Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 116 of 120
Found at i:35159803 original size:29 final size:29
Alignment explanation
Indices: 35159770--35159825 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
35159760 CTCATTTTGT
35159770 TTTTTCTTAAATTA-AAA-AATATTAATATA
1 TTTTT-TTAAATTATAAATAA-ATTAATATA
*
35159799 TTTTTTTAATTTATAAATAAATTAATA
1 TTTTTTTAAATTATAAATAAATTAATA
35159826 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 7 0.29
29 15 0.62
30 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTTTTAAATTATAAATAAATTAATATA
Found at i:35160737 original size:38 final size:38
Alignment explanation
Indices: 35160677--35160767 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
35160667 AAATGGAACG
* *
35160677 ATATGTTTATACA-ATGTATTAAAATATATCATGTGTAA
1 ATAT-TTTATATATATGCATTAAAATATATCATGTGTAA
* * * *
35160715 ATCTTTTATATATATGCATTAAATTATATTATGTTTAA
1 ATATTTTATATATATGCATTAAAATATATCATGTGTAA
35160753 ATATTTTATATATAT
1 ATATTTTATATATAT
35160768 ATATATATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 7 0.16
38 38 0.84
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (38 bp):
ATATTTTATATATATGCATTAAAATATATCATGTGTAA
Found at i:35166170 original size:2 final size:2
Alignment explanation
Indices: 35166165--35166190 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35166155 TGTTCATATA
35166165 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
35166191 AACAGGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35166948 original size:43 final size:44
Alignment explanation
Indices: 35166901--35166988 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 44
35166891 TAGTAATACT
*
35166901 TAAATATAATAATAATAA-GATTTTTACTTCGATCGGAAAAATA
1 TAAATATAATAATAATAACGATTTTTACTTCAATCGGAAAAATA
35166944 TAAATATAATAATAATAATCGGATTTTTACTTCAATCGGAAAAAT
1 TAAATATAATAATAATAA-C-GATTTTTACTTCAATCGGAAAAAT
35166989 GTAAGTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 18 0.44
46 23 0.56
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.35
Consensus pattern (44 bp):
TAAATATAATAATAATAACGATTTTTACTTCAATCGGAAAAATA
Found at i:35171177 original size:60 final size:60
Alignment explanation
Indices: 35171107--35171228 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
35171097 GAGGACATAT
35171107 AAGTACCATTTGTACATGTCATTTCACACAAAATAAATACACCTTGTCTTGCAATCTTCC
1 AAGTACCATTTGTACATGTCATTTCACACAAAATAAATACACCTTGTCTTGCAATCTTCC
35171167 AAGTACCATTTGTACATGTCATTTCACACAAAATAAATACACCTTGTCTTGCAATCTTCC
1 AAGTACCATTTGTACATGTCATTTCACACAAAATAAATACACCTTGTCTTGCAATCTTCC
35171227 AA
1 AA
35171229 TGTTGATGTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (60 bp):
AAGTACCATTTGTACATGTCATTTCACACAAAATAAATACACCTTGTCTTGCAATCTTCC
Found at i:35171941 original size:23 final size:24
Alignment explanation
Indices: 35171902--35171951 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
35171892 TAATAGGGAT
35171902 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
35171925 TTTCAA-TTCCAATTTCACTTTCAC
1 TTTCAATTTACAA-TTCACTATCAC
35171949 TTT
1 TTT
35171952 TGATCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 10 0.43
24 8 0.35
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Found at i:35174031 original size:41 final size:41
Alignment explanation
Indices: 35173986--35174065 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
35173976 TATTGTCAAT
*
35173986 GTGGAGATAGTTAGAATTGGGTGACTAGAATTCTTGTTATG
1 GTGGAGATAGTTAGAATTGAGTGACTAGAATTCTTGTTATG
*
35174027 GTGGAGATTGTTAGAATTGAGTGACTAGAATTCTTGTTA
1 GTGGAGATAGTTAGAATTGAGTGACTAGAATTCTTGTTA
35174066 AAATAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.05, G:0.30, T:0.38
Consensus pattern (41 bp):
GTGGAGATAGTTAGAATTGAGTGACTAGAATTCTTGTTATG
Found at i:35190521 original size:29 final size:30
Alignment explanation
Indices: 35190460--35190525 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
35190450 GGTGGAGAGC
*
35190460 TTAATTGATATTTTATTATTTTACAATAAT
1 TTAATTGATATTTTATTATTTTACAAGAAT
* * **
35190490 TTAATTGAT-TTTTTTTATTTTGCAAGGGT
1 TTAATTGATATTTTATTATTTTACAAGAAT
35190519 TTAATTG
1 TTAATTG
35190526 GTAATTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.58
Consensus pattern (30 bp):
TTAATTGATATTTTATTATTTTACAAGAAT
Found at i:35190897 original size:11 final size:11
Alignment explanation
Indices: 35190881--35190905 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35190871 TATTGTGTGG
35190881 GTGTCAAGTGA
1 GTGTCAAGTGA
35190892 GTGTCAAGTGA
1 GTGTCAAGTGA
35190903 GTG
1 GTG
35190906 GTGTGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.40, T:0.28
Consensus pattern (11 bp):
GTGTCAAGTGA
Found at i:35193583 original size:15 final size:16
Alignment explanation
Indices: 35193563--35193592 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35193553 CTAAATATTC
35193563 TAAAATAA-AAAATTG
1 TAAAATAATAAAATTG
35193578 TAAAATAATAAAATT
1 TAAAATAATAAAATT
35193593 TTTATTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAAAATAATAAAATTG
Found at i:35193865 original size:2 final size:2
Alignment explanation
Indices: 35193858--35193931 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
35193848 CTATTGATTA
35193858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
35193900 AT AT AT AT AT AT AT AT AA AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35193932 TTATTGAATA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35194172 original size:25 final size:24
Alignment explanation
Indices: 35194144--35194191 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
35194134 TTTTTAAAAA
35194144 TTATATAAAAATTATTGATTATTAT
1 TTATATAAAAATTATT-ATTATTAT
*
35194169 TTATTTAAAAATTATTATTATTA
1 TTATATAAAAATTATTATTATTA
35194192 AAAATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATATAAAAATTATTATTATTAT
Found at i:35194182 original size:18 final size:16
Alignment explanation
Indices: 35194161--35194196 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
35194151 AAAATTATTG
35194161 ATTATTATTTATTTAAAA
1 ATTATTA-TTA-TTAAAA
35194179 ATTATTATTATTAAAA
1 ATTATTATTATTAAAA
35194195 AT
1 AT
35194197 ATTTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 3 0.17
18 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATTATTATTAAAA
Found at i:35194297 original size:26 final size:27
Alignment explanation
Indices: 35194268--35194321 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
35194258 TTATTTCATC
*
35194268 AAATAAAT-TTAAAAATTC-AAAACCTA
1 AAATAAATATGAAAAA-TCGAAAACCTA
*
35194294 AAATTAATATGAAAAATCGAAAACCTA
1 AAATAAATATGAAAAATCGAAAACCTA
35194321 A
1 A
35194322 TTAAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.61, C:0.11, G:0.04, T:0.24
Consensus pattern (27 bp):
AAATAAATATGAAAAATCGAAAACCTA
Found at i:35201658 original size:22 final size:24
Alignment explanation
Indices: 35201633--35201678 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
35201623 AAAATTCAAT
*
35201633 AAAAATTTTC-AAAATTT-TAAAA
1 AAAAATATTCTAAAATTTATAAAA
*
35201655 AAAAATATTCTTAAATTTATAAAA
1 AAAAATATTCTAAAATTTATAAAA
35201679 GATACAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 6 0.30
24 5 0.25
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAAATATTCTAAAATTTATAAAA
Found at i:35202394 original size:29 final size:27
Alignment explanation
Indices: 35202328--35202396 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
35202318 TAGAGTTTCA
* *
35202328 CATGTATAATTACACCAAATTAAAATT
