Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 26 of 27
Found at i:4657671 original size:2 final size:2
Alignment explanation
Indices: 4657664--4657701 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
4657654 TCCTGCCAAA
*
4657664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4657702 GTATGTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4657706 original size:12 final size:12
Alignment explanation
Indices: 4657664--4657709 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
4657654 TCCTGCCAAA
*
4657664 ATATATATATAT
1 ATATATGTATAT
*
4657676 ATATATATATAT
1 ATATATGTATAT
4657688 ATATATGTATAT
1 ATATATGTATAT
*
4657700 ATGTATGTAT
1 ATATATGTAT
4657710 GTATTAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:4657710 original size:8 final size:8
Alignment explanation
Indices: 4657664--4657713 Score: 64
Period size: 8 Copynumber: 6.2 Consensus size: 8
4657654 TCCTGCCAAA
*
4657664 ATATATAT
1 ATATATGT
*
4657672 ATATATAT
1 ATATATGT
*
4657680 ATATATAT
1 ATATATGT
4657688 ATATATGT
1 ATATATGT
4657696 ATATATGT
1 ATATATGT
*
4657704 ATGTATGT
1 ATATATGT
4657712 AT
1 AT
4657714 TAGTATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (8 bp):
ATATATGT
Found at i:4675880 original size:75 final size:74
Alignment explanation
Indices: 4675787--4676041 Score: 298
Period size: 75 Copynumber: 3.4 Consensus size: 74
4675777 TTATAACTAA
* * * * *
4675787 GATTTATGTGGCGGGTACAAGTCTCGCAGTCAGAGTAAATATTGACTACCAGGATTCTGTCTTTT
1 GATTTATGTGACGAGTACAAGTCTAGCAGTCAGAGTGAGTATTGACTACCAGGATTCTGTC-TTT
4675852 TGGCGATCAG
65 TGGCGATCAG
* * * * * *
4675862 GATTTATGTGACGAGTACAAGTCTGGCAGCCAGAGTGAGTATTGGCTACTATGATTCCGTCATTT
1 GATTTATGTGACGAGTACAAGTCTAGCAGTCAGAGTGAGTATTGACTACCAGGATTCTGTC-TTT
4675927 TGGCGATCAG
65 TGGCGATCAG
* * *
4675937 GATTTATGTGACGAGCACAAGTCTAACAGTCAGAGTGAGTATT-ATCTATCAGGATTCTGTCTTT
1 GATTTATGTGACGAGTACAAGTCTAGCAGTCAGAGTGAGTATTGA-CTACCAGGATTCTGTCTTT
** *
4676001 T-GTAATCAA
65 TGGCGATCAG
* *
4676010 GATTTATGTGACGAGTATAAGTCTAACAGTCA
1 GATTTATGTGACGAGTACAAGTCTAGCAGTCA
4676042 AAGTCAGAGT
Statistics
Matches: 154, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
73 35 0.23
74 4 0.03
75 115 0.75
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (74 bp):
GATTTATGTGACGAGTACAAGTCTAGCAGTCAGAGTGAGTATTGACTACCAGGATTCTGTCTTTT
GGCGATCAG
Found at i:4675918 original size:149 final size:149
Alignment explanation
Indices: 4675638--4675909 Score: 323
Period size: 149 Copynumber: 1.8 Consensus size: 149
4675628 TGACGACCAG
* * * * *
4675638 GATTTATGTGGCGAGCACAGGTCTAGTAGTCAGAGTGAATGTTGACTATCAGGATTTCGTCCTTC
1 GATTTATGTGGCGAGCACAAGTCTAGCAGTCAGAGTAAATATTGACTACCAGGATTTCGTCCTTC
* * * * *
4675703 TAACGATCAAGATTTATGTGACGAGCACAGATTTGATAACTAGAGTGAGTGTTGTCTATCAAGAT
66 TAACGATCAAGATTTATGTGACGAGCACAGATCTGACAACCAGAGTGAGTATTGGCTATCAAGAT
4675768 TCTATTTTTTTATAACTAA
131 TCTATTTTTTTATAACTAA
* * * *
4675787 GATTTATGTGGCGGGTACAAGTCTCGCAGTCAGAGTAAATATTGACTACCAGGA-TTCTGTCTTT
1 GATTTATGTGGCGAGCACAAGTCTAGCAGTCAGAGTAAATATTGACTACCAGGATTTC-GTCCTT
* ** * * * *
4675851 TTGGCGATCAGGATTTATGTGACGAGTACA-AGTCTGGCAGCCAGAGTGAGTATTGGCTA
65 CTAACGATCAAGATTTATGTGACGAGCACAGA-TCTGACAACCAGAGTGAGTATTGGCTA
4675910 CTATGATTCC
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
148 4 0.04
149 96 0.96
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (149 bp):
GATTTATGTGGCGAGCACAAGTCTAGCAGTCAGAGTAAATATTGACTACCAGGATTTCGTCCTTC
TAACGATCAAGATTTATGTGACGAGCACAGATCTGACAACCAGAGTGAGTATTGGCTATCAAGAT
TCTATTTTTTTATAACTAA
Found at i:4676134 original size:42 final size:42
Alignment explanation
Indices: 4676038--4676164 Score: 211
Period size: 42 Copynumber: 3.0 Consensus size: 42
4676028 AAGTCTAACA
*
4676038 GTCAAAGTCAGAGTGAATGTTGGCTACTAGAATTTCAGTCTTT
1 GTCAAAGCCAGAGTGAATGTTGGCTACTAGAATTTC-GTCTTT
4676081 GTCAAAGCCAGAGTGAATGTTGGCTACTAGAATTTCGTCTTT
1 GTCAAAGCCAGAGTGAATGTTGGCTACTAGAATTTCGTCTTT
*
4676123 GTCAAAGCCAGAGTGAATGTTGGTTACTA-AGATTTCGTCTTT
1 GTCAAAGCCAGAGTGAATGTTGGCTACTAGA-ATTTCGTCTTT
4676165 CTGACGATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
41 1 0.01
42 45 0.56
43 35 0.43
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (42 bp):
GTCAAAGCCAGAGTGAATGTTGGCTACTAGAATTTCGTCTTT
Found at i:4676262 original size:75 final size:75
Alignment explanation
Indices: 4676170--4676311 Score: 203
Period size: 75 Copynumber: 1.9 Consensus size: 75
4676160 TCTTTCTGAC
* * * *
4676170 GATCAGAATTTACGTGATGAGCATAAATCTAGCAGCTAGAGTGAGTATTGATTACCAAAATTTCA
1 GATCAGAATTTACGTGATGAGCACAAATCTAACAGCCAGAGTGAGTATTGACTACCAAAATTTCA
4676235 TCCTTCGGGT
66 TCCTTCGGGT
* ** * *
4676245 GATCAGAATTTATGTGATGAGCACAGGTTTAACAGCCAGAGTGAGTATTGACTATCAAAATTTCA
1 GATCAGAATTTACGTGATGAGCACAAATCTAACAGCCAGAGTGAGTATTGACTACCAAAATTTCA
4676310 TC
66 TC
4676312 TTTTTAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (75 bp):
GATCAGAATTTACGTGATGAGCACAAATCTAACAGCCAGAGTGAGTATTGACTACCAAAATTTCA
TCCTTCGGGT
Found at i:4678262 original size:18 final size:16
Alignment explanation
Indices: 4678168--4678262 Score: 54
Period size: 18 Copynumber: 5.7 Consensus size: 16
4678158 ATATTTAACT
*
4678168 ATTTGTATTATATTCGTA
1 ATTT-TATTATATT-ATA
4678186 TATTTTATTATATTATA
1 -ATTTTATTATATTATA
**
4678203 ATTTTATT-TAAAAT-
1 ATTTTATTATATTATA
*
4678217 ATTTTA-TATTTATATAA
1 ATTTTATTATAT-TAT-A
4678234 ATTTT-TATATATTAATA
1 ATTTTAT-TATATT-ATA
4678251 ATTTATATTATA
1 ATTT-TATTATA
4678263 AAAATTTAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
13 1 0.02
14 7 0.12
15 6 0.10
16 8 0.13
17 13 0.22
18 20 0.33
19 5 0.08
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTTTATTATATTATA
Found at i:4678268 original size:15 final size:15
Alignment explanation
Indices: 4678202--4678270 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 15
4678192 ATTATATTAT
4678202 AATTT-TATT-TAAA
1 AATTTATATTATAAA
*
4678215 ATATTTTATATTTATATA
1 A-A-TTTATA-TTATAAA
* *
4678233 AATTTTTATATATTAAT
1 AATTTATAT-TA-TAAA
4678250 AATTTATATTATAAA
1 AATTTATATTATAAA
4678265 AATTTA
1 AATTTA
4678271 AAATATATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
13 1 0.02
14 1 0.02
15 13 0.30
16 11 0.26
17 13 0.30
18 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTATATTATAAA
Found at i:4678277 original size:33 final size:33
Alignment explanation
Indices: 4678214--4678278 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
4678204 TTTTATTTAA
* * **
4678214 AATATTTTATATTTATATAAATTTTTATATATT
1 AATAATTTATATTTATAAAAATTTAAATATATT
4678247 AATAATTTATA-TTATAAAAATTTAAAATATAT
1 AATAATTTATATTTATAAAAATTT-AAATATAT
4678279 ATTTATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
AATAATTTATATTTATAAAAATTTAAATATATT
Found at i:4678290 original size:15 final size:15
Alignment explanation
Indices: 4678221--4678296 Score: 58
Period size: 15 Copynumber: 5.5 Consensus size: 15
4678211 TAAAATATTT
4678221 TATATTTATATAA-A
1 TATATTTATATAATA
*
4678235 T-T-TTTATATATTA
1 TATATTTATATAATA
*
4678248 -ATAATTTATATTATA
1 TAT-ATTTATATAATA
* *
4678263 AAAATTTA-A-AATA
1 TATATTTATATAATA
4678276 TATATTTATATAATA
1 TATATTTATATAATA
4678291 T-TATTT
1 TATATTT
4678297 TTTAACTATG
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
12 8 0.17
13 12 0.25
14 8 0.17
15 19 0.40
16 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATTTATATAATA
Found at i:4689060 original size:72 final size:72
Alignment explanation
Indices: 4688956--4689098 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
4688946 TTACTAACAA
* * * *
4688956 TTTAAAAATAAGATATAATTTTTTTATTATATTAAAATTTTAATAATTTTTTATCATGATTACAA
1 TTTAAAAATAAAAAATAATTTTTTTATCATATTAAAATTTTAATAATTTTTTATCATAATTACAA
4689021 AGCATGT
66 AGCATGT
