size:3 final size:3
Alignment explanation
Indices: 12822002--12822043 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
12821992 CTAAATTAAA
12822002 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12822044 ACAATAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12827634 original size:27 final size:26
Alignment explanation
Indices: 12827601--12827661 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
12827591 ATATTAATAT
12827601 AATTATTAAAAATTATTTATTGTTAA
1 AATTATTAAAAATTATTTATTGTTAA
12827627 AATATATT-AAAATTATTTATTGTTAA
1 AAT-TATTAAAAATTATTTATTGTTAA
12827653 AATTATTAA
1 AATTATTAA
12827662 TATTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 4 0.12
26 25 0.76
27 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
AATTATTAAAAATTATTTATTGTTAA
Found at i:12827654 original size:16 final size:16
Alignment explanation
Indices: 12827609--12827659 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
12827599 ATAATTATTA
12827609 AAAATTATTTATTGTT
1 AAAATTATTTATTGTT
12827625 AAAA-TA--TA---TT
1 AAAATTATTTATTGTT
12827635 AAAATTATTTATTGTT
1 AAAATTATTTATTGTT
12827651 AAAATTATT
1 AAAATTATT
12827660 AATATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
10 6 0.21
11 2 0.07
13 4 0.14
15 2 0.07
16 15 0.52
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (16 bp):
AAAATTATTTATTGTT
Found at i:12827670 original size:16 final size:15
Alignment explanation
Indices: 12827630--12827669 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
12827620 TTGTTAAAAT
12827630 ATATTAAAATTATTTA
1 ATATTAAAATTA-TTA
* *
12827646 TTGTTAAAATTATTA
1 ATATTAAAATTATTA
12827661 ATATTAAAA
1 ATATTAAAA
12827670 AATAATTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATATTAAAATTATTA
Found at i:12827723 original size:34 final size:33
Alignment explanation
Indices: 12827630--12827749 Score: 97
Period size: 34 Copynumber: 3.6 Consensus size: 33
12827620 TTGTTAAAAT
* *
12827630 ATATTAAAATTATTTATT-GT-TAAAATTATTA
1 ATATTAAAATTATTTATTAATATAAAAATATTA
* *
12827661 ATATTAAAAAATAATTATATTTGA-ATAAAAATATTTA
1 ATATT--AAAATTATT-TA-TTAATATAAAAATA-TTA
12827698 ATATTAAAA-TATTATATTAATATAAAAATACTTA
1 ATATTAAAATTATT-TATTAATATAAAAATA-TTA
*
12827732 A-AATAAAATTATTTATTA
1 ATATTAAAATTATTTATTA
12827750 TTCTTTATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
31 5 0.07
33 22 0.30
34 25 0.34
35 6 0.08
36 7 0.10
37 8 0.11
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (33 bp):
ATATTAAAATTATTTATTAATATAAAAATATTA
Found at i:12827848 original size:15 final size:16
Alignment explanation
Indices: 12827828--12827870 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
12827818 TTAAAATAGT
12827828 AATATTTAT-TATTAA
1 AATATTTATATATTAA
*
12827843 AATATTTATACTGTTAA
1 AATATTTATA-TATTAA
12827860 AATATTTATAT
1 AATATTTATAT
12827871 TTTATATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 9 0.36
16 1 0.04
17 15 0.60
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
AATATTTATATATTAA
Found at i:12828253 original size:18 final size:20
Alignment explanation
Indices: 12828232--12828268 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12828222 TTTTAATTAA
12828232 ATTAA-ATAA-AATATTTTT
1 ATTAATATAATAATATTTTT
*
12828250 ATTAATTTAATAATATTTT
1 ATTAATATAATAATATTTT
12828269 AAGTCAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 3 0.19
20 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTAATATAATAATATTTTT
Found at i:12828261 original size:22 final size:23
Alignment explanation
Indices: 12828218--12828270 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
12828208 TTAATATTTT
12828218 AATATTTTAATTAAATTAAATAA
1 AATATTTTAATTAAATTAAATAA
* *
12828241 AATATTTTTATT-AATTTAAT--
1 AATATTTTAATTAAATTAAATAA
12828261 AATATTTTAA
1 AATATTTTAA
12828271 GTCAAATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.33
22 7 0.26
23 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTTTAATTAAATTAAATAA
Found at i:12828843 original size:2 final size:2
Alignment explanation
Indices: 12828836--12828865 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12828826 ACTCTTATCA
12828836 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
12828866 TGATAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12829352 original size:20 final size:20
Alignment explanation
Indices: 12829327--12829365 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12829317 ATTTGTAAAA
12829327 TGAATAAAATTAAA-AATAAT
1 TGAAT-AAATTAAATAATAAT
12829347 TGAATAAATTAAATAATAA
1 TGAATAAATTAAATAATAA
12829366 AATAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
TGAATAAATTAAATAATAAT
Found at i:12835131 original size:17 final size:17
Alignment explanation
Indices: 12835109--12835141 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12835099 AAGATTAAAT
12835109 AATCTTGGT-AAAGAAAC
1 AATCTT-GTAAAAGAAAC
12835126 AATCTTGTAAAAGAAA
1 AATCTTGTAAAAGAAA
12835142 ATTGGAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (17 bp):
AATCTTGTAAAAGAAAC
Found at i:12840512 original size:26 final size:26
Alignment explanation
Indices: 12840483--12840532 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
12840473 AGGTATGTGC
12840483 ATGAAATTTTGAGCATAAATCTTATA
1 ATGAAATTTTGAGCATAAATCTTATA
12840509 ATGAAATTTTGAGCATAAATCTTA
1 ATGAAATTTTGAGCATAAATCTTA
12840533 GTCAAGGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (26 bp):
ATGAAATTTTGAGCATAAATCTTATA
Found at i:12842843 original size:12 final size:13
Alignment explanation
Indices: 12842818--12842845 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12842808 CAAAATGCTG
12842818 AAAAATTTTAAAA
1 AAAAATTTTAAAA
12842831 AAAAATTTTAAAA
1 AAAAATTTTAAAA
12842844 AA
1 AA
12842846 TTCTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAATTTTAAAA
Found at i:12842843 original size:21 final size:21
Alignment explanation
Indices: 12842819--12842873 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
12842809 AAAATGCTGA
*
12842819 AAAATTTTAAAAAAAAATTTT
1 AAAATTTTAAAAAAAAATGTT
** **
12842840 AAAAAATTCTAAAAAAATGTT
1 AAAATTTTAAAAAAAAATGTT
*
12842861 AATATTTTAAAAA
1 AAAATTTTAAAAA
12842874 TTCCAAACAA
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATTTTAAAAAAAAATGTT
Found at i:12842909 original size:19 final size:19
Alignment explanation
Indices: 12842885--12842921 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12842875 TCCAAACAAT
*
12842885 TTCTAATTTTTTTTAAATA
1 TTCTAAATTTTTTTAAATA
12842904 TTCTAAATTTTTTTAAAT
1 TTCTAAATTTTTTTAAAT
12842922 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCTAAATTTTTTTAAATA
Found at i:12842960 original size:16 final size:16
Alignment explanation
Indices: 12842916--12842960 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
12842906 CTAAATTTTT
*
12842916 TTAAATTTTAAAAAAA
1 TTAAATTTTTAAAAAA
* *
12842932 TTAAATTTCTAAAATA
1 TTAAATTTTTAAAAAA
*
12842948 TTAATTTTTTAAA
1 TTAAATTTTTAAA
12842961 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTTTTAAAAAA
Found at i:12842987 original size:40 final size:40
Alignment explanation
Indices: 12842912--12842989 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
12842902 TATTCTAAAT
* *
12842912 TTTTTTAAATTTTAAAAAAATTAAATTTCTAAAATATTAA
1 TTTTTTAAATTTTAAAAAAATTAAATATATAAAATATTAA
*
12842952 TTTTTTAAATTTTAAAAAAATTCAAA-ATATGAAATATT
1 TTTTTTAAATTTTAAAAAAATT-AAATATATAAAATATT
12842990 TTTATAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (40 bp):
TTTTTTAAATTTTAAAAAAATTAAATATATAAAATATTAA
Found at i:12843050 original size:21 final size:21
Alignment explanation
Indices: 12843026--12843093 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
12843016 TTTGAAAAAT
12843026 TAAAAATTATAAAAATTTTCA
1 TAAAAATTATAAAAATTTTCA
*
12843047 T-AAAATAATAAAAAATTTTCA
1 TAAAAATTAT-AAAAATTTTCA
* *
12843068 -AAAAA--ATGAAAA-TTTAA
1 TAAAAATTATAAAAATTTTCA
12843085 TAAAAATTA
1 TAAAAATTA
12843094 AGTTTTCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
17 4 0.10
18 9 0.23
19 2 0.05
20 8 0.21
21 16 0.41
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (21 bp):
TAAAAATTATAAAAATTTTCA
Found at i:12843057 original size:20 final size:19
Alignment explanation
Indices: 12843027--12843082 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
12843017 TTGAAAAATT
*
12843027 AAAAATTATAAAAATTTTC
1 AAAAATAATAAAAATTTTC
12843046 ATAAAATAATAAAAAATTTTC
1 A-AAAATAAT-AAAAATTTTC
*
12843067 AAAAA-AATGAAAATTT
1 AAAAATAATAAAAATTT
12843083 AATAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 11 0.33
21 11 0.33
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAATAATAAAAATTTTC
Found at i:12843133 original size:18 final size:16
Alignment explanation
Indices: 12843110--12843148 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
12843100 CTTAAAGTTT
12843110 AAAAAACAAAAAAATAA
1 AAAAAAC-AAAAAATAA
*
12843127 GAAAAAACTAAAAATAA
1 -AAAAAACAAAAAATAA
12843144 AAAAA
1 AAAAA
12843149 TCTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 8 0.40
18 7 0.35
ACGTcount: A:0.85, C:0.05, G:0.03, T:0.08
Consensus pattern (16 bp):
AAAAAACAAAAAATAA
Found at i:12843139 original size:17 final size:16
Alignment explanation
Indices: 12843119--12843155 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
12843109 TAAAAAACAA
12843119 AAAAATAAGAAAAAACT
1 AAAAATAA-AAAAAACT
*
12843136 AAAAATAAAAAAATCT
1 AAAAATAAAAAAAACT
12843152 AAAA
1 AAAA
12843156 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (16 bp):
AAAAATAAAAAAAACT
Found at i:12843309 original size:18 final size:17
Alignment explanation
Indices: 12843288--12843345 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
12843278 AATTTTAGGA
12843288 AATTTTGATTTTTATTTT
1 AATTTTGATTTTT-TTTT
* *
12843306 AATTGTCATTTTTTCTTT
1 AATTTTGATTTTTT-TTT
*
12843324 --TTTGGA-TTTTTTTT
1 AATTTTGATTTTTTTTT
12843338 AATTTTGA
1 AATTTTGA
12843346 GACTTTTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
14 3 0.10
15 5 0.16
16 8 0.26
17 1 0.03
18 14 0.45
ACGTcount: A:0.19, C:0.03, G:0.09, T:0.69
Consensus pattern (17 bp):
AATTTTGATTTTTTTTT
Found at i:12843417 original size:10 final size:10
Alignment explanation
Indices: 12843379--12843502 Score: 71
Period size: 10 Copynumber: 12.6 Consensus size: 10
12843369 ACATTTCCTT
*
12843379 AATTCTTTTAT
1 AATT-TTTTAG
*
12843390 AATTTTTTAA
1 AATTTTTTAG
**
12843400 AAAATTTTAG
1 AATTTTTTAG
12843410 AATTTTTTAG
1 AATTTTTTAG
12843420 AATTCTTTTA-
1 AATT-TTTTAG
*
12843430 AATTTTTTAC
1 AATTTTTTAG
*
12843440 AATTTTTT-T
1 AATTTTTTAG
12843449 AA-TTTTTA-
1 AATTTTTTAG
*
12843457 AATTGATTT-G
1 AATT-TTTTAG
* *
12843467 AA-TTTCTAA
1 AATTTTTTAG
* *
12843476 AAATTTTTAA
1 AATTTTTTAG
12843486 AATTATTTTAG
1 AATT-TTTTAG
12843497 AATTTT
1 AATTTT
12843503 GAAAAAAATT
Statistics
Matches: 90, Mismatches: 14, Indels: 19
0.73 0.11 0.15
Matches are distributed among these distances:
8 9 0.10
9 11 0.12
10 52 0.58
11 18 0.20
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.57
Consensus pattern (10 bp):
AATTTTTTAG
Found at i:12843542 original size:21 final size:21
Alignment explanation
Indices: 12843509--12843557 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
12843499 TTTTGAAAAA
*
12843509 AATTTTT-AGTTTTTATATAT
1 AATTTTTAATTTTTTATATAT
* * *
12843529 ATTTTTTAATTTTTTTTTTAT
1 AATTTTTAATTTTTTATATAT
12843550 AATTTTTA
1 AATTTTTA
12843558 GGATTTTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
AATTTTTAATTTTTTATATAT
Found at i:12843564 original size:31 final size:30
Alignment explanation
Indices: 12843529--12843596 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
12843519 TTTTATATAT
* *
12843529 ATTTTTTA-ATTTTTTTTTTATAATTTTTAGG
1 ATTTTTTAGATTTTTTTTTT-GAATTTTTA-A
*
12843560 ATTTTTAAGATTTTTTTTTTGAATTTTTAA
1 ATTTTTTAGATTTTTTTTTTGAATTTTTAA
12843590 ATTTTTT
1 ATTTTTT
12843597 TTTTGGAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 6 0.19
31 15 0.47
32 11 0.34
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (30 bp):
ATTTTTTAGATTTTTTTTTTGAATTTTTAA
Found at i:12843577 original size:22 final size:21
Alignment explanation
Indices: 12843552--12843613 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 21
12843542 TTTTTTATAA
*
12843552 TTTTTAGGATTTTTAAGATTTT
1 TTTTTTGGATTTTTAA-ATTTT
*
12843574 TTTTTTGAATTTTTAAATTTT
1 TTTTTTGGATTTTTAAATTTT
12843595 TTTTTTGGAATTTTCTAAA
1 TTTTTTGG-ATTTT-TAAA