1 CATGAATAATTACACCAAATCAAAATT
* *
35202355 CATATATATAATTACACATTAAATCAAAATT
1 CAT-GA-ATAATTACAC--CAAATCAAAATT
35202386 CATGAATAATT
1 CATGAATAATT
35202397 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.09
29 16 0.48
30 1 0.03
31 13 0.39
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (27 bp):
CATGAATAATTACACCAAATCAAAATT
Found at i:35205573 original size:2 final size:2
Alignment explanation
Indices: 35205566--35205592 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35205556 TCCCATATGA
35205566 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 A
35205593 CTGTGGATAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35217157 original size:15 final size:15
Alignment explanation
Indices: 35217132--35217185 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 15
35217122 TAAATTTCGT
35217132 AATTTTTTTA-TTTA
1 AATTTTTTTATTTTA
35217146 AATTTTTATTATTTTA
1 AATTTTT-TTATTTTA
*
35217162 AATTAATTTTTAAATTTA
1 AATT--TTTTT-ATTTTA
35217180 AATTTT
1 AATTTT
35217186 ATTAAAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 7 0.21
15 3 0.09
16 10 0.29
17 2 0.06
18 12 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTTTTTTATTTTA
Found at i:35218738 original size:2 final size:2
Alignment explanation
Indices: 35218731--35218771 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35218721 CAATCTTACT
35218731 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35218772 TTTTTTTTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35233688 original size:135 final size:136
Alignment explanation
Indices: 35233422--35233681 Score: 441
Period size: 135 Copynumber: 1.9 Consensus size: 136
35233412 AGCATATCCT
*
35233422 GTAATGTGCTAAGTCATTTTGCTTTTCGGTAATTCTATTACCAAAGTGAATCTTACACTCCTTGG
1 GTAATGTGCTAAGTCATTTTGCTTTTCGGTAATTCTATTACCAAAGTGAATCTTACACTCCTTGA
* * *
35233487 ATCAAATGCTCCGTAGTAATATATGTCGAACATAGTTGTGAATAGCTCTTACTCATCTACCAATT
66 ACCAAACGCTCCGTAGTAATATACGTCGAACATAGTTGTGAATAGCTCTTACTCATCTACCAATT
35233552 TTGTTG
131 TTGTTG
* *
35233558 GTAATGTGCTAAGTCATTTTGCTTTT-GGTAATTCTATTACTAAAGTTAATCTTACACTCCTTGA
1 GTAATGTGCTAAGTCATTTTGCTTTTCGGTAATTCTATTACCAAAGTGAATCTTACACTCCTTGA
* *
35233622 ACCAAACGCTCCTTAGTAATATGCGTCGAACATAGTTGTGAATAGCTCTTACTCATCTAC
66 ACCAAACGCTCCGTAGTAATATACGTCGAACATAGTTGTGAATAGCTCTTACTCATCTAC
35233682 TGATTTTATT
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
135 90 0.78
136 26 0.22
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (136 bp):
GTAATGTGCTAAGTCATTTTGCTTTTCGGTAATTCTATTACCAAAGTGAATCTTACACTCCTTGA
ACCAAACGCTCCGTAGTAATATACGTCGAACATAGTTGTGAATAGCTCTTACTCATCTACCAATT
TTGTTG
Found at i:35238992 original size:10 final size:11
Alignment explanation
Indices: 35238970--35239004 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
35238960 TATTATTACA
35238970 ATTTTTTATAT
1 ATTTTTTATAT
35238981 ATTTTTTA-AT
1 ATTTTTTATAT
35238991 ATTTATTTATAT
1 ATTT-TTTATAT
35239003 AT
1 AT
35239005 AACATCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 12 0.55
12 4 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTTTTTATAT
Found at i:35244906 original size:23 final size:23
Alignment explanation
Indices: 35244878--35244928 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
35244868 ATGATATAAA
35244878 TTTTATAACTGGTAAAAATACTT
1 TTTTATAACTGGTAAAAATACTT
*
35244901 TTTTATAACTGGTAAAAATAGTT
1 TTTTATAACTGGTAAAAATACTT
35244924 TTTTA
1 TTTTA
35244929 AAAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (23 bp):
TTTTATAACTGGTAAAAATACTT
Found at i:35256741 original size:22 final size:23
Alignment explanation
Indices: 35256703--35256747 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
35256693 TTGCCTATTT
35256703 TCACTATTTTTGCTGTTGTTTTG
1 TCACTATTTTTGCTGTTGTTTTG
*
35256726 TCACTA-TTTTGGTGTTGTTTTG
1 TCACTATTTTTGCTGTTGTTTTG
35256748 CTATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.09, C:0.11, G:0.20, T:0.60
Consensus pattern (23 bp):
TCACTATTTTTGCTGTTGTTTTG
Found at i:35258857 original size:2 final size:2
Alignment explanation
Indices: 35258850--35258889 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
35258840 AATTATGCAA
35258850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35258890 GTTTATAAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35259014 original size:2 final size:2
Alignment explanation
Indices: 35259007--35259035 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35258997 TTTCTATTCT
35259007 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
35259036 TTAAAGGGGT
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:35261239 original size:19 final size:19
Alignment explanation
Indices: 35261215--35261269 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
35261205 CGTAAAATAT
35261215 ATTTATTATTTATTTTTAA
1 ATTTATTATTTATTTTTAA
**
35261234 ATTTATTA-TTAAATTTAA
1 ATTTATTATTTATTTTTAA
*
35261252 ATTATATT-TATATTTTTA
1 ATT-TATTATTTATTTTTA
35261270 TGTACTGCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTATTATTTATTTTTAA
Found at i:35261526 original size:5 final size:5
Alignment explanation
Indices: 35261518--35261549 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
35261508 TAAAAGCAGT
35261518 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GG
1 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GG
35261550 GAATCTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (5 bp):
GGAAG
Found at i:35264467 original size:6 final size:6
Alignment explanation
Indices: 35264456--35264500 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
35264446 ACAATTCATA
35264456 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
35264501 ATTTTGATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:35264677 original size:22 final size:22
Alignment explanation
Indices: 35264651--35264696 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
35264641 TAAACATATA
35264651 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
35264673 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
35264695 AT
1 AT
35264697 CACATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATTTCACATATACATTGTTC
Found at i:35264701 original size:18 final size:20
Alignment explanation
Indices: 35264655--35264704 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
35264645 CATATAATAT
35264655 TTCACATATACATTGTTCATA
1 TTCACATATACATTGTTCA-A
35264676 TTTCACATATACATTGTTC-A
1 -TTCACATATACATTGTTCAA
35264696 -TCACATATA
1 TTCACATATA
35264705 TATCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.32
20 1 0.04
22 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (20 bp):
TTCACATATACATTGTTCAA
Found at i:35269533 original size:43 final size:42
Alignment explanation
Indices: 35269451--35269547 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 42
35269441 TTTAGCTACC
35269451 ATTAAAAGATTCTGAAAAAAATTAAAAACAATGCCTACCTACAA
1 ATTAAAA-ATTCTGAAAAAAATTAAAAACAAT-CCTACCTACAA
* * * *
35269495 TTTTAAAATTCTGAAAAAAGATTAAAAACTTAT-TTACCTACAA
1 ATTAAAAATTCTGAAAAAA-ATTAAAAAC-AATCCTACCTACAA
35269538 ATTAAAAATT
1 ATTAAAAATT
35269548 AAAAAATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 29 0.64
44 14 0.31
45 2 0.04
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (42 bp):
ATTAAAAATTCTGAAAAAAATTAAAAACAATCCTACCTACAA
Found at i:35280491 original size:2 final size:2
Alignment explanation
Indices: 35280486--35280530 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
35280476 ACACACACAC