* *
4689028 TTTAAGAAATAAAAAATAA-TTTTTTATCATATTAAAATTTTAATAATTTTTTATTATAATTACG
1 TTTAA-AAATAAAAAATAATTTTTTTATCATATTAAAATTTTAATAATTTTTTATCATAATTACA
4689092 AAGCATG
65 AAGCATG
4689099 CATTACCTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 53 0.83
73 11 0.17
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (72 bp):
TTTAAAAATAAAAAATAATTTTTTTATCATATTAAAATTTTAATAATTTTTTATCATAATTACAA
AGCATGT
Found at i:4689064 original size:22 final size:22
Alignment explanation
Indices: 4688997--4689064 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
4688987 TTAAAATTTT
*
4688997 AATAATTTTTTATCATGATTACA
1 AATAATTTTTTATCAT-ATTAAA
** * ** * *
4689020 AAGCATGTTTTAAGAAATAAAA
1 AATAATTTTTTATCATATTAAA
4689042 AATAATTTTTTATCATATTAAA
1 AATAATTTTTTATCATATTAAA
4689064 A
1 A
4689065 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 15, Indels: 1
0.65 0.33 0.02
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (22 bp):
AATAATTTTTTATCATATTAAA
Found at i:4690682 original size:20 final size:20
Alignment explanation
Indices: 4690657--4690695 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4690647 TTTCAACAGA
4690657 TTGAGAGCAGAGTTGTTGGC
1 TTGAGAGCAGAGTTGTTGGC
*
4690677 TTGAGAGCAGAGTTTTTGG
1 TTGAGAGCAGAGTTGTTGG
4690696 ACTGGGCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.08, G:0.38, T:0.33
Consensus pattern (20 bp):
TTGAGAGCAGAGTTGTTGGC
Found at i:4695736 original size:3 final size:3
Alignment explanation
Indices: 4695730--4695768 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
4695720 CCCCAAACTT
4695730 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TCTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TT
4695769 TATTGTTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:4704716 original size:2 final size:2
Alignment explanation
Indices: 4704709--4704737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4704699 CATACATAAT
4704709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4704738 TGAATTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4705901 original size:3 final size:3
Alignment explanation
Indices: 4705893--4705967 Score: 75
Period size: 3 Copynumber: 25.3 Consensus size: 3
4705883 TTCCAATTAC
* *
4705893 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA CTA A-A ATTCA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-T-A
* *
4705942 A-C ATA A-A ATA ACA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4705968 AATCATAACT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.08
3 52 0.88
5 2 0.03
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:4717001 original size:21 final size:20
Alignment explanation
Indices: 4716963--4717001 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4716953 GTTGTTGTTG
4716963 TTTTTTTTTTTAAGAATATT
1 TTTTTTTTTTTAAGAATATT
4716983 TTTTTATTTATTTAA-AATA
1 TTTTT-TTT-TTTAAGAATA
4717002 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTTTTTTTTAAGAATATT
Found at i:4726256 original size:2 final size:2
Alignment explanation
Indices: 4726251--4726280 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4726241 CATCTCTCGT
4726251 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4726281 CTTCGTTCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4727937 original size:3 final size:3
Alignment explanation
Indices: 4727929--4727972 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4727919 TCTGTATTTA
4727929 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4727973 AGCATAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4728827 original size:2 final size:2
Alignment explanation
Indices: 4728820--4728846 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4728810 TTTAGAAATA
4728820 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
4728847 TGGAGAATTG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4739395 original size:2 final size:2
Alignment explanation
Indices: 4739388--4739417 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4739378 TCACGAAGAT
4739388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4739418 ATAGTGAAGA
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):
TA
Found at i:4739891 original size:6 final size:6
Alignment explanation
Indices: 4739874--4739906 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
4739864 TAAATACTAT
4739874 TAGTTC -AGTTC TAGTTC TAGTTC TAGTTC TAGT
1 TAGTTC TAGTTC TAGTTC TAGTTC TAGTTC TAGT
4739907 AGTGAAAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (6 bp):
TAGTTC
Found at i:4753077 original size:2 final size:2
Alignment explanation
Indices: 4753070--4753111 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
4753060 TAAGGATTTC
* *
4753070 TA TA TA TA TG TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4753112 CGCACCTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4754179 original size:2 final size:2
Alignment explanation
Indices: 4754172--4754196 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4754162 TATTATTGTG
4754172 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
4754197 GTAAATACAC
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:4754290 original size:2 final size:2
Alignment explanation
Indices: 4754283--4754309 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4754273 AATTTCTTTT
4754283 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
4754310 GTTTGACTAC
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:4755097 original size:32 final size:32
Alignment explanation
Indices: 4755022--4755122 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 32
4755012 GAGAACTTAA
* * *
4755022 TTTATATAAATTTTAATATCA-TAATTA-TAAA
1 TTTATATAAATTTTAATAT-ATTAATAATTTAT
4755053 TTTATATAAATTTTAATATATTAATAATTTAT
1 TTTATATAAATTTTAATATATTAATAATTTAT
* * *
4755085 TTTATATCAATTTTAACATATTTATATATTTAT
1 TTTATATAAATTTTAATATATTAATA-ATTTAT
*
4755118 ATTAT
1 TTTAT
4755123 GTTTTCATTA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
30 1 0.02
31 24 0.40
32 25 0.42
33 10 0.17
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (32 bp):
TTTATATAAATTTTAATATATTAATAATTTAT
Found at i:4755711 original size:16 final size:17
Alignment explanation
Indices: 4755685--4755716 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4755675 TACTTTATTT
4755685 TAAAAATTATTTTTAAA
1 TAAAAATTATTTTTAAA
4755702 TAAAAA-TATTTTTAA
1 TAAAAATTATTTTTAA
4755717 TAATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAATTATTTTTAAA
Found at i:4756388 original size:23 final size:21
Alignment explanation
Indices: 4756356--4756399 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4756346 TATGATTATA
4756356 AATTTAAAAGATATAAAAATATT
1 AATTTAAAAG-T-TAAAAATATT
*
4756379 AATTTTAAAGTTAAAAATATT
1 AATTTAAAAGTTAAAAATATT
4756400 TATAGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 1 0.05
23 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
AATTTAAAAGTTAAAAATATT
Found at i:4761898 original size:14 final size:14
Alignment explanation
Indices: 4761879--4761906 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4761869 TGCATACATG
4761879 TATACATACATACA
1 TATACATACATACA
4761893 TATACATACATACA
1 TATACATACATACA
4761907 AACTGACATT
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:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
TATACATACATACA
Found at i:4762517 original size:2 final size:2
Alignment explanation
Indices: 4762510--4762536 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4762500 TGTTCCTTTT
4762510 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
4762537 TTTCATCTAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4762812 original size:7 final size:7
