Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 35
Found at i:3244730 original size:6 final size:6
Alignment explanation
Indices: 3244719--3244781 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
3244709 TATCTACTCC
* * * * *
3244719 TGATGA TGATGA TGATGA CGATGA TGATGG TGATGG TGATGG TGATGG
1 TGATGA TGATGA TGATGA TGATGA TGATGA TGATGA TGATGA TGATGA
*
3244767 TGATGG TGATGA TGA
1 TGATGA TGATGA TGA
3244782 CGAGAGTGAG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.25, C:0.02, G:0.41, T:0.32
Consensus pattern (6 bp):
TGATGA
Found at i:3244736 original size:12 final size:12
Alignment explanation
Indices: 3244719--3244781 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
3244709 TATCTACTCC
*
3244719 TGATGATGATGA
1 TGATGGTGATGA
**
3244731 TGATGACGATGA
1 TGATGGTGATGA
*
3244743 TGATGGTGATGG
1 TGATGGTGATGA
*
3244755 TGATGGTGATGG
1 TGATGGTGATGA
3244767 TGATGGTGATGA
1 TGATGGTGATGA
3244779 TGA
1 TGA
3244782 CGAGAGTGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.25, C:0.02, G:0.41, T:0.32
Consensus pattern (12 bp):
TGATGGTGATGA
Found at i:3244743 original size:18 final size:18
Alignment explanation
Indices: 3244719--3244781 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
3244709 TATCTACTCC
* *
3244719 TGATGATGATGATGATGA
1 TGATGATGATGGTGATGG
*
3244737 CGATGATGATGGTGATGG
1 TGATGATGATGGTGATGG
*
3244755 TGATGGTGATGGTGATGG
1 TGATGATGATGGTGATGG
3244773 TGATGATGA
1 TGATGATGA
3244782 CGAGAGTGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.25, C:0.02, G:0.41, T:0.32
Consensus pattern (18 bp):
TGATGATGATGGTGATGG
Found at i:3244913 original size:13 final size:13
Alignment explanation
Indices: 3244895--3244920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3244885 ACATTTCATT
3244895 ATTTTTTTATTTA
1 ATTTTTTTATTTA
3244908 ATTTTTTTATTTA
1 ATTTTTTTATTTA
3244921 CCAACAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTTTTATTTA
Found at i:3245039 original size:25 final size:24
Alignment explanation
Indices: 3244981--3245040 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
3244971 ATTTTGTTTG
3244981 TTAATTTTTTATTACTTAATTGTT
1 TTAATTTTTTATTACTTAATTGTT
* *
3245005 TGAATGTTTTTATTATTTAA-TGCTTT
1 TTAAT-TTTTTATTACTTAATTG--TT
3245031 TTAATTTTTT
1 TTAATTTTTT
3245041 TGTTGTATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 6 0.20
25 18 0.60
26 6 0.20
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (24 bp):
TTAATTTTTTATTACTTAATTGTT
Found at i:3248473 original size:10 final size:10
Alignment explanation
Indices: 3248454--3248483 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3248444 TTTTGCGAGG
3248454 TTACTATTCA
1 TTACTATTCA
*
3248464 TTATTATTCA
1 TTACTATTCA
3248474 TTACTATTCA
1 TTACTATTCA
3248484 CATGAATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (10 bp):
TTACTATTCA
Found at i:3252369 original size:6 final size:6
Alignment explanation
Indices: 3252361--3252395 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
3252351 CTGCTACTGA
*
3252361 TGATGA TGATGG TGATGG TGATGG TGATGG TGATG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATG
3252396 ATGACGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.46, T:0.34
Consensus pattern (6 bp):
TGATGG
Found at i:3252657 original size:25 final size:24
Alignment explanation
Indices: 3252599--3252658 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
3252589 ATTTTGTTTG
3252599 TTAATTTTTTATTACTTAATTGTT
1 TTAATTTTTTATTACTTAATTGTT
* *
3252623 TGAATGTTTTTATTATTTAA-TGCTTT
1 TTAAT-TTTTTATTACTTAATTG--TT
3252649 TTAATTTTTT
1 TTAATTTTTT
3252659 TTGTATCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 6 0.20
25 18 0.60
26 6 0.20
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (24 bp):
TTAATTTTTTATTACTTAATTGTT
Found at i:3254189 original size:66 final size:63
Alignment explanation
Indices: 3254053--3254217 Score: 183
Period size: 66 Copynumber: 2.5 Consensus size: 63
3254043 TTTGCAAAGG
*
3254053 CATGCACCGATGCATCAATACATGCATCGATGCA-TCATTGAATAAATTGAACATCGAGTGCATT
1 CATGCACCGATGCA-C-ATACATGCATCGATGCACTCATT-AATAAATTGAACATCGAATGCATT
3254117 T
63 T
*
3254118 CATGCACCGATGCACTATACATGCATCGATGCACTCTGATT-TTAAA-TGAAAACATCGAATGCA
1 CATGCACCGATGCAC-ATACATGCATCGATGCACTC--ATTAATAAATTG--AACATCGAATGCA
3254181 TTT
61 TTT
* * *
3254184 GATGCATCGATGCACACACCATGCATCGATGCAC
1 CATGCACCGATGCACATA-CATGCATCGATGCAC
3254218 ACACCATGCA
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
64 20 0.23
65 22 0.25
66 43 0.49