35280486 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35280528 AG A
1 AG A
35280531 AAGATCGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35295343 original size:18 final size:18
Alignment explanation
Indices: 35295320--35295367 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
35295310 ACAATTCATA
35295320 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * *
35295338 TCACTTTCACTTTCATTT
1 TCACTTTCAATTCCAATT
35295356 TCACTTTCAATT
1 TCACTTTCAATT
35295368 TTGATCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:35295345 original size:6 final size:6
Alignment explanation
Indices: 35295320--35295364 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
35295310 ACAATTCATA
* * * *
35295320 TCACTT TCAATT CCAATT TCACTT TCACTT TCATTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
35295365 ATTTTGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:35295351 original size:12 final size:12
Alignment explanation
Indices: 35295320--35295368 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
35295310 ACAATTCATA
35295320 TCACTTTCAATT
1 TCACTTTCAATT
* * *
35295332 CCAATTTCACTT
1 TCACTTTCAATT
*
35295344 TCACTTTCATTT
1 TCACTTTCAATT
35295356 TCACTTTCAATT
1 TCACTTTCAATT
35295368 T
1 T
35295369 TGATCACAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:35303954 original size:18 final size:18
Alignment explanation
Indices: 35303931--35303979 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
35303921 ACAATTCATA
35303931 TCACTTTCAATTTCACTT
1 TCACTTTCAATTTCACTT
*
35303949 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCACTT
*
35303967 TCAATTTCAATTT
1 TCACTTTCAATTT
35303980 TGATCACAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (18 bp):
TCACTTTCAATTTCACTT
Found at i:35303979 original size:6 final size:6
Alignment explanation
Indices: 35303931--35303975 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
35303921 ACAATTCATA
* *
35303931 TCACTT TCAATT TCACTT TCACTT TCACTT TCACTT TCAATT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
35303976 ATTTTGATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:35313178 original size:15 final size:16
Alignment explanation
Indices: 35313135--35313178 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
35313125 AAAAATTATT
*
35313135 TTTTTTATCTTTCTAA
1 TTTTTTATCATTCTAA
*
35313151 TTTTTTAGCCATTC-AA
1 TTTTTTA-TCATTCTAA
35313167 TTTTTTATCATT
1 TTTTTTATCATT
35313179 TCAAAATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 16 0.67
17 4 0.17
ACGTcount: A:0.20, C:0.14, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTTTATCATTCTAA
Found at i:35319776 original size:28 final size:28
Alignment explanation
Indices: 35319736--35319793 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
35319726 AACCAAATGT
*
35319736 TAATTCATACATAACATTTTCAATTGCA
1 TAATTCATACATAACATTTTCAATTACA
35319764 TAATTCATACATAACATTTTCAATTACA
1 TAATTCATACATAACATTTTCAATTACA
35319792 TA
1 TA
35319794 CCTACATCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.40
Consensus pattern (28 bp):
TAATTCATACATAACATTTTCAATTACA
Found at i:35319793 original size:17 final size:17
Alignment explanation
Indices: 35319743--35319793 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
35319733 TGTTAATTCA
35319743 TACATAACATTTTCAAT
1 TACATAACATTTTCAAT
*
35319760 TGCAT-A-A--TTC-A-
1 TACATAACATTTTCAAT
35319771 TACATAACATTTTCAAT
1 TACATAACATTTTCAAT
35319788 TACATA
1 TACATA
35319794 CCTACATCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 12
0.65 0.05 0.30
Matches are distributed among these distances:
11 4 0.15
12 2 0.08
13 4 0.15
15 4 0.15
16 2 0.08
17 10 0.38
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (17 bp):
TACATAACATTTTCAAT
Found at i:35323175 original size:31 final size:31
Alignment explanation
Indices: 35323140--35323199 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
35323130 AGTTTAGGCT
*
35323140 CCAATGTGAGA-ACAATTGCCAAGTTCAAGTC
1 CCAATATGAGACA-AATTGCCAAGTTCAAGTC
35323171 CCAATATGAGACAAATTGCCAAGTTCAAG
1 CCAATATGAGACAAATTGCCAAGTTCAAG
35323200 GACTAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (31 bp):
CCAATATGAGACAAATTGCCAAGTTCAAGTC
Found at i:35342268 original size:29 final size:30
Alignment explanation
Indices: 35342215--35342276 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
35342205 ATATCCTATA
* **
35342215 TTTTATAATTTTTAAAGTATTAAATCA-AAT
1 TTTTATAATTTTTAAAGGAAAAAAT-ATAAT
35342245 TTTTATAATTTTT-AAGGAAAAAATATAAT
1 TTTTATAATTTTTAAAGGAAAAAATATAAT
35342274 TTT
1 TTT
35342277 ATCTTTACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 14 0.50
30 13 0.46
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (30 bp):
TTTTATAATTTTTAAAGGAAAAAATATAAT
Found at i:35343316 original size:19 final size:19
Alignment explanation
Indices: 35343292--35343358 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 19
35343282 TATCCAAATC
35343292 CAATAACAAATTTAATATT
1 CAATAACAAATTTAATATT
35343311 CAATAA-ATAATTT-AT-TT
1 CAATAACA-AATTTAATATT
*
35343328 -AAT-TCAAATTTAAATATT
1 CAATAACAAATTT-AATATT
35343346 C-A-AACAAATTTAA
1 CAATAACAAATTTAA
35343359 AAAATTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 16
0.68 0.04 0.28
Matches are distributed among these distances:
15 5 0.13
16 4 0.10
17 6 0.15
18 13 0.33
19 11 0.28
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (19 bp):
CAATAACAAATTTAATATT
Found at i:35347435 original size:3 final size:3
Alignment explanation
Indices: 35347427--35347469 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
35347417 ATAATCACAA
35347427 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35347470 ACAGTGATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35349947 original size:110 final size:110
Alignment explanation
Indices: 35349748--35349966 Score: 368
Period size: 110 Copynumber: 2.0 Consensus size: 110
35349738 ATAACCACTG
* *
35349748 TGAACTGGGAGCTCGAGTTGCAATGCAACATCTTCTAAGGTGATGGTGCACTCCCTACATAGGAA
1 TGAACTGGGAGCTCAAGTTGCAATGCAACATCTTCTAAGGTAATGGTGCACTCCCTACATAGGAA
* * *
35349813 ATGGAATGCGTGGATCTTTGAACGGTACTGCATCACCATCAACTA
66 ATAGAATGCGTGGATCTCTAAACGGTACTGCATCACCATCAACTA
35349858 TGAACTGGGAGCTCAAGTTGCAATGCAACATCTTCTAAGGTAATGGTGCACTTCCC-ACATAGGA
1 TGAACTGGGAGCTCAAGTTGCAATGCAACATCTTCTAAGGTAATGGTGCAC-TCCCTACATAGGA
*
35349922 AATAGAATGTGTGGATCTCTAAACGGTACTGCATCACCATCAACT
65 AATAGAATGCGTGGATCTCTAAACGGTACTGCATCACCATCAACT
35349967 CAAACATACA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
110 98 0.96
111 4 0.04
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (110 bp):
TGAACTGGGAGCTCAAGTTGCAATGCAACATCTTCTAAGGTAATGGTGCACTCCCTACATAGGAA
ATAGAATGCGTGGATCTCTAAACGGTACTGCATCACCATCAACTA
Found at i:35357528 original size:29 final size:30
Alignment explanation
Indices: 35357473--35357557 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 30
35357463 AGGTATAATA
**
35357473 TTAAATTTAGCTTTTAATATTTATATTTTTTTG
1 TTAAATTTAGCTTTT-AT-TTT-TATTTTTAAG
35357506 TT-AATTTAG-TTATTATTTTTATTTTTAAG
1 TTAAATTTAGCTT-TTATTTTTATTTTTAAG
35357535 TTAAATTTAGCTTTTAATTTTTA
1 TTAAATTTAGCTTTT-ATTTTTA
35357558 AAAAAATTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
29 10 0.22
30 12 0.26
31 13 0.28
32 9 0.20
33 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (30 bp):
TTAAATTTAGCTTTTATTTTTATTTTTAAG
Found at i:35366898 original size:2 final size:2
Alignment explanation
Indices: 35366887--35366936 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