12843614 AAGCTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.34
22 19 0.54
23 4 0.11
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.65
Consensus pattern (21 bp):
TTTTTTGGATTTTTAAATTTT
Found at i:12843699 original size:10 final size:10
Alignment explanation
Indices: 12843684--12843734 Score: 63
Period size: 9 Copynumber: 5.4 Consensus size: 10
12843674 TATTAAAAAG
12843684 TTTTATAATT
1 TTTTATAATT
12843694 TTTTATAATT
1 TTTTATAATT
*
12843704 TTTTACAA-T
1 TTTTATAATT
12843713 TTTT-TAATT
1 TTTTATAATT
*
12843722 TTTT-TTATT
1 TTTTATAATT
12843731 TTTT
1 TTTT
12843735 TTGGAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
8 2 0.05
9 18 0.49
10 17 0.46
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTATAATT
Found at i:12843716 original size:11 final size:10
Alignment explanation
Indices: 12843684--12843718 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
12843674 TATTAAAAAG
*
12843684 TTTTATAATT
1 TTTTACAATT
*
12843694 TTTTATAATT
1 TTTTACAATT
12843704 TTTTACAATT
1 TTTTACAATT
12843714 TTTTA
1 TTTTA
12843719 ATTTTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTACAATT
Found at i:12844594 original size:13 final size:13
Alignment explanation
Indices: 12844572--12844617 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
12844562 TTAAATTTTG
12844572 TATTTGATTATTA
1 TATTTGATTATTA
*
12844585 TATTTAATTATTA
1 TATTTGATTATTA
12844598 TGAATTTGATTATATA
1 T--ATTTGATTAT-TA
12844614 TATT
1 TATT
12844618 ATCATATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 13 0.46
14 3 0.11
15 9 0.32
16 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (13 bp):
TATTTGATTATTA
Found at i:12852552 original size:2 final size:2
Alignment explanation
Indices: 12852540--12852574 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12852530 CTAAGGGCTT
* *
12852540 TA TA AA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12852575 TGTTAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12856658 original size:19 final size:19
Alignment explanation
Indices: 12856637--12856672 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12856627 AATTGTTAGA
*
12856637 AAAAATAA-ATAAGAGAAG
1 AAAAATAATATAAAAGAAG
12856655 AAAAATAATATAAAAGAA
1 AAAAATAATATAAAAGAA
12856673 TTTTAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (19 bp):
AAAAATAATATAAAAGAAG
Found at i:12862854 original size:15 final size:13
Alignment explanation
Indices: 12862815--12862844 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12862805 CTTTTTTCTC
*
12862815 TTTTGTATTTTTA
1 TTTTGTGTTTTTA
12862828 TTTTGTGTTTTTA
1 TTTTGTGTTTTTA
12862841 TTTT
1 TTTT
12862845 TTGCCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (13 bp):
TTTTGTGTTTTTA
Found at i:12863161 original size:10 final size:10
Alignment explanation
Indices: 12863146--12863205 Score: 57
Period size: 11 Copynumber: 5.7 Consensus size: 10
12863136 GCCTAATCAA
12863146 TTTTTTTTTC
1 TTTTTTTTTC
12863156 TTTTTTTTTC
1 TTTTTTTTTC
** *
12863166 TTACTCTTTC
1 TTTTTTTTTC
12863176 TTTTTTTTTTCC
1 -TTTTTTTTT-C
12863188 TTTTTTTTATC
1 TTTTTTTT-TC
*
12863199 ATTTTTT
1 TTTTTTT
12863206 AAAAAAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
10 17 0.43
11 21 0.52
12 2 0.05
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:12873089 original size:2 final size:2
Alignment explanation
Indices: 12873082--12873121 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12873072 GAATATGAAC
12873082 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12873122 TCTTTTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12875968 original size:27 final size:27
Alignment explanation
Indices: 12875934--12875989 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
12875924 GAATGTGCAT
12875934 ATGACAAATAGGAATCCATCCATCATA
1 ATGACAAATAGGAATCCATCCATCATA
* * *
12875961 ATGACAAATAGTAATCCATTCGTCATA
1 ATGACAAATAGGAATCCATCCATCATA
12875988 AT
1 AT
12875990 TGCAACTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.27
Consensus pattern (27 bp):
ATGACAAATAGGAATCCATCCATCATA
Found at i:12880091 original size:15 final size:15
Alignment explanation
Indices: 12880071--12880101 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12880061 TTACAAAAAA
12880071 TTTTAACTAAAATGG
1 TTTTAACTAAAATGG
*
12880086 TTTTAAGTAAAATGG
1 TTTTAACTAAAATGG
12880101 T
1 T
12880102 CAAAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (15 bp):
TTTTAACTAAAATGG
Found at i:12880696 original size:24 final size:22
Alignment explanation
Indices: 12880669--12880763 Score: 54
Period size: 24 Copynumber: 4.1 Consensus size: 22
12880659 TAAAATTTAT
12880669 ATTTAATGTATTATTAATATATAA
1 ATTTAAT-TATTATTAATA-ATAA
* *
12880693 ATTTTATATAATATTAATGAATTAA
1 ATTTAAT-TATTATTAAT-AA-TAA
*
12880718 ATTAAATTACTTTATTAATAAATAA
1 ATTTAATTA--TTATTAAT-AATAA
12880743 ATATT-ATT-TT-TTAA-AATAA
1 AT-TTAATTATTATTAATAATAA
12880762 AT
1 AT
12880764 ATATAAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
19 7 0.12
21 4 0.07
22 2 0.03
24 18 0.31
25 17 0.29
26 10 0.17
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTAATTATTATTAATAATAA
Found at i:12880756 original size:21 final size:21
Alignment explanation
Indices: 12880715--12880765 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
12880705 ATTAATGAAT
*
12880715 TAAATTAA-ATTACTTTATTAA
1 TAAATAAATATTACTTTATT-A
*
12880736 TAAATAAATATTA-TTTTTTA
1 TAAATAAATATTACTTTATTA
12880756 -AAATAAATAT
1 TAAATAAATAT
12880766 ATAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.37
20 1 0.04
21 12 0.44
22 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATAAATATTACTTTATTA
Found at i:12880782 original size:31 final size:33
Alignment explanation
Indices: 12880735--12880816 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 33
12880725 TACTTTATTA
*
12880735 ATAAAT-AAATATTATTTTTTAAAA-TAAATAT
1 ATAAATAAAATAATATTTTTTAAAATTAAATAT
* ** *
12880766 ATAAA-AAATTAATA-TTTTTAAAATTTTATTT
1 ATAAATAAAATAATATTTTTTAAAATTAAATAT
12880797 ATAAATAAAATAATATTTTT
1 ATAAATAAAATAATATTTTT
12880817 ATTTTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
30 9 0.22
31 20 0.49
32 8 0.20
33 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATAAATAAAATAATATTTTTTAAAATTAAATAT