Alignment explanation
Indices: 4762800--4762845 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
4762790 GTGTATGGAT
4762800 TGGCAAA
1 TGGCAAA
4762807 TGGCAAA
1 TGGCAAA
4762814 TGGCAAA
1 TGGCAAA
4762821 TGGCAAA
1 TGGCAAA
4762828 TGGCAAA
1 TGGCAAA
4762835 TGGC-AA
1 TGGCAAA
4762841 TGGCA
1 TGGCA
4762846 TTCTAGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.15
Consensus pattern (7 bp):
TGGCAAA
Found at i:4763649 original size:16 final size:17
Alignment explanation
Indices: 4763628--4763660 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4763618 TGGTGGCGCC
4763628 AGTG-AAACAATAATTA
1 AGTGAAAACAATAATTA
*
4763644 AGTGAAAACTATAATTA
1 AGTGAAAACAATAATTA
4763661 GTATTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (17 bp):
AGTGAAAACAATAATTA
Found at i:4766517 original size:5 final size:5
Alignment explanation
Indices: 4766507--4766531 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4766497 TGGCATGCAA
4766507 GAGAG GAGAG GAGAG GAGAG GAGAG
1 GAGAG GAGAG GAGAG GAGAG GAGAG
4766532 TAATTAAGTG
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:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
GAGAG
Found at i:4767805 original size:3 final size:3
Alignment explanation
Indices: 4767797--4767850 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
4767787 GGCTTTCATG
4767797 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4767845 ATA ATA
1 ATA ATA
4767851 TAAGTGTGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4768387 original size:2 final size:2
Alignment explanation
Indices: 4768380--4768409 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4768370 AATTAGTTTT
*
4768380 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4768410 CACCCGCAAA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4768718 original size:2 final size:2
Alignment explanation
Indices: 4768707--4768747 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4768697 CAATACATGC
4768707 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4768748 GCATGCCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4769308 original size:2 final size:2
Alignment explanation
Indices: 4769301--4769338 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4769291 ACTTACAGCA
* *
4769301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4769339 TAAAATTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4770723 original size:10 final size:10
Alignment explanation
Indices: 4770708--4770747 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 10
4770698 TACACGTGTC
4770708 AATATAATAT
1 AATATAATAT
4770718 AATATAATA-
1 AATATAATAT
4770727 AATA-AATAT
1 AATATAATAT
4770736 -ATATAA-AT
1 AATATAATAT
4770744 AATA
1 AATA
4770748 ATTAGATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 9 0.33
9 9 0.33
10 9 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AATATAATAT
Found at i:4770747 original size:13 final size:13
Alignment explanation
Indices: 4770709--4770747 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
4770699 ACACGTGTCA
4770709 ATATAATATAATAT
1 ATATAA-ATAATAT
4770723 A-ATAAATAAATAT
1 ATATAAAT-AATAT
4770736 ATATAAATAATA
1 ATATAAATAATA
4770748 ATTAGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 14 0.61
14 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:4770747 original size:21 final size:22
Alignment explanation
Indices: 4770708--4770758 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
4770698 TACACGTGTC
4770708 AATATAATATAATATAATAAATA
1 AATAT-ATATAATATAATAAATA
*
4770731 AATATATATAA-ATAATAATTA
1 AATATATATAATATAATAAATA
*
4770752 GATATAT
1 AATATAT
4770759 TAGAGATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 15 0.58
22 6 0.23
23 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AATATATATAATATAATAAATA
Found at i:4770823 original size:25 final size:28
Alignment explanation
Indices: 4770784--4770837 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
4770774 TATTCTTGTT
*
4770784 TTTTTATAAGAATAT-T-T-TTTATTTA
1 TTTTTACAAGAATATATCTATTTATTTA
*
4770809 TTTTTACAAGTATATATCTATTTATTTA
1 TTTTTACAAGAATATATCTATTTATTTA
4770837 T
1 T
4770838 ATAATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.54
26 1 0.04
27 1 0.04
28 9 0.38
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (28 bp):
TTTTTACAAGAATATATCTATTTATTTA
Found at i:4770860 original size:15 final size:15
Alignment explanation
Indices: 4770819--4770860 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
4770809 TTTTTACAAG
4770819 TATATATCTATTTATT
1 TATATAT-TATTTATT
*
4770835 TATATAATATTTATT
1 TATATATTATTTATT
4770850 T-TAATATTATT
1 TAT-ATATTATT
4770861 AAAAATTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.04
15 16 0.70
16 6 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATATTATTTATT
Found at i:4771790 original size:6 final size:7
Alignment explanation
Indices: 4771761--4771789 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4771751 TGTTCAAAAA
4771761 AAATCTC
1 AAATCTC
4771768 AAATCTC
1 AAATCTC
4771775 AAATCTC
1 AAATCTC
4771782 -AATCTC
1 AAATCTC
4771788 AA
1 AA
4771790 TGTCATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATCTC
Found at i:4774141 original size:2 final size:2
Alignment explanation
Indices: 4774134--4774172 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4774124 TTTCCCATTG
*
4774134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4774173 AAATCAATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4776748 original size:20 final size:20
Alignment explanation
Indices: 4776725--4776763 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4776715 AAAAAGTTGA
4776725 AATAAAATTAAAAAATAATT
1 AATAAAATTAAAAAATAATT
*
4776745 AATAAAATTAATAAATAAT
1 AATAAAATTAAAAAATAAT
4776764 ATTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAATTAAAAAATAATT
Found at i:4777002 original size:22 final size:22
Alignment explanation
Indices: 4776962--4777008 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
4776952 AAATACTATT
4776962 AAAAATAGTTAATACAAAATTCAA
1 AAAAATAGTTAATA-AAAATT-AA
*
4776986 AAAAATATTTAAT-AAAATTAA
1 AAAAATAGTTAATAAAAATTAA
4777007 AA
1 AA
4777009 TATGAGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 6 0.27
24 12 0.55
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAATAGTTAATAAAAATTAA
Found at i:4777580 original size:17 final size:17
Alignment explanation
Indices: 4777560--4777597 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4777550 AAATAAAATT
4777560 AATTAAT-ATTATAAAAA
1 AATTAATGATT-TAAAAA
*
4777577 AATTATTGATTTAAAAA
1 AATTAATGATTTAAAAA
4777594 AATT
1 AATT
4777598 TCGAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTAATGATTTAAAAA
Found at i:4777593 original size:18 final size:20
Alignment explanation
Indices: 4777549--4777595 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
4777539 ATTAAAAAAA
*
4777549 TAAATAAAATTAATTAATAT
1 TAAAAAAAATTAATTAATAT
*
4777569 TATAAAAAAATT-ATTGAT-T
1 TA-AAAAAAATTAATTAATAT
4777588 TAAAAAAA
1 TAAAAAAA
4777596 TTTCGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 3 0.12
20 7 0.29
21 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAAAAAATTAATTAATAT
Found at i:4777832 original size:194 final size:194
Alignment explanation
Indices: 4777454--4777834 Score: 554
Period size: 194 Copynumber: 2.0 Consensus size: 194
4777444 AATCTATATA
* * *
4777454 TATTTATTAATTAATATTATGAAGTTTAAATTTAATGAATCTATATAAATTAAAAAAAGAGTTAA
1 TATTTATTAATTAATATTATAAAATTTAAACTTAATGAATCTATATAAATTAAAAAAAGAGTTAA
* * * *
4777519 AGCAGAATTCTTAATAATTTATTAAAAAAATAAATAAAATTAATTAATATTATAAAAAAATTATT