35366877 GTGTCTCAAT
* * **
35366887 TC TC -C TC TC TC TC TC TC TC TC TC TC TT TC TT TC TC TC TC AG
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
35366928 TC TC TC TC T
1 TC TC TC TC T
35366937 GAGTGTTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.02, C:0.44, G:0.02, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35367753 original size:2 final size:2
Alignment explanation
Indices: 35367746--35367771 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35367736 GTCGCCTTTT
35367746 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
35367772 ATTTAAGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35368843 original size:2 final size:2
Alignment explanation
Indices: 35368836--35368863 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35368826 TTAAAATAAG
35368836 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
35368864 AATAAGAGAT
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):
TA
Found at i:35386804 original size:23 final size:24
Alignment explanation
Indices: 35386778--35386824 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
35386768 TAAACCGAAT
35386778 TTAAAATACTCATA-TTTATATTA
1 TTAAAATACTCATATTTTATATTA
* * *
35386801 TTAAATTATTTATATTTTATATTA
1 TTAAAATACTCATATTTTATATTA
35386825 ATTACTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAAAATACTCATATTTTATATTA
Found at i:35392170 original size:20 final size:20
Alignment explanation
Indices: 35392122--35392159 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35392112 GATGCCTTAG
35392122 AAATATTTTTAATAATTTAT
1 AAATATTTTTAATAATTTAT
* *
35392142 AAATCTTTTTTATAATTT
1 AAATATTTTTAATAATTT
35392160 TTTAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
AAATATTTTTAATAATTTAT
Found at i:35392664 original size:17 final size:17
Alignment explanation
Indices: 35392639--35392671 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35392629 TGCTGCAATT
*
35392639 TTTATAAATATTTTAAA
1 TTTAAAAATATTTTAAA
35392656 TTTAAAAATATTTTAA
1 TTTAAAAATATTTTAA
35392672 TTTTTTGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAAAATATTTTAAA
Found at i:35397204 original size:18 final size:18
Alignment explanation
Indices: 35397183--35397217 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35397173 ATTTAGATTA
35397183 AAATCTCGATTTAAAAAT
1 AAATCTCGATTTAAAAAT
* *
35397201 AAATTTTGATTTAAAAA
1 AAATCTCGATTTAAAAA
35397218 GAGGCATGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATCTCGATTTAAAAAT
Found at i:35399893 original size:16 final size:16
Alignment explanation
Indices: 35399872--35399904 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35399862 TCTTTTAATA
*
35399872 TTTTATTTTATTTTTG
1 TTTTATTTTAATTTTG
35399888 TTTTATTTTAATTTTG
1 TTTTATTTTAATTTTG
35399904 T
1 T
35399905 CGCTGCCGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTATTTTAATTTTG
Found at i:35400516 original size:8 final size:9
Alignment explanation
Indices: 35400486--35400527 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
35400476 ATAAATTTAG
*
35400486 TTTTTAATG
1 TTTTTAATT
* *
35400495 TTTATATTT
1 TTTTTAATT
35400504 TTTTTAATT
1 TTTTTAATT
35400513 TTTTTAATT
1 TTTTTAATT
35400522 TTTTTA
1 TTTTTA
35400528 TTAATTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTTAATT
Found at i:35401954 original size:26 final size:26
Alignment explanation
Indices: 35401909--35401972 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 26
35401899 AGATTTATTT
35401909 TATTTTTATATTTAATAA-T-TTTATA
1 TATTTTT-TATTTAATAATTATTTATA
*
35401934 TATTTTTTATTTATTGAAATTATTTATA
1 TATTTTTTATTTAAT--AATTATTTATA
35401962 TAATTATTTTA
1 T-ATT-TTTTA
35401973 ATGTTTACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 7 0.22
25 7 0.22
26 2 0.06
27 1 0.03
28 7 0.22
29 3 0.09
30 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TATTTTTTATTTAATAATTATTTATA
Found at i:35426298 original size:11 final size:13
Alignment explanation
Indices: 35426282--35426340 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
35426272 CTTGAATGTT
35426282 TAATTTT-TTA-A
1 TAATTTTATTATA
35426293 TAATTTTATTATA
1 TAATTTTATTATA
35426306 -AATTTTGATTATA
1 TAATTTT-ATTATA
35426319 TAAATTTT-TTATA
1 T-AATTTTATTATA
35426332 TAATATTTA
1 TAAT-TTTA
35426341 AATTTATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
11 7 0.17
12 12 0.29
13 16 0.39
15 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TAATTTTATTATA
Found at i:35426332 original size:13 final size:13
Alignment explanation
Indices: 35426283--35426339 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 13
35426273 TTGAATGTTT
35426283 AATTTTTTA-AT-
1 AATTTTTTATATA
*
35426294 AATTTTAT-TATA
1 AATTTTTTATATA
35426306 AATTTTGATTATATA
1 AATTTT--TTATATA
35426321 AATTTTTTATATA
1 AATTTTTTATATA
35426334 ATATTT
1 A-ATTT
35426340 AAATTTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 9 0.24
12 6 0.16
13 8 0.21
14 5 0.13
15 10 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
AATTTTTTATATA
Found at i:35429444 original size:25 final size:28
Alignment explanation
Indices: 35429407--35429466 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
35429397 AAATTTTTAG
35429407 GTAAAAAT-TAA-ATTATATATTTTTATAATA
1 GTAAAAATATAATATTAT-TA--TTT-TAATA
35429437 GTAAAAATATAATATTATTATTTTAATA
1 GTAAAAATATAATATTATTATTTTAATA
35429465 GT
1 GT
35429467 TTTAATCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 8 0.29
31 5 0.18
32 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (28 bp):
GTAAAAATATAATATTATTATTTTAATA
Found at i:35429512 original size:29 final size:30
Alignment explanation
Indices: 35429474--35429533 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 30
35429464 AGTTTTAATC
*
35429474 TTTATAATTTTTAAAAAATTAAAT-TAATTT
1 TTTATAA-TTTTAAAAAATAAAATATAATTT
*
35429504 TTTAT-ATTTTAAAGAATAAAATATAATTT
1 TTTATAATTTTAAAAAATAAAATATAATTT
35429533 T
1 T
35429534 ATCATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 14 0.52
29 8 0.30
30 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTATAATTTTAAAAAATAAAATATAATTT
Found at i:35444852 original size:188 final size:188
Alignment explanation
Indices: 35444535--35444900 Score: 588
Period size: 188 Copynumber: 1.9 Consensus size: 188
35444525 CCTATAGTCC
* * *
35444535 CAAAAATATTAAGATCGAACTTAAAAAAGGATAGATAAAACTAAGTAGGATTTAAATAAATTCTT
1 CAAAAATATCAAGAACGAACTTAAAAAAGGATAGATAAAACTAAGTAGGATTTAAATAAATTCTC
* * * *
35444600 GTATTTATATTATTACAATATTCATATTTTATTATTATATATTGTTTGGACTTGCAATTAATATT
66 ATATTTATATTATTACAATATTCATATATTATTATTATATATTGTCTGGACTTACAATTAATATT
*
35444665 AACAACACAATTATAGAAAAACATTGGATCTCAAGTATTTTGTGGGTGCTTAGGATCT
131 AACAACACAATTATAAAAAAACATTGGATCTCAAGTATTTTGTGGGTGCTTAGGATCT
** * * *
35444723 CAAAAATATCAAGAACGGGCTTGAAAAGGGATAGATAAAGCTAAGTAGGATTTAAATAAATTCTC
1 CAAAAATATCAAGAACGAACTTAAAAAAGGATAGATAAAACTAAGTAGGATTTAAATAAATTCTC
*
35444788 ATATTTATATTATTACAATATTTATATATTATTATTATATATTGTCTGGACTTACAATTAATATT
66 ATATTTATATTATTACAATATTCATATATTATTATTATATATTGTCTGGACTTACAATTAATATT
* *
35444853 AACAACACAATTGTAAAAAAATATTGGATCTCAAGTATTTTGTGGGTG
131 AACAACACAATTATAAAAAAACATTGGATCTCAAGTATTTTGTGGGTG
35444901 AAGACCATTG
Statistics
Matches: 162, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
188 162 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (188 bp):
CAAAAATATCAAGAACGAACTTAAAAAAGGATAGATAAAACTAAGTAGGATTTAAATAAATTCTC
ATATTTATATTATTACAATATTCATATATTATTATTATATATTGTCTGGACTTACAATTAATATT