Found at i:12880834 original size:30 final size:30
Alignment explanation
Indices: 12880765--12880841 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 30
12880755 AAAATAAATA
*
12880765 TATAAA-AAATTAATATTTTTAAAATTTTATT
1 TATAAATAAAATAATATTTTT--AATTTTATT
12880796 TATAAATAAAATAATATTTTT-ATTTTATTT
1 TATAAATAAAATAATATTTTTAATTTTA-TT
*
12880826 TATTAATAAAATAATA
1 TATAAATAAAATAATA
12880842 GCATATTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 6 0.14
30 17 0.40
31 6 0.14
32 13 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TATAAATAAAATAATATTTTTAATTTTATT
Found at i:12881478 original size:11 final size:11
Alignment explanation
Indices: 12881464--12881502 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
12881454 TTTTATTAAA
12881464 TTTTATTTTAT
1 TTTTATTTTAT
* *
12881475 TTTTATGTAAT
1 TTTTATTTTAT
12881486 TTTTATTTTAT
1 TTTTATTTTAT
12881497 TTTTAT
1 TTTTAT
12881503 ATATACATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:12881492 original size:22 final size:21
Alignment explanation
Indices: 12881454--12881502 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
12881444 ATTATGTACA
12881454 TTTTATTAAATTTTATTTTAT
1 TTTTATTAAATTTTATTTTAT
*
12881475 TTTTATGTAATTTTTATTTTAT
1 TTTTAT-TAAATTTTATTTTAT
12881497 TTTTAT
1 TTTTAT
12881503 ATATACATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTATTAAATTTTATTTTAT
Found at i:12882891 original size:2 final size:2
Alignment explanation
Indices: 12882884--12882924 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
12882874 AGCTGAAAAA
*
12882884 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12882925 ATATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:12884275 original size:5 final size:5
Alignment explanation
Indices: 12884265--12884294 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
12884255 TCCTTTTTTC
*
12884265 CTTCT CTTCT CTTCT CTTCT CTTTT CTTCT
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT
12884295 TTCATCAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
CTTCT
Found at i:12884982 original size:24 final size:23
Alignment explanation
Indices: 12884955--12885000 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
12884945 TTTTTCTTTC
* *
12884955 TTTGCATGTTTAGTATTTTTTTAT
1 TTTGCATGTATA-TAATTTTTTAT
*
12884979 TTTGCTTGTATATAATTTTTTA
1 TTTGCATGTATATAATTTTTTA
12885001 GATTTATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (23 bp):
TTTGCATGTATATAATTTTTTAT
Found at i:12890757 original size:96 final size:96
Alignment explanation
Indices: 12890649--12890840 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
12890639 GAAAAGAGTT
12890649 GGTGGGAGGTGAAAATTAAGTATGTAGAGTCGGTGGAAGATAGAGGTAAAGAAAATGATTTAATT
1 GGTGGGAGGTGAAAATTAAGTATGTAGAGTCGGTGGAAGATAGAGGTAAAGAAAATGATTTAATT
12890714 TCATAAGCCTGCCATTTTTTTTTTATTACTC
66 TCATAAGCCTGCCATTTTTTTTTTATTACTC
12890745 GGTGGGAGGTGAAAATTAAGTATGTAGAGTCGGTGGAAGATAGAGGTAAAGAAAATGATTTAATT
1 GGTGGGAGGTGAAAATTAAGTATGTAGAGTCGGTGGAAGATAGAGGTAAAGAAAATGATTTAATT
12890810 TCATAAGCCTGCCATTTTTTTTTTATTACTC
66 TCATAAGCCTGCCATTTTTTTTTTATTACTC
12890841 AATGTGTTAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.34
Consensus pattern (96 bp):
GGTGGGAGGTGAAAATTAAGTATGTAGAGTCGGTGGAAGATAGAGGTAAAGAAAATGATTTAATT
TCATAAGCCTGCCATTTTTTTTTTATTACTC
Found at i:12892901 original size:3 final size:3
Alignment explanation
Indices: 12892893--12892922 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12892883 ACATGCATTC
12892893 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12892923 ATTTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12899784 original size:23 final size:23
Alignment explanation
Indices: 12899732--12899785 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
12899722 AAACAATTGA
*
12899732 AATTATTTATTTTGAATAGACTT
1 AATTATTTATTTTGAATAAACTT
*
12899755 -ATCTATTTATTTTGAATAAATTT
1 AAT-TATTTATTTTGAATAAACTT
12899778 AATTATTT
1 AATTATTT
12899786 GTCTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
AATTATTTATTTTGAATAAACTT
Found at i:12901866 original size:21 final size:22
Alignment explanation
Indices: 12901826--12901867 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
12901816 GATTAATTTT
* *
12901826 TTAAAAAATCCATATTTTTTCC
1 TTAAAAAATCCACATGTTTTCC
12901848 TTAAAAAAT-CACATGTTTTC
1 TTAAAAAATCCACATGTTTTC
12901868 AATCCTTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAAAAAATCCACATGTTTTCC
Found at i:12902148 original size:22 final size:22
Alignment explanation
Indices: 12902123--12902167 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
12902113 CTTAGCAATC
12902123 CCATTTCCAACCTTGTCAATTT
1 CCATTTCCAACCTTGTCAATTT
* *
12902145 CCATTTCCACCCTTGTCATTTT
1 CCATTTCCAACCTTGTCAATTT
12902167 C
1 C
12902168 TTTCGGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.36, G:0.04, T:0.42
Consensus pattern (22 bp):
CCATTTCCAACCTTGTCAATTT
Found at i:12904606 original size:22 final size:23
Alignment explanation
Indices: 12904557--12904620 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 23
12904547 TCATAAATTA
12904557 AAATATAAATAATAT---AATCT
1 AAATATAAATAATATAAAAATCT
*
12904577 AAATATAAATAATATAAAAATGT
1 AAATATAAATAATATAAAAATCT
*
12904600 -AATATAAATAAAAATAAAAAT
1 AAATATAAAT-AATATAAAAAT
12904621 TTTATGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 15 0.39
22 9 0.24
23 14 0.37
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATATAAATAATATAAAAATCT
Found at i:12904607 original size:28 final size:29
Alignment explanation
Indices: 12904558--12904616 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
12904548 CATAAATTAA
* *
12904558 AATATAAATAATATAATCTAAATATAAAT
1 AATATAAATAATATAATATAAATAAAAAT
*
12904587 AATATAAA-AATGTAATATAAATAAAAAT
1 AATATAAATAATATAATATAAATAAAAAT
12904615 AA
1 AA
12904617 AAATTTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (29 bp):
AATATAAATAATATAATATAAATAAAAAT
Found at i:12913192 original size:68 final size:67
Alignment explanation
Indices: 12913082--12913217 Score: 184
Period size: 68 Copynumber: 2.0 Consensus size: 67
12913072 TAGAATAAAA
* * * *
12913082 TCGTGAGACTTTTGGGTCAAGCGGACAATACTTAGCAAGTTGGTGTGTTGATAGTGACATCAAGC