66 AACAAAATTCTTAATAATTCATGAAAAAAATAAAT-AAATTAATTAATATTATAAAAAAATTATT
4777584 GATTTAAAAAAATTTCGAGAAAAAACCAATATAAACATTAGCATTTATGTTAAAAAACTATTTTT
130 GATTTAAAAAAATTTCGAGAAAAAACCAATATAAACATTAGCATTTATGTTAAAAAACTATTTTT
* *
4777649 TATTTATTAATTAATATTATAAAATTTAAACTTAATGAATTTATATAAATT-AAAAATGAGTTAA
1 TATTTATTAATTAATATTATAAAATTTAAACTTAATGAATCTATATAAATTAAAAAAAGAGTTAA
* *
4777713 AACAAAATTCTTAGTAATTCACTGAAAAAAA-AAAT-TATTAATTAATATTATAAAAAAATTATT
66 AACAAAATTCTTAATAATTCA-TGAAAAAAATAAATAAATTAATTAATATTATAAAAAAATTATT
* * * *
4777776 GATTTCCAAAAAATCTTTGAG-AAAAACTTAATATAAATATTAGCATTTATGTTAAAAAA
130 GATTT-AAAAAAAT-TTCGAGAAAAAAC-CAATATAAACATTAGCATTTATGTTAAAAAA
4777835 ATTATATTTT
Statistics
Matches: 167, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
192 32 0.19
193 13 0.08
194 67 0.40
195 55 0.33
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.38
Consensus pattern (194 bp):
TATTTATTAATTAATATTATAAAATTTAAACTTAATGAATCTATATAAATTAAAAAAAGAGTTAA
AACAAAATTCTTAATAATTCATGAAAAAAATAAATAAATTAATTAATATTATAAAAAAATTATTG
ATTTAAAAAAATTTCGAGAAAAAACCAATATAAACATTAGCATTTATGTTAAAAAACTATTTTT
Found at i:4780052 original size:2 final size:2
Alignment explanation
Indices: 4780045--4780075 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4780035 TGATGAGCCC
4780045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4780076 GTTTTGTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4781132 original size:2 final size:2
Alignment explanation
Indices: 4781125--4781154 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4781115 AAGTCTGACA
4781125 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
4781155 TAGGATAATA
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:4781719 original size:2 final size:2
Alignment explanation
Indices: 4781714--4781738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4781704 ATATATATAT
4781714 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
4781739 AATTACTCAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4782251 original size:2 final size:2
Alignment explanation
Indices: 4782244--4782278 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4782234 GTACATCACA
4782244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4782279 ATCAAAATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4784321 original size:14 final size:14
Alignment explanation
Indices: 4784302--4784328 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4784292 ATTCAAAATA
4784302 ATATATATACATAT
1 ATATATATACATAT
4784316 ATATATATACATA
1 ATATATATACATA
4784329 AAGAGTGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATACATAT
Found at i:4784859 original size:16 final size:16
Alignment explanation
Indices: 4784838--4784900 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
4784828 AAATTTTAAA
4784838 TAAATTTTTA-TATTTT
1 TAAATTTTTATTA-TTT
4784854 TAAATTTTTATTATTT
1 TAAATTTTTATTATTT
**
4784870 TAAA-TAATATTATTT
1 TAAATTTTTATTATTT
*
4784885 TAATTTTTTATT-TTT
1 TAAATTTTTATTATTT
4784900 T
1 T
4784901 TTATAATACT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
15 16 0.40
16 22 0.55
17 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TAAATTTTTATTATTT
Found at i:4784901 original size:16 final size:15
Alignment explanation
Indices: 4784840--4784892 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
4784830 ATTTTAAATA
4784840 AATTTTTA-TATTTTT
1 AATTTTTATTA-TTTT
4784855 AAATTTTTATTATTTT
1 -AATTTTTATTATTTT
* **
4784871 AAATAATATTATTTT
1 AATTTTTATTATTTT
4784886 AATTTTT
1 AATTTTT
4784893 TATTTTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 16 0.53
16 12 0.40
17 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTTTATTATTTT
Found at i:4785511 original size:14 final size:15
Alignment explanation
Indices: 4785492--4785521 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4785482 CAGAACTTCA
4785492 CATTTCTCT-CTTTC
1 CATTTCTCTCCTTTC
4785506 CATTTCTCTCCTTTC
1 CATTTCTCTCCTTTC
4785521 C
1 C
4785522 CCTTTCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (15 bp):
CATTTCTCTCCTTTC
Found at i:4790537 original size:21 final size:22
Alignment explanation
Indices: 4790511--4790586 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 22
4790501 GGTTCAAGTC
4790511 TTTTTTCTTATTCTT-ATTTCT
1 TTTTTTCTTATTCTTCATTTCT
* *
4790532 TTTTTTCTTTTTCTTCCTTTCT
1 TTTTTTCTTATTCTTCATTTCT
*
4790554 TTTCCTTTCTTCCTTCATTC-TTT-T
1 TTT--TTTCTT-ATTC-TTCATTTCT
4790578 TTTTTTCTT
1 TTTTTTCTT
4790587 TTTTGGTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 14 0.30
22 14 0.30
24 10 0.21
25 6 0.13
26 3 0.06
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTTCTTATTCTTCATTTCT
Found at i:4790710 original size:32 final size:32
Alignment explanation
Indices: 4790670--4790731 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
4790660 CGTATTTCTT
*
4790670 TTTTTCTTTCTTTATTCTTCT-TTTCTTTTCCC
1 TTTTTCTTTCATTATT-TTCTCTTTCTTTTCCC
*
4790702 TTTTTCTTTCATTCTTTTCTCTTTCTTTTC
1 TTTTTCTTTCATTATTTTCTCTTTCTTTTC
4790732 TGATTCACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (32 bp):
TTTTTCTTTCATTATTTTCTCTTTCTTTTCCC
Found at i:4793589 original size:16 final size:16
Alignment explanation
Indices: 4793568--4793600 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4793558 AATTACGTAA
4793568 ATTTTATGTAT-TTTTT
1 ATTTTAT-TATATTTTT
4793584 ATTTTATTATATTTTT
1 ATTTTATTATATTTTT
4793600 A
1 A
4793601 CCCTATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
ATTTTATTATATTTTT
Found at i:4797439 original size:5 final size:5
Alignment explanation
Indices: 4797429--4797457 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4797419 CCAATGCAGG
4797429 TCTTC TCTTC TCTTC TCTTC TCTTC TCTT
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTT
4797458 TTCTCCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCTTC
Found at i:4798903 original size:18 final size:18
Alignment explanation
Indices: 4798877--4798925 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
4798867 ATAATTAGAA
*
4798877 TTAAATTTTTATAATTAT
1 TTAATTTTTTATAATTAT
4798895 TTAATTTTTTATAA--AT
1 TTAATTTTTTATAATTAT
*
4798911 TTAATATTTTA-AATT
1 TTAATTTTTTATAATT
4798926 TAAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
18 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAATTTTTTATAATTAT
Found at i:4798939 original size:14 final size:14
Alignment explanation
Indices: 4798903--4798937 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
4798893 ATTTAATTTT
4798903 TTATAAATTTAATA
1 TTATAAATTTAATA
*
4798917 TTTTAAATTTAAATA
1 TTATAAATTT-AATA
4798932 TTATAA
1 TTATAA
4798938 TTATTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTATAAATTTAATA
Found at i:4799616 original size:12 final size:12
Alignment explanation
Indices: 4799599--4799632 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4799589 TATTGTGTTC
4799599 ATATTATTTTTT
1 ATATTATTTTTT
*
4799611 ATATTATGTTTT
1 ATATTATTTTTT
4799623 A-ATTATTTTT
1 ATATTATTTTT
4799633 ATTTATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:4799638 original size:10 final size:11
Alignment explanation
Indices: 4799602--4799643 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
4799592 TGTGTTCATA
*
4799602 TTATTTTTTAT
1 TTATGTTTTAT
*
4799613 ATTATGTTTTAA
1 -TTATGTTTTAT
4799625 TTAT-TTTTAT
1 TTATGTTTTAT
4799635 TTATGTTTT
1 TTATGTTTT
4799644 GTTCATATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 9 0.35
11 8 0.31
12 9 0.35
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (11 bp):
TTATGTTTTAT
Found at i:4799638 original size:21 final size:23
Alignment explanation
Indices: 4799601--4799643 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