AACAACACAATTATAAAAAAACATTGGATCTCAAGTATTTTGTGGGTGCTTAGGATCT
Found at i:35448242 original size:3 final size:3
Alignment explanation
Indices: 35448236--35448261 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35448226 CAACAACAAC
35448236 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
35448262 AACACCCAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35451857 original size:31 final size:30
Alignment explanation
Indices: 35451781--35451861 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
35451771 TATTAGTTGG
* * *
35451781 GTGATCAATTTAAAAAAAATTCATAGTTAG
1 GTGATCAATTTAGAAAAAATCCATAGTTAA
***
35451811 GTGA-CTAAAAAAGAAATAAATCCATAGTTAA
1 GTGATC-AATTTAGAAA-AAATCCATAGTTAA
35451842 GTGATCAATTTAGAAAAAAT
1 GTGATCAATTTAGAAAAAAT
35451862 AATAGTTTGC
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
29 1 0.03
30 14 0.36
31 23 0.59
32 1 0.03
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (30 bp):
GTGATCAATTTAGAAAAAATCCATAGTTAA
Found at i:35458762 original size:26 final size:25
Alignment explanation
Indices: 35458716--35458771 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
35458706 TAAAGGGTAC
*
35458716 AACGTATATAGAATAAGTTATATTT
1 AACGTATATAGAATAAATTATATTT
* *
35458741 AACGTAATTTAGAGTAAATTATATTT
1 AACGT-ATATAGAATAAATTATATTT
35458767 AACGT
1 AACGT
35458772 CAGTAAACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.39
Consensus pattern (25 bp):
AACGTATATAGAATAAATTATATTT
Found at i:35460116 original size:19 final size:20
Alignment explanation
Indices: 35460092--35460135 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
35460082 TTTACCTTTT
*
35460092 AATTTAATTAAT-ATTTAAA
1 AATTTAATAAATAATTTAAA
35460111 AATTT-ATAAATAATTTAAA
1 AATTTAATAAATAATTTAAA
35460130 AATTTA
1 AATTTA
35460136 TTACAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTAATAAATAATTTAAA
Found at i:35460145 original size:12 final size:11
Alignment explanation
Indices: 35460106--35460158 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
35460096 TAATTAATAT
35460106 TTAAAAATTTA
1 TTAAAAATTTA
35460117 -TAAATAA--T-
1 TTAAA-AATTTA
35460125 TTAAAAATTTA
1 TTAAAAATTTA
35460136 TTACAAAATTTTA
1 TTA-AAAA-TTTA
35460149 TTAAAAATTT
1 TTAAAAATTT
35460159 GGCAAGTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
8 2 0.06
9 5 0.14
10 5 0.14
11 8 0.23
12 8 0.23
13 7 0.20
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAAAAATTTA
Found at i:35460148 original size:13 final size:12
Alignment explanation
Indices: 35460125--35460158 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
35460115 TATAAATAAT
35460125 TTAAAAA-TTTA
1 TTAAAAATTTTA
35460136 TTACAAAATTTTA
1 TTA-AAAATTTTA
35460149 TTAAAAATTT
1 TTAAAAATTT
35460159 GGCAAGTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 11 0.52
13 7 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAAAATTTTA
Found at i:35461582 original size:13 final size:12
Alignment explanation
Indices: 35461564--35461604 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
35461554 CAAGTAATTA
35461564 TTTTCCTTTTCTT
1 TTTTCCTTTT-TT
35461577 TTTTCCTTTTTT
1 TTTTCCTTTTTT
*
35461589 TTTT-CTTTTTG
1 TTTTCCTTTTTT
35461600 TTTTC
1 TTTTC
35461605 TGTTCACTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.38
12 6 0.23
13 10 0.38
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTCCTTTTTT
Found at i:35470911 original size:13 final size:13
Alignment explanation
Indices: 35470878--35470912 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
35470868 TGCTAATTTT
35470878 AAAAAATATAAAAA
1 AAAAAAT-TAAAAA
*
35470892 AAAAAATTTAAAA
1 AAAAAATTAAAAA
35470905 AAAAAATT
1 AAAAAATT
35470913 GATTTACTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAATTAAAAA
Found at i:35470918 original size:17 final size:14
Alignment explanation
Indices: 35470878--35470910 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
35470868 TGCTAATTTT
*
35470878 AAAAAATATAAAAA
1 AAAAAATTTAAAAA
35470892 AAAAAATTTAAAAA
1 AAAAAATTTAAAAA
35470906 AAAAA
1 AAAAA
35470911 TTGATTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAAATTTAAAAA
Found at i:35474956 original size:66 final size:66
Alignment explanation
Indices: 35474850--35474984 Score: 243
Period size: 66 Copynumber: 2.0 Consensus size: 66
35474840 AATCTCTTGG
* *
35474850 TGAAGAAAGTAGATGCGTGAGCTATTGACTTTGTCAAACCTCTCTTTGAGATCCTTCCAAACGAG
1 TGAAGAAAGTAGATGCGTGAGCCATCGACTTTGTCAAACCTCTCTTTGAGATCCTTCCAAACGAG
35474915 A
66 A
*
35474916 TGAAGAAAGTAGATGCGTGAGCCATCGACTTTGTCAAACCTCTCTTTGAGATCCTTCCAGACGAG
1 TGAAGAAAGTAGATGCGTGAGCCATCGACTTTGTCAAACCTCTCTTTGAGATCCTTCCAAACGAG
35474981 A
66 A
35474982 TGA
1 TGA
35474985 GCACTGGTTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (66 bp):
TGAAGAAAGTAGATGCGTGAGCCATCGACTTTGTCAAACCTCTCTTTGAGATCCTTCCAAACGAG
A
Found at i:35479748 original size:11 final size:12
Alignment explanation
Indices: 35479725--35479754 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
35479715 CTCCACCCAA
35479725 TTTTCTAATTTT
1 TTTTCTAATTTT
35479737 TTTTCTAATTTT
1 TTTTCTAATTTT
35479749 TTTTCT
1 TTTTCT
35479755 TAGCCTTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTAATTTT
Found at i:35481662 original size:22 final size:24
Alignment explanation
Indices: 35481613--35481662 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 24
35481603 TTATTTCTCT
**
35481613 TAATAATATTATTTTTAAAATTTA
1 TAATAATATTATTTTTAAAACGTA
35481637 -AATAA-ATT-TTTTTAAAACGTA
1 TAATAATATTATTTTTAAAACGTA
35481658 TAATA
1 TAATA
35481663 TACCTTATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 11 0.48
22 7 0.30
23 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TAATAATATTATTTTTAAAACGTA
Found at i:35506393 original size:24 final size:24
Alignment explanation
Indices: 35506357--35506414 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
35506347 AGTGCAAGTC
* *
35506357 CAGCTGCATCCGCCGCCGCTGCAG
1 CAGCTGCAGCCGCCGCCACTGCAG
* * *
35506381 CAGCTGCCGCCGCTGCCACTGCAA
1 CAGCTGCAGCCGCCGCCACTGCAG
*
35506405 CTGCTGCAGC
1 CAGCTGCAGC
35506415 TAAAGGTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.14, C:0.45, G:0.28, T:0.14
Consensus pattern (24 bp):
CAGCTGCAGCCGCCGCCACTGCAG
Found at i:35513673 original size:31 final size:30
Alignment explanation
Indices: 35513608--35513666 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
35513598 ATTAAATGAA
*
35513608 AAAAATAAAAAAATTATATTTCGATCTCTC
1 AAAAATAAAAAAATTATATTTCAATCTCTC
*
35513638 AAAAATAAAAAAAATTCTATTT-AATCTCT
1 AAAAAT-AAAAAAATTATATTTCAATCTCT
35513667 TTAAAAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAAATAAAAAAATTATATTTCAATCTCTC
Found at i:35516582 original size:23 final size:22
Alignment explanation
Indices: 35516534--35516582 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
35516524 ATACCCATTC
* *
35516534 TAAAAATAAGTAGACCAATTTG
1 TAAAAATAAGTAGACCAAATTA
* *
35516556 TAAAAATTAGATAGATCAAATTA
1 TAAAAATAAG-TAGACCAAATTA
35516579 TAAA
1 TAAA
35516583 TATACCTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (22 bp):
TAAAAATAAGTAGACCAAATTA
Found at i:35516968 original size:18 final size:18
Alignment explanation
Indices: 35516947--35516981 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35516937 ATATGAAAGT
*
35516947 TGATTAAGGGGTGTTCGG
1 TGATTAAGCGGTGTTCGG
*
35516965 TGATTAATCGGTGTTCG
1 TGATTAAGCGGTGTTCG
35516982 ATTCGTCGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (18 bp):
TGATTAAGCGGTGTTCGG