1 TCGTGAGACTTTCGGGTCAAGCGAACAATACCTAGCAAGTTGGTGTGTTGATAGGGACATCAAGC
12913147 TT
66 TT
* * *
12913149 TCGTGAGA-TCTTCGGGTCAAAGCGAACAATACCTATCAGGTTGGTGTGTTGATAGGGACGTCAA
1 TCGTGAGACT-TTCGGGTC-AAGCGAACAATACCTAGCAAGTTGGTGTGTTGATAGGGACATCAA
12913213 GCTT
64 GCTT
12913217 T
1 T
12913218 AAGGTTATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
66 1 0.02
67 15 0.25
68 44 0.73
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (67 bp):
TCGTGAGACTTTCGGGTCAAGCGAACAATACCTAGCAAGTTGGTGTGTTGATAGGGACATCAAGC
TT
Found at i:12915030 original size:18 final size:20
Alignment explanation
Indices: 12914994--12915032 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
12914984 TTAAACTGAA
*
12914994 TTATATATTTTTATTAATTT
1 TTATATATTTTTATAAATTT
12915014 TTATAT-TTTTTA-AAATTT
1 TTATATATTTTTATAAATTT
12915032 T
1 T
12915033 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATATATTTTTATAAATTT
Found at i:12915032 original size:17 final size:18
Alignment explanation
Indices: 12914992--12915035 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
12914982 AATTAAACTG
* *
12914992 AATTATATATTTTTATTA
1 AATTTTATATTTTTATAA
*
12915010 ATTTTTATATTTTT-TAA
1 AATTTTATATTTTTATAA
12915027 AATTTTATA
1 AATTTTATA
12915036 AAATAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTTTATATTTTTATAA
Found at i:12919341 original size:40 final size:40
Alignment explanation
Indices: 12919297--12919386 Score: 180
Period size: 40 Copynumber: 2.2 Consensus size: 40
12919287 TAAAATTTTT
12919297 TGTTTTCTGATCATCAGTATATTAATCCTATCTGTTCAAC
1 TGTTTTCTGATCATCAGTATATTAATCCTATCTGTTCAAC
12919337 TGTTTTCTGATCATCAGTATATTAATCCTATCTGTTCAAC
1 TGTTTTCTGATCATCAGTATATTAATCCTATCTGTTCAAC
12919377 TGTTTTCTGA
1 TGTTTTCTGA
12919387 AATCGACCTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (40 bp):
TGTTTTCTGATCATCAGTATATTAATCCTATCTGTTCAAC
Found at i:12921114 original size:8 final size:7
Alignment explanation
Indices: 12921098--12921142 Score: 54
Period size: 8 Copynumber: 6.0 Consensus size: 7
12921088 GCTTATGGTT
12921098 TTTTTAA
1 TTTTTAA
12921105 TTTTTAAA
1 TTTTT-AA
*
12921113 TTTTTGTA
1 TTTTT-AA
12921121 TTTTGTAA
1 TTTT-TAA
12921129 TTTTTAA
1 TTTTTAA
12921136 TTTTTAA
1 TTTTTAA
12921143 ATAGATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 15 0.45
8 17 0.52
9 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (7 bp):
TTTTTAA
Found at i:12921123 original size:16 final size:15
Alignment explanation
Indices: 12921098--12921144 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
12921088 GCTTATGGTT
12921098 TTTTTAATTTTTAAA
1 TTTTTAATTTTTAAA
*
12921113 TTTTTGTATTTTGT-AA
1 TTTTT-AATTTT-TAAA
12921129 TTTTTAATTTTTAAA
1 TTTTTAATTTTTAAA
12921144 T
1 T
12921145 AGATAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 1 0.04
15 13 0.48
16 12 0.44
17 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (15 bp):
TTTTTAATTTTTAAA
Found at i:12921341 original size:16 final size:16
Alignment explanation
Indices: 12921303--12921350 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
12921293 CACATATATG
12921303 TCTTTTTCTATCT-TTT
1 TCTTTTTCTAT-TATTT
12921319 TCATTTTTCTATTATTT
1 TC-TTTTTCTATTATTT
12921336 TCTTTTTCTA-TATTT
1 TCTTTTTCTATTATTT
12921351 AATAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.17
16 11 0.37
17 14 0.47
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (16 bp):
TCTTTTTCTATTATTT
Found at i:12921680 original size:14 final size:13
Alignment explanation
Indices: 12921661--12921691 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
12921651 TAGAATTTGA
12921661 TTTTTTTTTATCTT
1 TTTTTTTTTAT-TT
12921675 TTTTTTTTTATTT
1 TTTTTTTTTATTT
12921688 TTTT
1 TTTT
12921692 GCCTTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.06, C:0.03, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTATTT
Found at i:12921691 original size:22 final size:23
Alignment explanation
Indices: 12921663--12921707 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
12921653 GAATTTGATT
*
12921663 TTTTTTTATCTTTTT-TTTTTTA
1 TTTTTTTACCTTTTTGTTTTTTA
*
12921685 TTTTTTTGCCTTTTTGTTTTTTA
1 TTTTTTTACCTTTTTGTTTTTTA
12921708 AATCTGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.82
Consensus pattern (23 bp):
TTTTTTTACCTTTTTGTTTTTTA
Found at i:12921981 original size:19 final size:20
Alignment explanation
Indices: 12921957--12921997 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12921947 CTTCAATACA
* *
12921957 TTTCCT-TTTTTTTTCTTTT
1 TTTCCTATTTTATTTATTTT
12921976 TTTCCTATTTTATTTATTTT
1 TTTCCTATTTTATTTATTTT
12921996 TT
1 TT
12921998 CTTTGTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCCTATTTTATTTATTTT
Found at i:12922105 original size:9 final size:8
Alignment explanation
Indices: 12922080--12922104 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12922070 TGATTAAAAA
12922080 TATTTTTT
1 TATTTTTT
12922088 TATTTTTT
1 TATTTTTT
12922096 TATTTTTT
1 TATTTTTT
12922104 T
1 T
12922105 TCCTTTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:12923612 original size:15 final size:16
Alignment explanation
Indices: 12923592--12923633 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
12923582 TTTTCCCTTT
*
12923592 TTTTTTCTTTA-TTTA
1 TTTTTTATTTATTTTA
12923607 TTTTTTATTTATTTTA
1 TTTTTTATTTATTTTA
*
12923623 TTTTTAATTTA
1 TTTTTTATTTA
12923634 ATGAAGTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTATTTATTTTA
Found at i:12925311 original size:14 final size:14
Alignment explanation
Indices: 12925278--12925315 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
12925268 ACTTTTGTTG
*
12925278 ATTTTTGTTGCGATT
1 ATTTTTGTT-TGATT
12925293 A-TTTTGTTTGATT
1 ATTTTTGTTTGATT
12925306 ATTTTTGTTT
1 ATTTTTGTTT
12925316 TTTGACATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 5 0.24
14 15 0.71
15 1 0.05
ACGTcount: A:0.13, C:0.03, G:0.16, T:0.68
Consensus pattern (14 bp):
ATTTTTGTTTGATT
Found at i:12931656 original size:24 final size:24
Alignment explanation
Indices: 12931629--12931676 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
12931619 ATGTTTGGGT
12931629 GTGCTTGGACTATTGAGATTTGAA
1 GTGCTTGGACTATTGAGATTTGAA