4799591 TTGTGTTCAT
4799601 ATTATTTTTTATATTATGTTTTA
1 ATTATTTTTTATATTATGTTTTA
4799624 ATTA-TTTTTAT-TTATGTTTT
1 ATTATTTTTTATATTATGTTTT
4799644 GTTCATATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (23 bp):
ATTATTTTTTATATTATGTTTTA
Found at i:4800315 original size:27 final size:29
Alignment explanation
Indices: 4800278--4800337 Score: 88
Period size: 27 Copynumber: 2.1 Consensus size: 29
4800268 TGATCTGTAT
4800278 TTATGTCATGTTTAAATTA-TTTTT-ATA
1 TTATGTCATGTTTAAATTATTTTTTCATA
* *
4800305 TTATGTTATGTTTTAATTATTTTTTCATA
1 TTATGTCATGTTTAAATTATTTTTTCATA
4800334 TTAT
1 TTAT
4800338 ATTTGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 17 0.59
28 5 0.17
29 7 0.24
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (29 bp):
TTATGTCATGTTTAAATTATTTTTTCATA
Found at i:4800382 original size:35 final size:35
Alignment explanation
Indices: 4800295--4800383 Score: 85
Period size: 35 Copynumber: 2.6 Consensus size: 35
4800285 ATGTTTAAAT
* *
4800295 TATTTTTAT-ATTATGTTATGTTTTAATTATTTTT
1 TATTTTTATAATTATATTATGTTTTAATTATTTTA
* * * *
4800329 TCA-TATTATATTTGTATTATGTTTTGATTCATTTTA
1 T-ATTTTTATAATTATATTATGTTTTAATT-ATTTTA
4800365 TATTTTTATAATT-TATTAT
1 TATTTTTATAATTATATTAT
4800384 AATAATTCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
34 6 0.14
35 23 0.53
36 14 0.33
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (35 bp):
TATTTTTATAATTATATTATGTTTTAATTATTTTA
Found at i:4800433 original size:17 final size:18
Alignment explanation
Indices: 4800411--4800444 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4800401 TTCAAATTCA
*
4800411 ATTATATAAAAT-TTTAG
1 ATTATAAAAAATATTTAG
4800428 ATTATAAAAAATATTTA
1 ATTATAAAAAATATTTA
4800445 AATAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATTATAAAAAATATTTAG
Found at i:4802345 original size:3 final size:3
Alignment explanation
Indices: 4802339--4802363 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4802329 AAAAAAAAAA
4802339 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
4802364 GCAGCCAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4806696 original size:2 final size:2
Alignment explanation
Indices: 4806689--4806729 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4806679 ACATACACCA
4806689 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4806730 TGTAATGACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4812779 original size:21 final size:21
Alignment explanation
Indices: 4812755--4812794 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4812745 ACTTTTGAAT
*
4812755 TTTAAAAATTACATTTTTTTA
1 TTTAAAAAATACATTTTTTTA
*
4812776 TTTAAAAAATATATTTTTT
1 TTTAAAAAATACATTTTTT
4812795 CATTCATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAAAAAATACATTTTTTTA
Found at i:4814707 original size:3 final size:3
Alignment explanation
Indices: 4814701--4814731 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4814691 ATCTGCCCTT
4814701 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4814732 ATGAGAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4814942 original size:30 final size:30
Alignment explanation
Indices: 4814908--4814969 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
4814898 TATATATATA
4814908 TACTACTATATAAATTAATACTAATGAAAG
1 TACTACTATATAAATTAATACTAATGAAAG
4814938 TACTACTATATAAATTAATACTAATGAAAG
1 TACTACTATATAAATTAATACTAATGAAAG
4814968 TA
1 TA
4814970 GTTAGTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (30 bp):
TACTACTATATAAATTAATACTAATGAAAG
Found at i:4814944 original size:15 final size:15
Alignment explanation
Indices: 4814911--4814969 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
4814901 ATATATATAC
*
4814911 TACTATATAAATTAA
1 TACTATATAAAGTAA
*
4814926 TACTA-ATGAAAGTAC
1 TACTATAT-AAAGTAA
*
4814941 TACTATATAAATTAA
1 TACTATATAAAGTAA
4814956 TACTA-ATGAAAGTA
1 TACTATAT-AAAGTA
4814970 GTTAGTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 4 0.11
15 30 0.83
16 2 0.06
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (15 bp):
TACTATATAAAGTAA
Found at i:4815414 original size:2 final size:2
Alignment explanation
Indices: 4815409--4815439 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4815399 TATATATATA
4815409 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4815440 ATAGATTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4819796 original size:2 final size:2
Alignment explanation
Indices: 4819789--4819816 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4819779 TTTCTTATGA
4819789 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
4819817 TTGTTTTCAT
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:4820754 original size:2 final size:2
Alignment explanation
Indices: 4820747--4820775 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4820737 CTTTTAGGAG
4820747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4820776 CACATATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4824306 original size:36 final size:34
Alignment explanation
Indices: 4824244--4824330 Score: 102
Period size: 36 Copynumber: 2.5 Consensus size: 34
4824234 TTAATCAAGG
*
4824244 TTCAAGTCAAGTTTGTTTTTCCGTTTTCTTGGGT
1 TTCAAGTCAAGTTTGTTTTTCCGTTTTCTTGAGT
* * *
4824278 TTCAAGTCAATTTTTTCGTTTTCTGTTTTCTTGAGT
1 TTCAAGTCAAGTTTGT--TTTTCCGTTTTCTTGAGT
* *
4824314 TTCAAGTTAAGGTTGTT
1 TTCAAGTCAAGTTTGTT
4824331 AGCTTAGAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
34 15 0.35
36 28 0.65
ACGTcount: A:0.15, C:0.13, G:0.18, T:0.54
Consensus pattern (34 bp):
TTCAAGTCAAGTTTGTTTTTCCGTTTTCTTGAGT
Found at i:4826108 original size:19 final size:18
Alignment explanation
Indices: 4826084--4826127 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
4826074 TTTTTTATAG
4826084 TTATTTAGTTAAGAAATTA
1 TTATTTA-TTAAGAAATTA
**
4826103 TTATTTTATTAATTAATTA
1 TTA-TTTATTAAGAAATTA
4826122 TTATTT
1 TTATTT
4826128 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 3 0.14
19 15 0.68
20 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
TTATTTATTAAGAAATTA
Found at i:4826145 original size:19 final size:19
Alignment explanation
Indices: 4826102--4826145 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4826092 TTAAGAAATT
*
4826102 ATTATTTTATTAATTAATT
1 ATTATTTTATTAATTAATA
*
4826121 ATTATTTTATT-TTTAATA
1 ATTATTTTATTAATTAATA
4826139 ATATATT
1 AT-TATT
4826146 CAAAGTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTATTTTATTAATTAATA
Found at i:4826924 original size:17 final size:16
Alignment explanation
Indices: 4826881--4826948 Score: 55
Period size: 17 Copynumber: 4.0 Consensus size: 16
4826871 TAGGGGAAGG
*
4826881 AAGAAAAGGAAAGAGAAA
1 AAGAAAA-GAAA-AAAAA
* *
4826899 TAGAGAAGAAAAAAATA
1 AAGAAAAGAAAAAAA-A
* *
4826916 AATAAAAGAGAAAAAAG
1 AAGAAAAGA-AAAAAAA
4826933 AAGAAAAGAAAAAAAA
1 AAGAAAAGAAAAAAAA
4826949 GTATTTTTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
16 9 0.23
17 19 0.49
18 11 0.28
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (16 bp):
AAGAAAAGAAAAAAAA
Found at i:4826931 original size:9 final size:8
Alignment explanation
Indices: 4826904--4826947 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
4826894 AGAAATAGAG
4826904 AAGAAAAA
1 AAGAAAAA
*
4826912 AATAAATAA
1 AAGAAA-AA
4826921 AAGAGAAAA
1 AAGA-AAAA
*
4826930 AAGAAGAA
1 AAGAAAAA
4826938 AAGAAAAA
1 AAGAAAAA
4826946 AA
1 AA
4826948 AGTATTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 17 0.57
9 11 0.37
10 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (8 bp):
AAGAAAAA
Found at i:4826949 original size:17 final size:17
Alignment explanation
Indices: 4826904--4826949 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