Found at i:35519173 original size:4 final size:4
Alignment explanation
Indices: 35519164--35519216 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
35519154 TTCCAAATTT
35519164 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
35519212 ATAC A
1 ATAC A
35519217 CATAAGTGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:35523542 original size:29 final size:29
Alignment explanation
Indices: 35523500--35523564 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
35523490 ATGGCAATCC
*
35523500 ACATATATGACATATCAGTAAAGTTAACAT
1 ACAT-TATGACATACCAGTAAAGTTAACAT
*
35523530 ACATTATGCCATACCAGTAAAGTTAACAT
1 ACATTATGACATACCAGTAAAGTTAACAT
35523559 ACATTA
1 ACATTA
35523565 ACTTTTCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.29
Consensus pattern (29 bp):
ACATTATGACATACCAGTAAAGTTAACAT
Found at i:35525378 original size:20 final size:20
Alignment explanation
Indices: 35525353--35525419 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
35525343 AGCGTAATGG
*
35525353 TAAATTTAATTTTTAATATT
1 TAAATTTAATTTTTATTATT
35525373 TAAA-TT--TTTTTATTAATT
1 TAAATTTAATTTTTATT-ATT
* *
35525391 TAATTTTAATTTTT-TTAGT
1 TAAATTTAATTTTTATTATT
35525410 TAAATTTAAT
1 TAAATTTAAT
35525420 CATTAACATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 7 0.18
18 6 0.15
19 15 0.38
20 6 0.15
21 5 0.13
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
TAAATTTAATTTTTATTATT
Found at i:35525412 original size:24 final size:26
Alignment explanation
Indices: 35525364--35525419 Score: 82
Period size: 25 Copynumber: 2.2 Consensus size: 26
35525354 AAATTTAATT
35525364 TTTAATATTTAAATTTTTTTATT-AA
1 TTTAATATTTAAATTTTTTTATTAAA
35525389 TTTAAT-TTT-AATTTTTTTAGTTAAA
1 TTTAATATTTAAATTTTTTTA-TTAAA
35525414 TTTAAT
1 TTTAAT
35525420 CATTAACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.34
24 5 0.17
25 14 0.48
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTAATATTTAAATTTTTTTATTAAA
Found at i:35525807 original size:23 final size:22
Alignment explanation
Indices: 35525781--35525831 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
35525771 CGAATTGAGG
35525781 CAAAAAAATAAAAATTTAAGTAT
1 CAAAAAAA-AAAAATTTAAGTAT
** *
35525804 CAAACTGAAAAAATTTTAAGTAT
1 CAAA-AAAAAAAAATTTAAGTAT
35525827 CAAAA
1 CAAAA
35525832 TTGAATAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (22 bp):
CAAAAAAAAAAAATTTAAGTAT
Found at i:35534010 original size:20 final size:20
Alignment explanation
Indices: 35533985--35534023 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35533975 AGATTGGATT
*
35533985 TAGAAA-AAAGAAAATGGTAA
1 TAGAAATAAA-AAAAGGGTAA
35534005 TAGAAATAAAAAAAGGGTA
1 TAGAAATAAAAAAAGGGTA
35534024 CTAAAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (20 bp):
TAGAAATAAAAAAAGGGTAA
Found at i:35535812 original size:25 final size:25
Alignment explanation
Indices: 35535784--35535833 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
35535774 AATTAAACAG
35535784 GTCAACGAATTTGAATTGAAGGATA
1 GTCAACGAATTTGAATTGAAGGATA
35535809 GTCAACGAATTTGAATTGAAGGATA
1 GTCAACGAATTTGAATTGAAGGATA
35535834 TCATTTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (25 bp):
GTCAACGAATTTGAATTGAAGGATA
Found at i:35538923 original size:97 final size:96
Alignment explanation
Indices: 35538757--35538970 Score: 286
Period size: 97 Copynumber: 2.2 Consensus size: 96
35538747 TTATGTATTC
* * * ** *
35538757 AAAAATTAAACCAAGTAAAGCGGAAATGTAGAAATGGAGAACTACGAGGTAATTTAATCAAACAA
1 AAAAATTAAACTAAGTAAAGAGGAAATGTAGAAATGGAAAACTACGAGACAACTTAATCAAACAA
*
35538822 AAGAACATATCATGAATCTTACAACAAATTAA
66 AAGAACATATCAAGAATCTTACAACAAA-TAA
35538854 AAAAATTAAACTAAGTAAAGAGGAAATGTAGAAAT-GAAAAGCTACGAGACAACTTAATCAAACA
1 AAAAATTAAACTAAGTAAAGAGGAAATGTAGAAATGGAAAA-CTACGAGACAACTTAATCAAACA
* ** **
35538918 AAAGAACATATCAAGAATCTTGCTTCAAATCC
65 AAAGAACATATCAAGAATCTTACAACAAATAA
*
35538950 AAAAATTAAACTAAATAAAGA
1 AAAAATTAAACTAAGTAAAGA
35538971 AGACATACAG
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
96 25 0.24
97 78 0.76
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (96 bp):
AAAAATTAAACTAAGTAAAGAGGAAATGTAGAAATGGAAAACTACGAGACAACTTAATCAAACAA
AAGAACATATCAAGAATCTTACAACAAATAA
Found at i:35539058 original size:42 final size:42
Alignment explanation
Indices: 35539011--35539093 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
35539001 TGATCAAATA
* * *
35539011 TAAACTGAAACATAATCTAAATCTTACTTCGGATCCAAAAAG
1 TAAACTGAAACATAATATAAATCTTACTTCGAATCAAAAAAG
* *
35539053 TAAACTGAAACATACTATTAATCTTACTTCGAATCAAAAAA
1 TAAACTGAAACATAATATAAATCTTACTTCGAATCAAAAAA
35539094 TGAACTAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (42 bp):
TAAACTGAAACATAATATAAATCTTACTTCGAATCAAAAAAG
Found at i:35539359 original size:42 final size:42
Alignment explanation
Indices: 35539244--35539360 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
35539234 AATCACACAT
* *
35539244 TATTAATCTTACTT-GCAATCCGAAAATTAAACTGAAACATAC
1 TATTAATCTTACTTCG-AATTCAAAAATTAAACTGAAACATAC
** * *
35539286 TAAGAATCTTACTCCGAA-TCAAAAAAGTAAACTGAAACATAC
1 TATTAATCTTACTTCGAATTC-AAAAATTAAACTGAAACATAC
*
35539328 TATTAACCTTACTTCGAATTCAAAAATTAAACT
1 TATTAATCTTACTTCGAATTCAAAAATTAAACT
35539361 AAGTAAAGCG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.02
42 57 0.93
43 3 0.05
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (42 bp):
TATTAATCTTACTTCGAATTCAAAAATTAAACTGAAACATAC
Found at i:35544518 original size:24 final size:25
Alignment explanation
Indices: 35544462--35544518 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
35544452 GAAAATTGTT
*
35544462 TTTCAAAAGTGTTGTGATAAAGTAA
1 TTTCAAAAGTGTTGTGATAAAATAA
* *
35544487 TTTGAAAA-TGTTGTGATAAAATAC
1 TTTCAAAAGTGTTGTGATAAAATAA
35544511 TTTCAAAA
1 TTTCAAAA
35544519 AATGTGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (25 bp):
TTTCAAAAGTGTTGTGATAAAATAA
Found at i:35556424 original size:21 final size:21
Alignment explanation
Indices: 35556398--35556437 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35556388 TGATTGATTT
35556398 AAATCA-AATAAATTATAAAAA
1 AAATCATAA-AAATTATAAAAA
*
35556419 AAATCATAAAAATTTTAAA
1 AAATCATAAAAATTATAAA
35556438 TTTTAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCATAAAAATTATAAAAA
Found at i:35559202 original size:22 final size:20
Alignment explanation
Indices: 35559175--35559229 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
35559165 AATATCTGAA
*
35559175 TAATAACAATAAAATAGTAG
1 TAATAACAATAAAATAATAG
* *
35559195 TACTATAATAACAAAATAATAG
1 TA--ATAACAATAAAATAATAG
35559217 TAA-AACAATAAAA
1 TAATAACAATAAAA
35559230 ATATATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 8 0.29
20 3 0.11
22 17 0.61
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (20 bp):
TAATAACAATAAAATAATAG
Found at i:35559227 original size:25 final size:25
Alignment explanation
Indices: 35559173--35559227 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
35559163 ATAATATCTG
**
35559173 AATAATAACAATAAAATAGTAGTAC
1 AATAATAACAATAAAATAGTAAAAC
*
35559198 TATAATAACAA-AATAATAGTAAAAC
1 AATAATAACAATAA-AATAGTAAAAC
35559223 AATAA
1 AATAA
35559228 AAATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (25 bp):
AATAATAACAATAAAATAGTAAAAC
Found at i:35569907 original size:2 final size:2
Alignment explanation
Indices: 35569902--35569950 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
35569892 TTTAAAAAGT
35569902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35569944 TA TA TA T