67 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (63 bp):
CATGCACCGATGCACATACATGCATCGATGCACTCATTAATAAATTGAACATCGAATGCATTT
Found at i:3254209 original size:19 final size:19
Alignment explanation
Indices: 3254185--3254235 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
3254175 AATGCATTTG
3254185 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
3254204 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
*
3254223 ATGCATCAATGCA
1 ATGCATCGATGCA
3254236 TTCAGGCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.33, C:0.33, G:0.16, T:0.18
Consensus pattern (19 bp):
ATGCATCGATGCACACACC
Found at i:3254226 original size:85 final size:83
Alignment explanation
Indices: 3254118--3254302 Score: 196
Period size: 83 Copynumber: 2.2 Consensus size: 83
3254108 GAGTGCATTT
* * * *
3254118 CATGCACCGATGCACTATACATGCATCGATGCACTC-TGATTTTAAATGAAAACATCGAATGCAT
1 CATGCACCGATGCACTACACATGCATCAATGCACTCAGGATTTT---TCAAAACATCGAATGCAT
*
3254182 TTGATGCATCGATGCACACAC
63 TTGATACATCGATGCACACAC
* * *
3254203 CATGCATCGATGCAC-ACACCATGCATCAATGCATTCAGGCTTTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTACA-CATGCATCAATGCACTCAGGATTTTTCAAAACATCGAATGCATTT
* * *
3254267 TATACATCGATGCATAC-T
65 GATACATCGATGCACACAC
*
3254285 TAGTGCACCGATGCACTA
1 CA-TGCACCGATGCACTA
3254303 AGTGTTCAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
82 1 0.01
83 45 0.54
84 3 0.04
85 29 0.35
86 5 0.06
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (83 bp):
CATGCACCGATGCACTACACATGCATCAATGCACTCAGGATTTTTCAAAACATCGAATGCATTTG
ATACATCGATGCACACAC
Found at i:3260074 original size:24 final size:24
Alignment explanation
Indices: 3260054--3260135 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 24
3260044 ACACTTGTCA
3260054 GTGCATCGATGCATCCCCTTGAAT
1 GTGCATCGATGCATCCCCTTGAAT
*
3260078 GTGCATCGATGCAT---CATGAA-
1 GTGCATCGATGCATCCCCTTGAAT
* *
3260098 GATGCACCGATGCAT-GCCTTGAAT
1 G-TGCATCGATGCATCCCCTTGAAT
*
3260122 ATGCATCGATGCAT
1 GTGCATCGATGCAT
3260136 GAAGGCCATG
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.02
21 17 0.35
23 17 0.35
24 14 0.29
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (24 bp):
GTGCATCGATGCATCCCCTTGAAT
Found at i:3260125 original size:23 final size:23
Alignment explanation
Indices: 3260055--3260136 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
3260045 CACTTGTCAG
* *
3260055 TGCATCGATGCATCCCCTTGAATG
1 TGCATCGATGCAT-GCCTTGAATA
* *
3260079 TGCATCGATGCAT--CATGAAGA
1 TGCATCGATGCATGCCTTGAATA
*
3260100 TGCACCGATGCATGCCTTGAATA
1 TGCATCGATGCATGCCTTGAATA
3260123 TGCATCGATGCATG
1 TGCATCGATGCATG
3260137 AAGGCCATGC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
21 17 0.35
23 19 0.39
24 13 0.27
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (23 bp):
TGCATCGATGCATGCCTTGAATA
Found at i:3260147 original size:44 final size:43
Alignment explanation
Indices: 3260055--3260160 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 43
3260045 CACTTGTCAG
* * *
3260055 TGCATCGATGCATCCCCTTGAATGTGCATCGATGCATCATGAAGA
1 TGCATCGATGCAT--CCTTGAATATGCATCGATGCATCAAGAACA
* * **
3260100 TGCACCGATGCATGCCTTGAATATGCATCGATGCATGAAGGCCA
1 TGCATCGATGCAT-CCTTGAATATGCATCGATGCATCAAGAACA
3260144 TGCATCGATGCATCCTT
1 TGCATCGATGCATCCTT
3260161 CGGGTTTTAG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 4 0.08
44 36 0.69
45 12 0.23
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (43 bp):
TGCATCGATGCATCCTTGAATATGCATCGATGCATCAAGAACA
Found at i:3260581 original size:13 final size:13
Alignment explanation
Indices: 3260565--3260589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3260555 AAATCGAAAA
3260565 TCTAAATTTAATT
1 TCTAAATTTAATT
3260578 TCTAAATTTAAT
1 TCTAAATTTAAT
3260590 GTTTTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TCTAAATTTAATT
Found at i:3261414 original size:23 final size:23
Alignment explanation
Indices: 3261388--3261432 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3261378 CACCACAGCT
*
3261388 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
3261411 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
3261433 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:3262665 original size:19 final size:19
Alignment explanation
Indices: 3262616--3262657 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3262606 CACGTTTGGA
3262616 AGAAGAGAAG-AGTGAAGAAG
1 AGAAGA-AAGAAG-GAAGAAG
*
3262636 ATAAGAAAGAAGGAAGAAG
1 AGAAGAAAGAAGGAAGAAG
3262655 AGA
1 AGA