12931653 GTGCTTGGACTATTGAGATTTGAA
1 GTGCTTGGACTATTGAGATTTGAA
12931677 CGAAGCAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.38
Consensus pattern (24 bp):
GTGCTTGGACTATTGAGATTTGAA
Found at i:12934703 original size:11 final size:12
Alignment explanation
Indices: 12934689--12934718 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
12934679 AAATTTTTCA
12934689 AAAAAAAAT-TT
1 AAAAAAAATCTT
12934700 AAAAAAAATCTT
1 AAAAAAAATCTT
12934712 AAAAAAA
1 AAAAAAA
12934719 TATATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAAAAATCTT
Found at i:12935080 original size:18 final size:18
Alignment explanation
Indices: 12935015--12935081 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 18
12935005 TGATAAATCC
*
12935015 AATAATAAAAAAAAAGATA
1 AATAATAAAAAACAA-ATA
12935034 AATCAACTAAAAAAATCAAAT-
1 AAT-AA-T-AAAAAA-CAAATA
12935055 -ATAGATAAAAAACAAATA
1 AATA-ATAAAAAACAAATA
12935073 AATAATAAA
1 AATAATAAA
12935082 TAAATAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
17 5 0.12
18 11 0.28
19 8 0.20
20 5 0.12
21 1 0.03
22 8 0.20
23 2 0.05
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (18 bp):
AATAATAAAAAACAAATA
Found at i:12935084 original size:22 final size:21
Alignment explanation
Indices: 12935042--12935109 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
12935032 TAAATCAACT
*
12935042 AAAAAAATCAAATATAGATAA
1 AAAAAAATCAAATATAAATAA
12935063 AAAACAAAT-AAATAATAAATAA
1 AAAA-AAATCAAAT-ATAAATAA
* * *
12935085 ATAAAAATGAAA-A-GAATAA
1 AAAAAAATCAAATATAAATAA
12935104 AAAAAA
1 AAAAAA
12935110 TGGCCAATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.25
20 1 0.03
21 12 0.30
22 17 0.43
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.16
Consensus pattern (21 bp):
AAAAAAATCAAATATAAATAA
Found at i:12938975 original size:43 final size:43
Alignment explanation
Indices: 12938927--12939212 Score: 224
Period size: 43 Copynumber: 6.6 Consensus size: 43
12938917 AAGCTTTTCT
* * *
12938927 AATTTTTCAAATTTGTTGAACCTCTGATGAAATAAGCCTTTTA
1 AATTTTTCAAATTTGTTGAGCCTCTAATGAAATGAGCCTTTTA
* *
12938970 AATTTTTCAAAAGTTT-TTGAGCCTCTGATGAGAA-GAGCTTTTTA
1 AATTTTTC-AAA-TTTGTTGAGCCTCTAATGA-AATGAGCCTTTTA
*
12939014 TAA-TTTTCAAATTTGTTGAGCTTCTAAT-AAGATGAGCCTTTTA
1 -AATTTTTCAAATTTGTTGAGCCTCTAATGAA-ATGAGCCTTTTA
** * * *
12939057 TGTTTTTCAAAATTGTTGAGCCTCTAATGAGATGAGTCTTTTA
1 AATTTTTCAAATTTGTTGAGCCTCTAATGAAATGAGCCTTTTA
* * * * *
12939100 TA-TTTTCAAAAGTTGTTGAGCCTCTAATGAGAGGAGTCTTTTA
1 AATTTTTC-AAATTTGTTGAGCCTCTAATGAAATGAGCCTTTTA
* * * * ** *
12939143 TATTCTTT-AAAGTTGTTAAGCCTTTCAATGAAATGAGTTTTTTT
1 AATT-TTTCAAATTTGTTGAGCCTCT-AATGAAATGAGCCTTTTA
* * *
12939187 AATTTTTCAAAGTCGTTGAACCTCTA
1 AATTTTTCAAATTTGTTGAGCCTCTA
12939213 TTTAGAGTGG
Statistics
Matches: 203, Mismatches: 26, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.00
42 10 0.05
43 120 0.59
44 62 0.31
45 10 0.05
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (43 bp):
AATTTTTCAAATTTGTTGAGCCTCTAATGAAATGAGCCTTTTA
Found at i:12939119 original size:86 final size:86
Alignment explanation
Indices: 12938920--12939212 Score: 272
Period size: 86 Copynumber: 3.4 Consensus size: 86
12938910 AGTTAAAAAG
* * * * ** *
12938920 CTTTTCTAATTTTTCAAATTTGTTGAACCTCTGATGAA-ATAAGCCTTTTAAATTTTTCAAAAGT
1 CTTTTATAA-TTTTCAAAGTTGTTGAGCCTCTAAT-AAGAGGAGCCTTTTATATTTTTCAAAA-T
* * *
12938984 TTTTGAGCCTCTGATGAGAAGAG-
63 TGTTGAGCCTCTAATGAGATGAGT
* * * *
12939007 CTTTTTATAATTTTCAAATTTGTTGAGCTTCTAATAAGATGAGCCTTTTATGTTTTTCAAAATTG
1 C-TTTTATAATTTTCAAAGTTGTTGAGCCTCTAATAAGAGGAGCCTTTTATATTTTTCAAAATTG
12939072 TTGAGCCTCTAATGAGATGAGT
65 TTGAGCCTCTAATGAGATGAGT
* * *
12939094 CTTTTAT-ATTTTCAAAAGTTGTTGAGCCTCTAATGAGAGGAGTCTTTTATATTCTTT-AAAGTT
1 CTTTTATAATTTTC-AAAGTTGTTGAGCCTCTAATAAGAGGAGCCTTTTATATT-TTTCAAAATT
* * *
12939157 GTTAAGCCTTTCAATGAAATGAGT
64 GTTGAGCCTCT-AATGAGATGAGT
* * *
12939181 -TTTTTTAATTTTTCAAAGTCGTTGAACCTCTA
1 CTTTTATAA-TTTTCAAAGTTGTTGAGCCTCTA
12939213 TTTAGAGTGG
Statistics
Matches: 175, Mismatches: 23, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
85 6 0.03
86 81 0.46
87 76 0.43
88 12 0.07
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (86 bp):
CTTTTATAATTTTCAAAGTTGTTGAGCCTCTAATAAGAGGAGCCTTTTATATTTTTCAAAATTGT
TGAGCCTCTAATGAGATGAGT
Found at i:12939228 original size:129 final size:130
Alignment explanation
Indices: 12938928--12939239 Score: 291
Period size: 130 Copynumber: 2.4 Consensus size: 130
12938918 AGCTTTTCTA
* * * * * * * *
12938928 ATTTTTCAAATTTGTTGAACCTCTGATGAAATAAGCCTTTTA-AATTTTTCAAAAGTTTTTGAGC
1 ATTTTTCAAAATCGTTGAACCTCTAATGAGATGAGTCTTTTATGA-TTTTCAAAAGTTGTTGAGC
* * *
12938992 CTCTGATGAGAAGAGCTTTTTATAATTTTCAAATTTGTTGAGCTTCTAATAAGATGAGCCTTTTA
65 CTCTAATGAGAAGAGCTTTTTATAATTTTCAAAGTTGTTAAGCTTCTAATAAGATGAGCCTTTTA
12939057 T
130 T
* * *
12939058 GTTTTTCAAAATTGTTGAGCCTCTAATGAGATGAGTCTTTTAT-ATTTTCAAAAGTTGTTGAGCC
1 ATTTTTCAAAATCGTTGAACCTCTAATGAGATGAGTCTTTTATGATTTTCAAAAGTTGTTGAGCC
* * *
12939122 TCTAATGAGAGGAG-TCTTTTAT-ATTCTTTAAAGTTGTTAAGCCTT-TCAATGAA-ATGAG-TT
66 TCTAATGAGAAGAGCT-TTTTATAATT-TTCAAAGTTGTTAAG-CTTCT-AAT-AAGATGAGCCT
*
12939182 TTTTT
126 TTTAT
* * * *
12939187 AATTTTTCAAAGTCGTTGAACCTCTATTTAGAGTG-GT-TTTTATGTTTTTCAAA
1 -ATTTTTCAAAATCGTTGAACCTCTAATGAGA-TGAGTCTTTTATGATTTTCAAA
12939240 GGTTTTTAAG
Statistics
Matches: 151, Mismatches: 22, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
128 4 0.03
129 61 0.40
130 82 0.54
131 4 0.03
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (130 bp):
ATTTTTCAAAATCGTTGAACCTCTAATGAGATGAGTCTTTTATGATTTTCAAAAGTTGTTGAGCC
TCTAATGAGAAGAGCTTTTTATAATTTTCAAAGTTGTTAAGCTTCTAATAAGATGAGCCTTTTAT
Found at i:12939249 original size:87 final size:86
Alignment explanation
Indices: 12938972--12939250 Score: 223
Period size: 86 Copynumber: 3.2 Consensus size: 86
12938962 GCCTTTTAAA
* * * * * *
12938972 TTTTTCAAAAGTTTTTGAGCCTCTGATGAGAA-GAG-CTTTTTATAATTTTC-AAATTTGTTGAG
1 TTTTTC-AAAGTTGTTAAGCCTCTAATGA-AATGAGTC-TTTTAT-ATTTTCAAAAGTCGTTGAA
* * * *
12939034 CTTCTAATAAGATGAGCCTTTTATG
62 CCTCTAATGAGAGGAGTCTTTTATG
* * * * *
12939059 TTTTTCAAAATTGTTGAGCCTCTAATGAGATGAGTCTTTTATATTTTCAAAAGTTGTTGAGCCTC
1 TTTTTCAAAGTTGTTAAGCCTCTAATGAAATGAGTCTTTTATATTTTCAAAAGTCGTTGAACCTC