1 TA TA TA T
35569951 TGGTGAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35571536 original size:20 final size:21
Alignment explanation
Indices: 35571499--35571542 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
35571489 GATATGTTGA
* * *
35571499 TATTGTATAATTTTATAA-AT
1 TATTGAATAATATAATAAGAT
35571519 TATTGAATAATATAATAAGAT
1 TATTGAATAATATAATAAGAT
35571540 TAT
1 TAT
35571543 GTTAAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (21 bp):
TATTGAATAATATAATAAGAT
Found at i:35578855 original size:21 final size:22
Alignment explanation
Indices: 35578825--35578866 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
35578815 CCTAATTTTT
*
35578825 AAATTTAAAA-AAAAATAAAAA
1 AAATTAAAAATAAAAATAAAAA
*
35578846 AAATTAAAAATAAAACTAAAA
1 AAATTAAAAATAAAAATAAAA
35578867 TAACTAAATT
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:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (22 bp):
AAATTAAAAATAAAAATAAAAA
Found at i:35579553 original size:13 final size:13
Alignment explanation
Indices: 35579535--35579575 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
35579525 TCTACACAGT
*
35579535 TCACATATTGAGG
1 TCACATATTGAGC
*
35579548 TCACATATTGACC
1 TCACATATTGAGC
*
35579561 TCACGTATTGAGC
1 TCACATATTGAGC
35579574 TC
1 TC
35579576 GTGATGTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (13 bp):
TCACATATTGAGC
Found at i:35585389 original size:2 final size:2
Alignment explanation
Indices: 35585384--35585415 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35585374 GTAATATATA
35585384 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
35585416 AGAGAGAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35585420 original size:2 final size:2
Alignment explanation
Indices: 35585415--35585448 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
35585405 GTGTGTGTGT
35585415 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35585449 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35605098 original size:24 final size:23
Alignment explanation
Indices: 35605065--35605134 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 23
35605055 AAAATATAAA
* * *
35605065 TTTATTATTTTAATAATTTAAATT
1 TTTATAATTTTAAAAAATT-AATT
35605089 TTTATAATTTTAAAAAAATTAATT
1 TTTATAATTTT-AAAAAATTAATT
*
35605113 TTTATACTTTTAAAATAATTAA
1 TTTATAATTTTAAAA-AATTAA
35605135 AATGTAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.10
24 30 0.75
25 6 0.15
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTATAATTTTAAAAAATTAATT
Found at i:35616173 original size:19 final size:19
Alignment explanation
Indices: 35616141--35616179 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
35616131 AAAATTAAAT
*
35616141 AAATTATAAGAAAAGAGTA
1 AAATTATAACAAAAGAGTA
* *
35616160 AAATTTTAACAAAAGCGTA
1 AAATTATAACAAAAGAGTA
35616179 A
1 A
35616180 TTTGAAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.13, T:0.23
Consensus pattern (19 bp):
AAATTATAACAAAAGAGTA
Found at i:35618992 original size:30 final size:30
Alignment explanation
Indices: 35618956--35619017 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
35618946 ACTTATTTTA
*
35618956 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAGAGACAT
35618986 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAGAGACAT
35619016 TT
1 TT
35619018 ACTTGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGACAT
Found at i:35624798 original size:9 final size:9
Alignment explanation
Indices: 35624784--35624949 Score: 50
Period size: 10 Copynumber: 18.6 Consensus size: 9
35624774 GAGAACACTT
35624784 TTTTTAATA
1 TTTTTAATA
35624793 TTTTTACA-A
1 TTTTTA-ATA
*
35624802 ATTTT-A--
1 TTTTTAATA
35624808 TTTTTAATAA
1 TTTTTAAT-A
35624818 TTTTTAAT-
1 TTTTTAATA
35624826 TTTTTAA-A
1 TTTTTAATA
**
35624834 -AATTACA-A
1 TTTTTA-ATA
35624842 T-TTTAATA
1 TTTTTAATA
**
35624850 TTTTTTACGA
1 -TTTTTAATA
35624860 TTTTTAAT-
1 TTTTTAATA
35624868 TTTTTAATA
1 TTTTTAATA
35624877 -TTTTAATAA
1 TTTTTAAT-A
35624886 TTTTT-ATAA
1 TTTTTAAT-A
* *
35624895 GATTTTAATTT
1 -TTTTTAA-TA
*
35624906 TTTTTATTA
1 TTTTTAATA
*
35624915 TTTTTTACATT
1 -TTTTTA-ATA
* *
35624926 TTTTTTAGA
1 TTTTTAATA
35624935 TTTTTAATGA
1 TTTTTAAT-A
35624945 TTTTT
1 TTTTT
35624950 GTCAATCTTT
Statistics
Matches: 116, Mismatches: 21, Indels: 39
0.66 0.12 0.22
Matches are distributed among these distances:
6 4 0.03
7 6 0.05
8 28 0.24
9 31 0.27
10 44 0.38
11 2 0.02
12 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTAATA
Found at i:35624837 original size:33 final size:33
Alignment explanation
Indices: 35624784--35624891 Score: 94
Period size: 33 Copynumber: 3.2 Consensus size: 33
35624774 GAGAACACTT
*
35624784 TTTTTAATATTTTTACAAATTTTATTTTTAATAA
1 TTTTTAAT-TTTTTAAAAATTTTATTTTTAATAA
** * *
35624818 TTTTTAATTTTTTAAAAATTACAATTTTAATAT
1 TTTTTAATTTTTTAAAAATTTTATTTTTAATAA
**
35624851 TTTTTACGA-TTTTT-AATTTTTTAATATTTTAATAA
1 TTTTTA--ATTTTTTAAAAATTTT-AT-TTTTAATAA
35624886 TTTTTA
1 TTTTTA
35624892 TAAGATTTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
33 30 0.51
34 14 0.24
35 15 0.25
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (33 bp):
TTTTTAATTTTTTAAAAATTTTATTTTTAATAA
Found at i:35624880 original size:35 final size:36
Alignment explanation
Indices: 35624841--35624908 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
35624831 AAAAATTACA
*
35624841 ATTTTAAT-ATTTTT-TACGATTTTTAATTTTTTAAT
1 ATTTTAATAATTTTTATAAGA-TTTTAATTTTTTAAT
35624876 ATTTTAATAATTTTTATAAGATTTTAATTTTTT
1 ATTTTAATAATTTTTATAAGATTTTAATTTTTT
35624909 TTATTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 8 0.27
36 18 0.60
37 4 0.13
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (36 bp):
ATTTTAATAATTTTTATAAGATTTTAATTTTTTAAT
Found at i:35624903 original size:17 final size:17
Alignment explanation
Indices: 35624849--35624908 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
35624839 CAATTTTAAT
*
35624849 ATTTTTTACGATTTTTA
1 ATTTTTTAAGATTTTTA
*
35624866 ATTTTTTAATATTTTAATA
1 ATTTTTTAAGATTTT--TA
35624885 ATTTTTATAAGA-TTTTA
1 ATTTTT-TAAGATTTTTA
35624902 ATTTTTT
1 ATTTTTT
35624909 TTATTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
19 11 0.30
20 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTTTTAAGATTTTTA
Found at i:35624909 original size:20 final size:20
Alignment explanation
Indices: 35624867--35624932 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
35624857 CGATTTTTAA
**
35624867 TTTTT-TAATATTTTAATAA
1 TTTTTATAATATTTTAATTT
*
35624886 TTTTTATAAGATTTTAATTT
1 TTTTTATAATATTTTAATTT
* *
35624906 TTTTTATTATTTTTTACATTT
1 TTTTTATAATATTTTA-ATTT
35624927 TTTTTA
1 TTTTTA
35624933 GATTTTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 5 0.13
20 24 0.62
21 10 0.26
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTATAATATTTTAATTT
Found at i:35624937 original size:20 final size:20
Alignment explanation
Indices: 35624842--35624939 Score: 66
Period size: 18 Copynumber: 5.2 Consensus size: 20
35624832 AAAATTACAA
* *
35624842 TTTTAATATTTTTTACGA-T
1 TTTTAATTTTTTTTATGATT
*
35624861 TTTTAA-TTTTTTAAT-ATT
1 TTTTAATTTTTTTTATGATT
* * *
35624879 TTAATAA-TTTTTATAAGA--
1 TT-TTAATTTTTTTTATGATT
*
35624897 TTTTAATTTTTTTTATTATT
1 TTTTAATTTTTTTTATGATT
35624917 TTTTACATTTTTTTTA-GATT
1 TTTTA-ATTTTTTTTATGATT
35624937 TTT
1 TTT
35624940 AATGATTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
17 4 0.07
18 19 0.32
19 15 0.25
20 12 0.20
21 10 0.17