4826894 AGAAATAGAG
*
4826904 AAGAAAAAAATA-AATAA
1 AAGAAAAAAA-AGAAGAA
*
4826921 AAGAGAAAAAAGAAGAA
1 AAGAAAAAAAAGAAGAA
4826938 AAGAAAAAAAAG
1 AAGAAAAAAAAG
4826950 TATTTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.04
17 24 0.96
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (17 bp):
AAGAAAAAAAAGAAGAA
Found at i:4829000 original size:79 final size:79
Alignment explanation
Indices: 4828896--4829091 Score: 223
Period size: 79 Copynumber: 2.5 Consensus size: 79
4828886 AACGGGGTTG
* * * *** * *
4828896 GAGTATCTCCTTGAAAATAATGGGGTTGGAGTATCCCTGGTTGTGAAAAATCGATGATT-GGGAA
1 GAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAAT-ATTCGGGAA
*
4828960 ATAAAATCGGGATTA
65 ATAAAACCGGGATTA
* * *
4828975 GAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTCTGGAAA
1 GAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTCGGGAAA
* * *
4829040 TAAAGCCGGGGTTG
66 TAAAACCGGGATTA
**
4829054 GAGTATCCCCTTGGAGGTAACGGGGTTGGAGTATCCCC
1 GAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCC
4829092 GATGAAAAAT
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 3 0.03
79 95 0.97
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.26
Consensus pattern (79 bp):
GAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTCGGGAAA
TAAAACCGGGATTA
Found at i:4829182 original size:51 final size:51
Alignment explanation
Indices: 4829074--4829770 Score: 384
Period size: 51 Copynumber: 13.5 Consensus size: 51
4829064 TTGGAGGTAA
* * *
4829074 CGGGGTTGGAGTATCCCCGA-TGAA--AAATTGGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAAAGGAAATTGGTG-TTTTGAAAATAAAAC
* *
4829123 TGGAGTTGGAGTATCCCCGATTAAAGGAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAAAGGAAATTGGTGTTTTGAAAATAAAAC
*
4829174 CGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTTGAAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAAAGGAAA-TTGGTGTTTTG-AAAATAAAAC
* * * *
4829227 CGGGGTTAGAGTATCCCCGATT-ATGGAAAGTTAGTGTTTT-AGAAATGAAAC
1 CGGGGTTGGAGTATCCCCGATTAAAGGAAA-TTGGTGTTTTGA-AAATAAAAC
*** * * *
4829278 CGGGGTTGGAGTATCCCC-ATT-AAGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTAAAG-GAAATTGGTGTTTTGAAAATAAAAC
* * ** * * **** *
4829328 CGGGGTTGGAGTATCCCTCGGAGGTAACGG-GGTTGGAGTATCCCCAATGAAATAA
1 CGGGGTTGGAGTATCCC-C-GA-TTAAAGGAAATTGGTGTTTTGAAAAT-AAA-AC
** * * ** * *
4829383 CAAGGTTGGAATATCCTCGATT-GTGAAAGATTGGTGTTTTTAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAAAGGAA-ATTGGTGTTTTGAAAATAAAAC
*
4829434 CGAGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTTGAAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAAAGGAAA-TTGGTGTTTTG-AAAATAAAAC
* * *
4829487 TGGGGTTAGAGTATCCCCGATTATGAA-G-AATTAGTGTTTT-AGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTA--AAGGAAATTGGTGTTTTGA-AAATAAAAC
* * *** * * *
4829538 C-GGGTTGGAGTATCCCCCATT-ATGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTAAAG-GAAATTGGTGTTTTGAAAATAAAAC
* * ** * * ***** *
4829588 CGGGGTTGGAGTATCCACTCGGAGGTAACGG-GGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCC-C-C-GA-TTAAAGGAAATTGGTGTTTTGAAAAT-AAA-AC
* * * * * *
4829644 CGAGGTTGGAGTATCCTCGATTATGAA--AAATTTGTCTTTTTTGAAAACAAAAT
1 CGGGGTTGGAGTATCCCCGATTA--AAGGAAA-TTG-GTGTTTTGAAAATAAAAC
* * * **
4829697 CAGAGTTGGAGTATCCCTGATTAAAGGAAATTGGTGTTTTGAAAATAATTC
1 CGGGGTTGGAGTATCCCCGATTAAAGGAAATTGGTGTTTTGAAAATAAAAC
*
4829748 TGGGGTTGGAGTATCCCCGATTA
1 CGGGGTTGGAGTATCCCCGATTA
4829771 TGAGCAATTG
Statistics
Matches: 481, Mismatches: 125, Indels: 82
0.70 0.18 0.12
Matches are distributed among these distances:
47 1 0.00
49 19 0.04
50 77 0.16
51 148 0.31
52 67 0.14
53 106 0.22
54 21 0.04
55 25 0.05
56 17 0.04
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTAAAGGAAATTGGTGTTTTGAAAATAAAAC
Found at i:4829223 original size:104 final size:101
Alignment explanation
Indices: 4829074--4829603 Score: 303
Period size: 104 Copynumber: 5.2 Consensus size: 101
4829064 TTGGAGGTAA
* * * *
4829074 CGGGGTTGGAGTATCCCCGA-TGAAAAATTGGTGTTTTTGGAAATAAAATTGGAGTTGGAGTATC
1 CGGGGTTGGAGTATCCCCGATTAAAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTAGAGTATC
*
4829138 CCCGATTAAAGGAAA-TTGGTGTTTT-GAAAATAAAAC
66 CCCGATT-AAGGAAAGTTAGTGTTTTAG-AAATAAAAC
*
4829174 CGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTG-TTTTGAAAAATAAAATCGGGGTTAGAG
1 CGGGGTTGGAGTATCCCCGATTAAA--AAA-TTGGTGTTTTTG-AAAATAAAATCGGAGTTAGAG
* *
4829238 TATCCCCGATTATGGAAAGTTAGTGTTTTAGAAATGAAAC
62 TATCCCCGATTAAGGAAAGTTAGTGTTTTAGAAATAAAAC
*** * * ** * *
4829278 CGGGGTTGGAGTATCCCC-ATTAAGAGAAATCAAT-ATTTTGGAAATAAAGCCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTAA-A-AAATTGGTGTTTTTGAAAATAAAATCGGAGTTAGAGTA
* * * * * **** *
4829341 TCCCTCGGAGGTAACGG--GGTTGGAGTATCCCCAATGAAATAA
64 TCCC-C-GA-TTAA-GGAAAGTTAGTGTTTTAGAAAT-AAA-AC
** * * * * * *
4829383 CAAGGTTGGAATATCCTCGATTGTGAAAGATTGGTGTTTTT-AAAATAAAA-CCGAGGTTGGAGT
1 CGGGGTTGGAGTATCCCCGA-T-TAAAAAATTGGTGTTTTTGAAAATAAAATCGGA-GTTAGAGT
* * *
4829446 ATCCCCGATTAAAGGAAATTTGGTGTTTTGAAAAATAAAAC
63 ATCCCCGATT-AAGGAAAGTTAGTGTTTT-AGAAATAAAAC
* * * * * * *
4829487 TGGGGTTAGAGTATCCCCGATTATGAAGAATTAGTGTTTTAG-AAATAAAACCGG-GTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTA--AAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTAGAGTA
* * * * * * *
4829550 TCCCCCATTATGAGAAA-TCAATATTTTGGAAATAAAGC
64 TCCCCGATTAAG-GAAAGTTAGTGTTTTAGAAATAAAAC
4829588 CGGGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
4829604 ACTCGGAGGT
Statistics
Matches: 327, Mismatches: 74, Indels: 57
0.71 0.16 0.12
Matches are distributed among these distances:
100 20 0.06
101 48 0.15
102 17 0.05
103 60 0.18
104 113 0.35
105 33 0.10
106 28 0.09
107 6 0.02
108 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (101 bp):
CGGGGTTGGAGTATCCCCGATTAAAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAGGAAAGTTAGTGTTTTAGAAATAAAAC
Found at i:4829418 original size:260 final size:263
Alignment explanation
Indices: 4829150--4829772 Score: 985
Period size: 260 Copynumber: 2.4 Consensus size: 263
4829140 CGATTAAAGG
4829150 AAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTT
1 AAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTT
* *
4829215 GAAAAATAAAATC-GGGGTTAGAGTATCCCCGATTATGGAA-AGTTAGTGTTTTAGAAATGAAAC
66 GAAAAATAAAATCTGGGGTTAGAGTATCCCCGATTATGGAAGAATTAGTGTTTTAGAAATAAAAC
4829278 CGGGGTTGGAGTAT-CCCCATTAAGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
131 C-GGGTTGGAGTATCCCCCATTAAGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
*
4829342 CC-CTCGGAGGTAACGGGGTTGGAGTATCCCCAATGAAATAACAAGGTTGGAATATCCTCGATTG
195 CCACTCGGAGGTAACGGGGTTGGAGTATCCCCAATGAAATAACAAGGTTGGAATATCCTCGATTA
4829406 TGAA
260 TGAA
* * *
4829410 AGATTGGTGTTTTTAAAATAAAACCGAGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTT
1 AAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTT
4829475 GAAAAATAAAA-CTGGGGTTAGAGTATCCCCGATTAT-GAAGAATTAGTGTTTTAGAAATAAAAC
66 GAAAAATAAAATCTGGGGTTAGAGTATCCCCGATTATGGAAGAATTAGTGTTTTAGAAATAAAAC
*
4829538 CGGGTTGGAGTATCCCCCATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATC
131 CGGGTTGGAGTATCCCCCATTAAGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATC
* * *
4829603 CACTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTAT
196 CACTCGGAGGTAACGGGGTTGGAGTATCCCCAATGAAATAACAAGGTTGGAATATCCTCGATTAT
4829668 GAA
261 GAA
* * * * * * *
4829671 AAATTTGTCTTTTTTGAAAACAAAATCAGAGTTGGAGTATCCCTGATTAAAGGAAA-TTGGTGTT
1 AAA-TTG-GTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTT
* *
4829735 TTG-AAAAT-AATTCTGGGGTTGGAGTATCCCCGATTATG
64 TTGAAAAATAAAATCTGGGGTTAGAGTATCCCCGATTATG
4829773 AGCAATTGAG
Statistics