*
12939124 TAATGAGAGGAGTCTTTTATA
66 TAATGAGAGGAGTCTTTTATG
* *
12939145 TTCTTT-AAAGTTGTTAAGCCTTTCAATGAAATGAGT-TTTTTTAATTTTTC-AAAGTCGTTGAA
1 TT-TTTCAAAGTTGTTAAGCCTCT-AATGAAATGAGTCTTTTAT-A-TTTTCAAAAGTCGTTGAA
* *
12939207 CCTCTATTTAGAGTG-GT-TTTTATG
62 CCTCTAATGAGAG-GAGTCTTTTATG
*
12939231 TTTTTCAAAGGTTTTTAAGC
1 TTTTTCAAA-GTTGTTAAGC
12939251 TTATGTTTTA
Statistics
Matches: 161, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
85 10 0.06
86 91 0.57
87 54 0.34
88 6 0.04
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (86 bp):
TTTTTCAAAGTTGTTAAGCCTCTAATGAAATGAGTCTTTTATATTTTCAAAAGTCGTTGAACCTC
TAATGAGAGGAGTCTTTTATG
Found at i:12940397 original size:20 final size:21
Alignment explanation
Indices: 12940359--12940398 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12940349 GGACAGAAAG
*
12940359 GAAAATTTTGGGTTTTTTTGT
1 GAAAATTCTGGGTTTTTTTGT
12940380 GAAAATTCTGGGTTTTTTT
1 GAAAATTCTGGGTTTTTTT
12940399 CTAGATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.55
Consensus pattern (21 bp):
GAAAATTCTGGGTTTTTTTGT
Found at i:12942433 original size:60 final size:58
Alignment explanation
Indices: 12942368--12942577 Score: 174
Period size: 58 Copynumber: 3.5 Consensus size: 58
12942358 CCAAATTTAT
* * * * *
12942368 TATAATACCTTTTACCATAATTACGAAAATACTCATATTTTCATAATTGATAAAAATTAT
1 TATAATACATTTTATCATAATTA-AAAAATACTC-TATTATCATAATTGATAAAAATTAC
* * * *
12942428 TATAATGACATCTTATCATAATTATATAAATACTC--CTA-CTATAATTGATTAAAATTAC
1 TATAAT-ACATTTTATCATAATTA-AAAAATACTCTATTATC-ATAATTGATAAAAATTAC
* * * *
12942486 TATAATATCTTTTTATCATAATTAAAAAAAATCTCTATTACCATAATTGATCAAAATTAC
1 TATAATA-CATTTTATCATAATTAAAAAATA-CTCTATTATCATAATTGATAAAAATTAC
* *
12942546 TATAATACTATTCATATCATACTTAAGAAAAT
1 TATAATAC-ATT-TTATCATAATTAA-AAAAT
12942578 GCCCATCCTA
Statistics
Matches: 120, Mismatches: 20, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
57 7 0.06
58 40 0.33
59 1 0.01
60 34 0.28
61 34 0.28
62 4 0.03
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (58 bp):
TATAATACATTTTATCATAATTAAAAAATACTCTATTATCATAATTGATAAAAATTAC
Found at i:12942490 original size:58 final size:59
Alignment explanation
Indices: 12942409--12942616 Score: 165
Period size: 58 Copynumber: 3.5 Consensus size: 59
12942399 CTCATATTTT
* * *
12942409 CATAATTGATAAAAATTATTATAATGA-CATCTTATCATAATT-ATATAAATACTC-CTAC
1 CATAATTGATAAAAATTACTATAAT-ATCATCTTATCATAATTAAAAAAAAT-CTCACTAC
* * * * *
12942467 TATAATTGATTAAAATTACTATAATATCTTTTTATCATAATTAAAAAAAATCTCTATTAC
1 CATAATTGATAAAAATTACTATAATATCATCTTATCATAATTAAAAAAAATCTC-ACTAC
* * * * *
12942527 CATAATTGATCAAAATTACTATAATA-CTATTCATATCATACTT-AAGAAAATGCCCATCCTAC
1 CATAATTGATAAAAATTACTATAATATC-A-TCTTATCATAATTAAAAAAAAT-CTCA--CTAC
* * *
12942589 CATAAGTGATTAAAATTACTATTATATC
1 CATAATTGATAAAAATTACTATAATATC
12942617 TTTTATACCA
Statistics
Matches: 120, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
57 1 0.01
58 38 0.32
59 7 0.06
60 35 0.29
61 12 0.10
62 26 0.22
63 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.38
Consensus pattern (59 bp):
CATAATTGATAAAAATTACTATAATATCATCTTATCATAATTAAAAAAAATCTCACTAC
Found at i:12944257 original size:2 final size:2
Alignment explanation
Indices: 12944244--12944277 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
12944234 ATAGCAATTC
*
12944244 AT AT AT AC AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
12944278 AAATGTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12944448 original size:26 final size:26
Alignment explanation
Indices: 12944399--12944449 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12944389 TTTTTTATAT
12944399 TATTTTAATATTATATTATTATATCA
1 TATTTTAATATTATATTATTATATCA
12944425 TATTTTAA-ATTACTA-TATTCATATC
1 TATTTTAATATTA-TATTATT-ATATC
12944450 CAGCTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTTAATATTATATTATTATATCA
Found at i:12944975 original size:32 final size:32
Alignment explanation
Indices: 12944901--12944976 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 32
12944891 CAAGATTGGT
*
12944901 TAATAATTTTAAATTTAAAAAATAGTTTTATAG
1 TAAT-ATTTAAAATTTAAAAAATAGTTTTATAG
* *
12944934 TATTTTTTAAAATATTAAAAAATA-TTTTATA-
1 TAATATTTAAAAT-TTAAAAAATAGTTTTATAG
12944965 TCAATATTTAAA
1 T-AATATTTAAA
12944977 TTATAATTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 1 0.03
32 22 0.61
33 13 0.36
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (32 bp):
TAATATTTAAAATTTAAAAAATAGTTTTATAG
Found at i:12945571 original size:30 final size:29
Alignment explanation
Indices: 12945515--12945574 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
12945505 AAAACCTATA
**
12945515 TTTTATTATATCCAAATAAATTTTTATTT
1 TTTTATTATATCCAAATAAACCTTTATTT
*
12945544 TTTTATTTATATCCAAATATACCTTTATTT
1 TTTTA-TTATATCCAAATAAACCTTTATTT
12945574 T
1 T
12945575 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTATTATATCCAAATAAACCTTTATTT
Found at i:12945949 original size:41 final size:41
Alignment explanation
Indices: 12945892--12945974 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
12945882 GCATCTAAGA
* * *
12945892 TAGTTTATTAGGATAATATTTATCCATTGGTGTCATTAGGT
1 TAGTTTATTAGCATAATAGTTATCCATTGGTATCATTAGGT
*
12945933 TAGTTTATTAGCATAATAGTTATCCTTTGGTATCATTAGGT
1 TAGTTTATTAGCATAATAGTTATCCATTGGTATCATTAGGT
12945974 T
1 T
12945975 TCCAACAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (41 bp):
TAGTTTATTAGCATAATAGTTATCCATTGGTATCATTAGGT
Found at i:12949707 original size:20 final size:21
Alignment explanation
Indices: 12949666--12949708 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
12949656 TCATAATAGG
12949666 AAAATATTGTTTTCCATCAAA
1 AAAATATTGTTTTCCATCAAA
* *
12949687 AAAATATT-TTTTCTATTAAA
1 AAAATATTGTTTTCCATCAAA
12949707 AA
1 AA
12949709 TATTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAATATTGTTTTCCATCAAA
Found at i:12949894 original size:18 final size:16
Alignment explanation
Indices: 12949867--12949902 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
12949857 ATCATTTATC
12949867 AAAAATATTTTTAATAA
1 AAAAATATTTTTAA-AA
12949884 AAAATATATTTTTAAAA
1 AAAA-ATATTTTTAAAA
12949901 AA
1 AA
12949903 TTAAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAAATATTTTTAAAA