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTAATTTTTTTTATGATT
Found at i:35624946 original size:10 final size:9
Alignment explanation
Indices: 35624806--35624949 Score: 52
Period size: 10 Copynumber: 15.8 Consensus size: 9
35624796 TTACAAATTT
35624806 TATTTTTAA
1 TATTTTTAA
35624815 TAATTTTTAA
1 T-ATTTTTAA
35624825 T-TTTTTAA
1 TATTTTTAA
**
35624833 -A-AATTACA
1 TATTTTTA-A
35624841 -A-TTTTAA
1 TATTTTTAA
*
35624848 TATTTTTTAC
1 TA-TTTTTAA
*
35624858 GATTTTTAA
1 TATTTTTAA
35624867 T-TTTTTAA
1 TATTTTTAA
35624875 TA-TTTTAA
1 TATTTTTAA
35624883 TAATTTTT-A
1 T-ATTTTTAA
*
35624892 TAAGATTTTAA
1 T-A-TTTTTAA
* *
35624903 TTTTTTTTAT
1 -TATTTTTAA
35624913 TATTTTTTACA
1 TA-TTTTTA-A
* *
35624924 TTTTTTTTA
1 TATTTTTAA
*
35624933 GATTTTTAA
1 TATTTTTAA
35624942 TGATTTTT
1 T-ATTTTT
35624950 GTCAATCTTT
Statistics
Matches: 100, Mismatches: 20, Indels: 29
0.67 0.13 0.19
Matches are distributed among these distances:
7 4 0.04
8 28 0.28
9 20 0.20
10 45 0.45
11 2 0.02
12 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (9 bp):
TATTTTTAA
Found at i:35624949 original size:20 final size:18
Alignment explanation
Indices: 35624842--35624942 Score: 80
Period size: 19 Copynumber: 5.4 Consensus size: 18
35624832 AAAATTACAA
*
35624842 TTTTAATATTTTTTACGAT
1 TTTTAATTTTTTTTA-GAT
* *
35624861 TTTTAA-TTTTTTAATAT
1 TTTTAATTTTTTTTAGAT
* *
35624878 TTTAATAATTTTTATAAGA-
1 TTT--TAATTTTTTTTAGAT
*
35624897 TTTTAATTTTTTTTATTATT
1 TTTTAATTTTTTTTA-GA-T
35624917 TTTTACATTTTTTTTAGAT
1 TTTTA-ATTTTTTTTAGAT
35624936 TTTTAAT
1 TTTTAAT
35624943 GATTTTTGTC
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
17 15 0.23
18 9 0.14
19 18 0.27
20 14 0.21
21 10 0.15
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTAATTTTTTTTAGAT
Found at i:35637753 original size:16 final size:16
Alignment explanation
Indices: 35637732--35637781 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
35637722 TGATTGGGAT
35637732 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
35637748 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
35637763 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
35637778 ATTA
1 ATTA
35637782 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:35637991 original size:27 final size:27
Alignment explanation
Indices: 35637958--35638030 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 27
35637948 AAAAATATTT
35637958 AAAATTTTATATTAATTTTTTATAACA
1 AAAATTTTATATTAATTTTTTATAACA
*
35637985 AAAATTTTAT-TTAA-TTTTTGTAACA
1 AAAATTTTATATTAATTTTTTATAACA
** *
35638010 AATTTTTTTTATTTAATTTTT
1 AAAATTTTATA-TTAATTTTT
35638031 ATCACCTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
25 17 0.44
26 4 0.10
27 14 0.36
28 4 0.10
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (27 bp):
AAAATTTTATATTAATTTTTTATAACA
Found at i:35638002 original size:25 final size:25
Alignment explanation
Indices: 35637958--35638032 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 25
35637948 AAAAATATTT
35637958 AAAATTTTATATTAATTTTTTATAACA
1 AAAATTTTAT-TTAA-TTTTTATAACA
*
35637985 AAAATTTTATTTAATTTTTGTAACA
1 AAAATTTTATTTAATTTTTATAACA
**
35638010 AATTTTTTTTATTTAATTTTTAT
1 AA--AATTTTATTTAATTTTTAT
35638033 CACCTACAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.29
26 4 0.10
27 26 0.62
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (25 bp):
AAAATTTTATTTAATTTTTATAACA
Found at i:35638811 original size:16 final size:16
Alignment explanation
Indices: 35638790--35638822 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35638780 AGAATCCAAT
*
35638790 AACAAATTAAAAATAA
1 AACAAATAAAAAATAA
35638806 AACAAATAAAAAATAA
1 AACAAATAAAAAATAA
35638822 A
1 A
35638823 GTTAGATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (16 bp):
AACAAATAAAAAATAA
Found at i:35642908 original size:30 final size:30
Alignment explanation
Indices: 35642864--35642931 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
35642854 AAATTTTAAA
*
35642864 TTAATAAA-AATAAAATTATAAATTAATCCT
1 TTAA-AAATAATAAAATTATAAATTAATCAT
* * *
35642894 TTAAAAATAATAAAATTTTGATTTAATCAT
1 TTAAAAATAATAAAATTATAAATTAATCAT
35642924 TTAAAAAT
1 TTAAAAAT
35642932 TACATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAAATTAATCAT
Found at i:35643954 original size:5 final size:6
Alignment explanation
Indices: 35643937--35643961 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35643927 AGCGCCGGTC
35643937 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
35643962 TCAAGCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:35656319 original size:19 final size:21
Alignment explanation
Indices: 35656297--35656346 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
35656287 TTTATTTCAT
35656297 GAAAAATAATT-T-AGTCAAC
1 GAAAAATAATTATAAGTCAAC
*
35656316 GAAAAATGATTTATAAGTCAAC
1 GAAAAAT-AATTATAAGTCAAC
35656338 GAAAAATAA
1 GAAAAATAA
35656347 ACTTATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 7 0.27
20 3 0.12
21 2 0.08
22 14 0.54
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (21 bp):
GAAAAATAATTATAAGTCAAC
Found at i:35656352 original size:23 final size:22
Alignment explanation
Indices: 35656297--35656352 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
35656287 TTTATTTCAT
35656297 GAAAAATAA-TT-T-AGTCAAC
1 GAAAAATAACTTATAAGTCAAC
* *
35656316 GAAAAATGATTTATAAGTCAAC
1 GAAAAATAACTTATAAGTCAAC
35656338 GAAAAATAAACTTAT
1 GAAAAAT-AACTTAT
35656353 TTCACTGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 8 0.27
20 2 0.07
21 1 0.03
22 14 0.47
23 5 0.17
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.27
Consensus pattern (22 bp):
GAAAAATAACTTATAAGTCAAC
Found at i:35671215 original size:19 final size:19
Alignment explanation
Indices: 35671170--35671218 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
35671160 TAAAAATGCT
*
35671170 AAATTATCTTTAAATAATAT
1 AAATTAT-TTTAAATAATAA
*
35671190 AATTTATTTTAAAT-ATAAA
1 AAATTATTTTAAATAAT-AA
35671209 AAATTATTTT
1 AAATTATTTT
35671219 TGTAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.68
20 6 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTATTTTAAATAATAA
Found at i:35671431 original size:24 final size:23
Alignment explanation
Indices: 35671403--35671454 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
35671393 ATACAAGCTA
*
35671403 TTTTTACTAAAATATTTATTATTG
1 TTTTTACTAAAA-ATTCATTATTG
* *
35671427 TTTTTATTAATAATTCATTATTG
1 TTTTTACTAAAAATTCATTATTG
35671450 TTTTT
1 TTTTT
35671455 TATTAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTTACTAAAAATTCATTATTG
Found at i:35671455 original size:24 final size:23
Alignment explanation
Indices: 35671420--35671467 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
35671410 TAAAATATTT
35671420 ATTATTGTTTTTATTAATAATTC
1 ATTATTGTTTTTATTAATAATTC
35671443 ATTATTGTTTTTTATTAATAATTC
1 ATTATTG-TTTTTATTAATAATTC
35671467 A
1 A
35671468 AAATCTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
ATTATTGTTTTTATTAATAATTC
Found at i:35682448 original size:25 final size:24
Alignment explanation
Indices: 35682400--35682448 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
35682390 GTATTCAACG
*
35682400 AACATGTAAATTTATTATTGATTT
1 AACATGTAAATTTATTATTCATTT
35682424 AACATGGTAAATTGTATT-TTCATTT
1 AACAT-GTAAATT-TATTATTCATTT
35682449 TATCTTAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 13 0.59
26 4 0.18
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (24 bp):
AACATGTAAATTTATTATTCATTT
Done.