Matches: 333, Mismatches: 22, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
259 16 0.05
260 171 0.51
261 93 0.28
262 14 0.04
263 39 0.12
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (263 bp):
AAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTT
GAAAAATAAAATCTGGGGTTAGAGTATCCCCGATTATGGAAGAATTAGTGTTTTAGAAATAAAAC
CGGGTTGGAGTATCCCCCATTAAGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATC
CACTCGGAGGTAACGGGGTTGGAGTATCCCCAATGAAATAACAAGGTTGGAATATCCTCGATTAT
GAA
Found at i:4829644 original size:28 final size:28
Alignment explanation
Indices: 4829588--4829664 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
4829578 GAAATAAAGC
**
4829588 CGGGGTTGGAGTATCCACTCG--GAGGTAA
1 CGGGGTTGGAGTATCC-C-CGATGAAATAA
4829616 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
4829644 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
4829665 TATGAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 40 0.93
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:4830753 original size:18 final size:19
Alignment explanation
Indices: 4830713--4830833 Score: 112
Period size: 18 Copynumber: 6.6 Consensus size: 19
4830703 GCTGCTCTCA
4830713 CTGGAGCTGCTGT-TGCGTG
1 CTGGAGCTGCTGTCTGC-TG
*
4830732 CTGGAGCTGCAGTC-GCTG
1 CTGGAGCTGCTGTCTGCTG
*
4830750 CTGGAGTTGCTG-CTGCTG
1 CTGGAGCTGCTGTCTGCTG
*
4830768 TTGGAGCTGCTGT-TGCGTG
1 CTGGAGCTGCTGTCTGC-TG
* *
4830787 CTAGAGCTG-TCG-CTGCCG
1 CTGGAGCTGCT-GTCTGCTG
*
4830805 CTGGAGCTGGTG-CTGCTG
1 CTGGAGCTGCTGTCTGCTG
4830823 CTGGAGCTGCT
1 CTGGAGCTGCT
4830834 TTTGCGTGTT
Statistics
Matches: 84, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.01
18 55 0.65
19 28 0.33
ACGTcount: A:0.07, C:0.24, G:0.40, T:0.29
Consensus pattern (19 bp):
CTGGAGCTGCTGTCTGCTG
Found at i:4830776 original size:55 final size:55
Alignment explanation
Indices: 4830692--4830847 Score: 183
Period size: 55 Copynumber: 2.8 Consensus size: 55
4830682 AGATTGCTAC
* *
4830692 CTGCTAGAGTTGCTGCT-CTCACTGGAGCTGCTGTTGCGTGCTGGAGCTG-CAG-TCG
1 CTGCTGGAGTTGCTGCTGCT-GCTGGAGCTGCTGTTGCGTGCTGGAGCTGTC-GCT-G
* *
4830747 CTGCTGGAGTTGCTGCTGCTGTTGGAGCTGCTGTTGCGTGCTAGAGCTGTCGCTG
1 CTGCTGGAGTTGCTGCTGCTGCTGGAGCTGCTGTTGCGTGCTGGAGCTGTCGCTG
* * * * *
4830802 CCGCTGGAGCTGGTGCTGCTGCTGGAGCTGCTTTTGCGTGTTGGAG
1 CTGCTGGAGTTGCTGCTGCTGCTGGAGCTGCTGTTGCGTGCTGGAG
4830848 TCGTTGGCTA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
55 83 0.95
56 4 0.05
ACGTcount: A:0.08, C:0.23, G:0.38, T:0.31
Consensus pattern (55 bp):
CTGCTGGAGTTGCTGCTGCTGCTGGAGCTGCTGTTGCGTGCTGGAGCTGTCGCTG
Found at i:4831337 original size:6 final size:6
Alignment explanation
Indices: 4831303--4831329 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4831293 ATTATTATTT
4831303 TTTGAA TTTGAA TTTGAA TTTGAA TTT
1 TTTGAA TTTGAA TTTGAA TTTGAA TTT
4831330 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTGAA
Found at i:4831563 original size:17 final size:17
Alignment explanation
Indices: 4831543--4831616 Score: 62
Period size: 17 Copynumber: 4.3 Consensus size: 17
4831533 TTTATAATTT
4831543 AATAATATATTATTAAA
1 AATAATATATTATTAAA
*
4831560 AATAATAAATTATTAATA
1 AATAATATATTATTAA-A
* *
4831578 TAATTATTATTTTATTAAA
1 -AA-TAATATATTATTAAA
* *
4831597 AATTAT-TATT-TTAAT
1 AATAATATATTATTAAA
4831612 AATAA
1 AATAA
4831617 ATTGTAATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
15 8 0.18
16 3 0.07
17 17 0.38
18 3 0.07
19 3 0.07
20 11 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATAATATATTATTAAA
Found at i:4831602 original size:18 final size:19
Alignment explanation
Indices: 4831569--4831619 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
4831559 AAATAATAAA
4831569 TTATTAATATAATTATTATT
1 TTATTAATA-AATTATTATT
4831589 TTATTAA-AAATTATTATT
1 TTATTAATAAATTATTATT
*
4831607 TTAATAATAAATT
1 TTATTAATAAATT
4831620 GTAATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 16 0.55
19 6 0.21
20 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTAATAAATTATTATT
Found at i:4832860 original size:15 final size:15
Alignment explanation
Indices: 4832840--4832868 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4832830 ATATATTATA
4832840 TTATTTTTATTTAAG
1 TTATTTTTATTTAAG
4832855 TTATTTTTATTTAA
1 TTATTTTTATTTAA
4832869 AAATAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATTTTTATTTAAG
Found at i:4833133 original size:23 final size:25
Alignment explanation
Indices: 4833080--4833134 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
4833070 TTATTCTCAT
* *
4833080 TAAATTTTTAAATAATAGTATTTAA
1 TAAATTTTAAAAAAATAGTATTTAA
*
4833105 TTAATTTTAAAAAAATA-T-TTTAA
1 TAAATTTTAAAAAAATAGTATTTAA
4833128 TAAATTT
1 TAAATTT
4833135 ATTTTAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 11 0.42
24 1 0.04
25 14 0.54
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TAAATTTTAAAAAAATAGTATTTAA
Found at i:4833804 original size:16 final size:15
Alignment explanation
Indices: 4833782--4833826 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
4833772 ACTCATAATT
4833782 AAAAATAAACAACTA
1 AAAAATAAACAACTA
* *
4833797 ATAAAATAAAAAAATA
1 A-AAAATAAACAACTA
4833813 AAAAATAAACAACT
1 AAAAATAAACAACT
4833827 TAGACAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAATAAACAACTA
Found at i:4844859 original size:3 final size:3
Alignment explanation
Indices: 4844853--4844891 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4844843 TTATTAGTGT
4844853 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4844892 GTAACAACGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4845886 original size:5 final size:5
Alignment explanation
Indices: 4845876--4845906 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
4845866 ATTATGTTCC
4845876 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
4845907 CACCTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:4847226 original size:31 final size:30
Alignment explanation
Indices: 4847183--4847246 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
4847173 AATAAAACAT
4847183 TAAAAAAATATTAATTATATTATAAATAAA
1 TAAAAAAATATTAATTATATTATAAATAAA
* *
4847213 TAAAAAAAGTATTAATTTTATTATAATTAAA
1 TAAAAAAA-TATTAATTATATTATAAATAAA
4847244 TAA
1 TAA
4847247 TAAATGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAAAAAATATTAATTATATTATAAATAAA
Found at i:4847387 original size:46 final size:43
Alignment explanation
Indices: 4847323--4847420 Score: 103
Period size: 46 Copynumber: 2.2 Consensus size: 43
4847313 ATTTATAAAT
* *
4847323 ATAAATAAA-TTAAATATA-TTATATTTAAATTCTA-TTGATTTA
1 ATAAATAAATTTAAATATATTTATAATT--ATTCTATTTAATTTA
*
4847365 ATAAATAAATCTTAAAATTATATTTATAATTATTTTATTTAATTTA
1 ATAAATAAAT-TT-AAA-TATATTTATAATTATTCTATTTAATTTA
4847411 ATAAATAAAT
1 ATAAATAAAT
4847421 AAAAATAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
42 9 0.19
44 2 0.04
45 8 0.17
46 21 0.45
47 7 0.15
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (43 bp):
ATAAATAAATTTAAATATATTTATAATTATTCTATTTAATTTA
Found at i:4847872 original size:2 final size:2
Alignment explanation
Indices: 4847867--4847907 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4847857 ATATATATAT
*
4847867 AG AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4847908 AAGTTTTAGT
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:0.51, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:4848711 original size:20 final size:22
Alignment explanation
Indices: 4848672--4848740 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
4848662 ATATTTATAT
4848672 ATTTTTAATTAAATTTAAATAA
1 ATTTTTAATTAAATTTAAATAA
*
4848694 ATTTTTTATT-AA-TTAAATAAA
1 ATTTTTAATTAAATTTAAAT-AA
* * * *
4848715 AATTTAAATCAAA-TTAAATTA