Found at i:12949972 original size:33 final size:33
Alignment explanation
Indices: 12949935--12950036 Score: 86
Period size: 33 Copynumber: 3.1 Consensus size: 33
12949925 TAACTCTTTT
*
12949935 TAAAAAATTCCATATCATTTTTAAAAAATTAAG
1 TAAAAAATTCCATATCATTTTTAAAAAATTAAA
* *
12949968 TAAAAACTT-C-TAT-ATTGATTTATAAAATTAAA
1 TAAAAAATTCCATATCATT--TTTAAAAAATTAAA
* * * *
12950000 TAAAAAAACTCTATATCA-TTTTAAAATATTAAT
1 T-AAAAAATTCCATATCATTTTTAAAAAATTAAA
12950033 TAAA
1 TAAA
12950037 TTTTTCATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
30 3 0.06
31 3 0.06
32 17 0.31
33 26 0.48
35 4 0.07
36 1 0.02
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (33 bp):
TAAAAAATTCCATATCATTTTTAAAAAATTAAA
Found at i:12951478 original size:22 final size:21
Alignment explanation
Indices: 12951430--12951479 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
12951420 TTTAAATAAA
12951430 TATGAATTTTTAAAAAATTCAT
1 TATGAATTTTTAAAAAATT-AT
*
12951452 AATGATATTTTTAAAAAAATT-T
1 TATGA-ATTTTT-AAAAAATTAT
12951474 TATGAA
1 TATGAA
12951480 ATTATAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 9 0.38
23 6 0.25
24 8 0.33
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (21 bp):
TATGAATTTTTAAAAAATTAT
Found at i:12951882 original size:23 final size:23
Alignment explanation
Indices: 12951856--12951902 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12951846 TTATATTTTT
* * *
12951856 ATTTTTATTTTAATTATAATACA
1 ATTTTTATATAAAATATAATACA
*
12951879 ATTTTTGTATAAAATATAATACA
1 ATTTTTATATAAAATATAATACA
12951902 A
1 A
12951903 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTTTATATAAAATATAATACA
Found at i:12954157 original size:20 final size:21
Alignment explanation
Indices: 12954120--12954158 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
12954110 GTGATAGGAA
* *
12954120 TTCTGAAATAACTGAAATGTT
1 TTCTGAAATAAATCAAATGTT
12954141 TTCTG-AATAAATCAAATG
1 TTCTGAAATAAATCAAATG
12954159 ACCAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (21 bp):
TTCTGAAATAAATCAAATGTT
Found at i:12965122 original size:29 final size:28
Alignment explanation
Indices: 12965055--12965123 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
12965045 ATTAGACTCG
* * *
12965055 AAATTAATAAAATATTATTTTTAAATAT
1 AAATAAATAAAATATCATTTATAAATAT
**
12965083 AAATATTTAAAATATCATTATATAAATAT
1 AAATAAATAAAATATCATT-TATAAATAT
*
12965112 ATATAAATAAAA
1 AAATAAATAAAA
12965124 AATTAATAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
AAATAAATAAAATATCATTTATAAATAT
Found at i:12968355 original size:2 final size:2
Alignment explanation
Indices: 12968342--12968371 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12968332 GCTTCAATTA
*
12968342 AT AT AT AC 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
12968372 GAAACTCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12976428 original size:8 final size:8
Alignment explanation
Indices: 12976415--12976441 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12976405 GAAATGATTC
12976415 AAATTTTA
1 AAATTTTA
12976423 AAATTTTA
1 AAATTTTA
12976431 AAATTTTA
1 AAATTTTA
12976439 AAA
1 AAA
12976442 AATTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATTTTA
Found at i:12980905 original size:109 final size:109
Alignment explanation
Indices: 12980714--12980933 Score: 422
Period size: 109 Copynumber: 2.0 Consensus size: 109
12980704 TAGCCACTCA
12980714 CATTAGGTTTGGTTATAGCAAGTTACATAAGGCCAAATCTAACAACATGCAAGTTTGCCAAGGCT
1 CATTAGGTTTGGTTATAGCAAGTTACATAAGGCCAAATCTAACAACATGCAAGTTTGCCAAGGCT
*
12980779 TGGTAAGAGTAAGCAAACCTAACTAAGATTTGTCTAAACAAAGG
66 TGGTAAGAGTAAGCAAACCTAACTAAGATCTGTCTAAACAAAGG
12980823 CATTAGGTTTGGTTATAGCAAGTTACATAAGGCCAAATCTAACAACATGCAAGTTTGCCAAGGCT
1 CATTAGGTTTGGTTATAGCAAGTTACATAAGGCCAAATCTAACAACATGCAAGTTTGCCAAGGCT
*
12980888 TGGTAAGAGTAAGCAAACCTAACTAGGATCTGTCTAAACAAAGG
66 TGGTAAGAGTAAGCAAACCTAACTAAGATCTGTCTAAACAAAGG
12980932 CA
1 CA
12980934 ACAAAGAAGT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (109 bp):
CATTAGGTTTGGTTATAGCAAGTTACATAAGGCCAAATCTAACAACATGCAAGTTTGCCAAGGCT
TGGTAAGAGTAAGCAAACCTAACTAAGATCTGTCTAAACAAAGG
Found at i:12982172 original size:16 final size:17
Alignment explanation
Indices: 12982151--12982183 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12982141 ATACGAGTAC
12982151 ACATG-TAACATATTTA
1 ACATGTTAACATATTTA
12982167 ACATGTTTAACATATTT
1 ACATG-TTAACATATTT
12982184 TTTATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (17 bp):
ACATGTTAACATATTTA
Found at i:12982206 original size:7 final size:7
Alignment explanation
Indices: 12982194--12982223 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
12982184 TTTATATTTA
12982194 TTTTAAT
1 TTTTAAT
12982201 TTTTAAT
1 TTTTAAT
12982208 TTTTAATT
1 TTTTAA-T
12982216 TTTTAAT
1 TTTTAAT
12982223 T
1 T
12982224 ATGATACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTAAT
Found at i:12982212 original size:19 final size:20
Alignment explanation
Indices: 12982180--12982217 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12982170 TGTTTAACAT
*
12982180 ATTTTTTATATTT-ATTTTA
1 ATTTTTAATATTTAATTTTA
*
12982199 ATTTTTAATTTTTAATTTT
1 ATTTTTAATATTTAATTTT
12982218 TTAATTATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTTAATATTTAATTTTA
Found at i:12982213 original size:14 final size:15
Alignment explanation
Indices: 12982194--12982223 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12982184 TTTATATTTA
12982194 TTTTAA-TTTTTAAT
1 TTTTAATTTTTTAAT
12982208 TTTTAATTTTTTAAT
1 TTTTAATTTTTTAAT
12982223 T
1 T
12982224 ATGATACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTAATTTTTTAAT
Found at i:12982356 original size:45 final size:45
Alignment explanation
Indices: 12982292--12982379 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
12982282 ATACTCATTC
12982292 AATAATTATTATAACATTATTTTTTATATTAATAATATAAATATT
1 AATAATTATTATAACATTATTTTTTATATTAATAATATAAATATT
12982337 AATAATTATTATATA-ATTATTTTTTATATTAATAATATAAATA
1 AATAATTATTATA-ACATTATTTTTTATATTAATAATATAAATA
12982380 CTATAAACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (45 bp):
AATAATTATTATAACATTATTTTTTATATTAATAATATAAATATT
Done.