1 ATTTTTAATTAAATTTAAATAA
4848736 ATTTT
1 ATTTT
4848741 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 6 0.16
21 15 0.39
22 17 0.45
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTTTAATTAAATTTAAATAA
Found at i:4854802 original size:19 final size:20
Alignment explanation
Indices: 4854771--4854811 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
4854761 TTAATTAATC
*
4854771 AAATTAATAAAAAATAATTA
1 AAATTAATAAAAAATAAATA
4854791 AAATTAAT-AAAAATAAATA
1 AAATTAATAAAAAATAAATA
4854810 AA
1 AA
4854812 GTTTACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATTAATAAAAAATAAATA
Found at i:4856063 original size:23 final size:22
Alignment explanation
Indices: 4856037--4856102 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
4856027 TAGACACGAT
*
4856037 TTTAGTTTAAAAATAATTATTCA
1 TTTA-TTTAAAAATAATTATCCA
*
4856060 TTTA---AAAAAT-A-TATCCT
1 TTTATTTAAAAATAATTATCCA
4856077 TTTATTTTAAAAATAATTATCCA
1 TTTA-TTTAAAAATAATTATCCA
4856100 TTT
1 TTT
4856103 TAAAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
17 8 0.24
18 1 0.03
19 6 0.18
21 6 0.18
22 1 0.03
23 12 0.35
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTATTTAAAAATAATTATCCA
Found at i:4856069 original size:19 final size:19
Alignment explanation
Indices: 4856045--4856107 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 19
4856035 ATTTTAGTTT
4856045 AAAAATAATTATTCATTTA
1 AAAAATAATTATTCATTTA
* *
4856064 AAAAATATATCCT-TTTATTTT
1 AAAAATA-AT--TATTCATTTA
*
4856085 AAAAATAATTATCCATTTTA
1 AAAAATAATTATTCA-TTTA
4856105 AAA
1 AAA
4856108 TATTACCTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
18 1 0.03
19 9 0.26
20 10 0.29
21 13 0.38
22 1 0.03
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAATAATTATTCATTTA
Found at i:4856324 original size:3 final size:3
Alignment explanation
Indices: 4856316--4856341 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4856306 CCAAGGGTGA
4856316 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
4856342 TATGATATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:4858736 original size:3 final size:3
Alignment explanation
Indices: 4858728--4858757 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4858718 CGCGTTGCTC
*
4858728 CTT CTT CTT CTT CTT CTT CTT CTA CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
4858758 TATCTTCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:4869240 original size:1 final size:1
Alignment explanation
Indices: 4869234--4869322 Score: 70
Period size: 1 Copynumber: 89.0 Consensus size: 1
4869224 AAATCTTCAC
* * ** * * * **
4869234 TTTTTTTTTGTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
4869299 TTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
4869323 CCAATTGCCA
Statistics
Matches: 68, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:4869282 original size:32 final size:32
Alignment explanation
Indices: 4869233--4869316 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
4869223 CAAATCTTCA
*
4869233 CTTTTTTTT-TGTT-TTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
4869263 CTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
4869295 CTTTTTTTTGTTTTGTTTTTTT
1 CTTTTTTTTGTTTTGTTTTTTT
4869317 CTTTTTCCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 9 0.18
31 3 0.06
32 39 0.76
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (32 bp):
CTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
Found at i:4878043 original size:21 final size:21
Alignment explanation
Indices: 4878019--4878062 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
4878009 TGAAATGATA
*
4878019 CATTGGTTAGATGAAAGAATG
1 CATTGGTTAGATGAAAAAATG
** *
4878040 CATTTTTTGGATGAAAAAATG
1 CATTGGTTAGATGAAAAAATG
4878061 CA
1 CA
4878063 ACTTTTAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (21 bp):
CATTGGTTAGATGAAAAAATG
Found at i:4878068 original size:21 final size:21
Alignment explanation
Indices: 4878028--4878068 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4878018 ACATTGGTTA
* **
4878028 GATGAAAGAATGCATTTTTTG
1 GATGAAAAAATGCAACTTTTG
4878049 GATGAAAAAATGCAACTTTT
1 GATGAAAAAATGCAACTTTT
4878069 AATAACCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (21 bp):
GATGAAAAAATGCAACTTTTG
Found at i:4888784 original size:10 final size:10
Alignment explanation
Indices: 4888750--4888784 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
4888740 TTCTTTTTCA
*
4888750 TTTTTCATTT
1 TTTTTCTTTT
4888760 TTTTTCTTTT
1 TTTTTCTTTT
*
4888770 CTTTTCTTTT
1 TTTTTCTTTT
4888780 TTTTT
1 TTTTT
4888785 TAATCCATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:4890764 original size:37 final size:38
Alignment explanation
Indices: 4890666--4890764 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 38
4890656 CTATGCCATC
*
4890666 AATTTAAAATAGT-AGTTTTTGTTTCAAATCGTACCTTG
1 AATTGAAAATAGTGA-TTTTTGTTTCAAATCGTACCTTG
** * **
4890704 AATTGAAAATAGTGATTAATGTTTCAAATTGTGTCTTG
1 AATTGAAAATAGTGATTTTTGTTTCAAATCGTACCTTG
*
4890742 -ATTGAGAATAGTGATTTTTGTTT
1 AATTGAAAATAGTGATTTTTGTTT
4890765 TGAATTTTGC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
37 20 0.39
38 30 0.59
39 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.45
Consensus pattern (38 bp):
AATTGAAAATAGTGATTTTTGTTTCAAATCGTACCTTG
Found at i:4896211 original size:6 final size:6
Alignment explanation
Indices: 4896141--4896238 Score: 94
Period size: 5 Copynumber: 18.3 Consensus size: 6
4896131 TGCTTTATCA
4896141 AAAAG- AAAAG- AAAAG- AAAAG- AAAAG- AAAAGC -AAAG- AAAAGC
1 AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC
* *
4896182 -AAAGC -AAAGC -AAGGC -AAAGC AAAAGT AAAAGC -AAAGC AAAAGC
1 AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC
4896225 AAAAGC AAAAGC AA
1 AAAAGC AAAAGC AA
4896239 TGTTTTCATA
Statistics
Matches: 84, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
5 56 0.67
6 28 0.33
ACGTcount: A:0.68, C:0.11, G:0.19, T:0.01
Consensus pattern (6 bp):
AAAAGC
Found at i:4896789 original size:2 final size:2
Alignment explanation
Indices: 4896782--4896819 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4896772 CTTCGGAAAT
4896782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4896820 GAAAATGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4899733 original size:22 final size:22
Alignment explanation
Indices: 4899708--4899750 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4899698 TCATGAGTAT
4899708 ACCAAATTAGAACCATAAGCAC
1 ACCAAATTAGAACCATAAGCAC
*
4899730 ACCAAATTAGAACCATGAGCA
1 ACCAAATTAGAACCATAAGCA
4899751 TGACTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.12, T:0.14
Consensus pattern (22 bp):
ACCAAATTAGAACCATAAGCAC
Found at i:4901751 original size:22 final size:24
Alignment explanation
Indices: 4901725--4901789 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
4901715 TTAATATCTT
*
4901725 TATTAAGAGTGTTAGGT-A-AACA
1 TATTAAGTGTGTTAGGTGAGAACA
* *
4901747 TATTAAGTGTGTTAAGTGAGTAATA
1 TATTAAGTGTGTTAGGTGAG-AACA
4901772 TATTAAGTGTGTTAGGTG
1 TATTAAGTGTGTTAGGTG
4901790 GTGTGTTAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 15 0.42
23 1 0.03
25 20 0.56
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (24 bp):
TATTAAGTGTGTTAGGTGAGAACA
Found at i:4901820 original size:22 final size:22
Alignment explanation
Indices: 4901789--4901830 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4901779 TGTGTTAGGT
*
4901789 GGTGTGTTAGGTAAACATATTA
1 GGTGTATTAGGTAAACATATTA
*
4901811 GGTGTATTAGGTGAACATAT
1 GGTGTATTAGGTAAACATAT
4901831 CTTGTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.36
Consensus pattern (22 bp):
GGTGTATTAGGTAAACATATTA
Done.