3262658 TGAGAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (19 bp):
AGAAGAAAGAAGGAAGAAG
Found at i:3268945 original size:21 final size:21
Alignment explanation
Indices: 3268921--3268963 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3268911 TTCATATTCG
* *
3268921 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3268942 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3268963 T
1 T
3268964 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3269473 original size:19 final size:19
Alignment explanation
Indices: 3269424--3269465 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3269414 CACGTTTGGA
3269424 AGAAGAGAAG-AGTGAAGAAG
1 AGAAGA-AAGAAG-GAAGAAG
*
3269444 ATAAGAAAGAAGGAAGAAG
1 AGAAGAAAGAAGGAAGAAG
3269463 AGA
1 AGA
3269466 TGAGAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (19 bp):
AGAAGAAAGAAGGAAGAAG
Found at i:3270593 original size:21 final size:21
Alignment explanation
Indices: 3270551--3270594 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3270541 ACTCCGGGAG
*
3270551 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
3270572 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
3270593 CT
1 CT
3270595 CCAGCTCCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:3271740 original size:66 final size:63
Alignment explanation
Indices: 3271604--3271768 Score: 199
Period size: 66 Copynumber: 2.5 Consensus size: 63
3271594 TTTGCAAAGG
3271604 CATGCACCGATGCATCAATACATGCATCGATGCATCATTGAATAAATTGAACATCGAATGCATTT
1 CATGCACCGATGCA-C-ATACATGCATCGATGCATCATTGAATAAATTGAACATCGAATGCATTT
* *
3271669 CATGCACCGATGCACTATACATGCATCGATGCA-CTTTGATTTTAAA-TGAAAACATCGAATGCA
1 CATGCACCGATGCAC-ATACATGCATCGATGCATCATTGA--ATAAATTG--AACATCGAATGCA
3271732 TTT
61 TTT
* * *
3271735 GATGCATCGATGCACACACCATGCATCGATGCAT
1 CATGCACCGATGCACATA-CATGCATCGATGCAT
3271769 TCAGGCTTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
63 5 0.06
64 20 0.23
65 20 0.23
66 43 0.49
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACATACATGCATCGATGCATCATTGAATAAATTGAACATCGAATGCATTT
Found at i:3272949 original size:25 final size:25
Alignment explanation
Indices: 3272887--3272951 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
3272877 TGATACAACA
3272887 AAAAAATTAA-AAAGCATTAAATAAT
1 AAAAAATTAACAAA-CATTAAATAAT
*
3272912 AAAAACATT--CAAACAGTTAAGTAAT
1 AAAAA-ATTAACAAACA-TTAAATAAT
3272937 -AAAAATTAACAAACA
1 AAAAAATTAACAAACA
3272952 AAATAAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
23 3 0.09
24 6 0.18
25 22 0.65
26 3 0.09
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.22
Consensus pattern (25 bp):
AAAAAATTAACAAACATTAAATAAT
Found at i:3272977 original size:19 final size:18
Alignment explanation
Indices: 3272951--3272993 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
3272941 ATTAACAAAC
3272951 AAAATAAATTAAGT-AATA
1 AAAATAAA-TAAGTAAATA
*
3272969 AAAAGTAAATAATTAAATA
1 AAAA-TAAATAAGTAAATA
3272988 AAAATA
1 AAAATA
3272994 TTGCAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAATAAATAAGTAAATA
Found at i:3273154 original size:3 final size:3
Alignment explanation
Indices: 3273146--3273187 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
3273136 CTCACTCTCG
* * *
3273146 TCA TCA TCA CCA TCA CCA TCA TCA TCA TCA TTA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
3273188 GGAGTAGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:3277099 original size:9 final size:9
Alignment explanation
Indices: 3277085--3277109 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3277075 TACATATACA
3277085 CATCATTTC
1 CATCATTTC
3277094 CATCATTTC
1 CATCATTTC
3277103 CATCATT
1 CATCATT
3277110 GACCTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTTC
Found at i:3277429 original size:18 final size:18
Alignment explanation
Indices: 3277406--3277441 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3277396 ACTGAATATT
3277406 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3277424 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3277442 ATAATCCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3277546 original size:24 final size:25
Alignment explanation
Indices: 3277509--3277568 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
3277499 TGGGCATTAT
* *
3277509 CATTCATGTTATTTCAT-ATTT-TCA
1 CATTCATATCATTT-ATCATTTATCA
*
3277533 CATTCATATCATTTATCTTTTATCA
1 CATTCATATCATTTATCATTTATCA
3277558 CATGTCATATC
1 CAT-TCATATC
3277569 TCTTATGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 2 0.07
24 15 0.50
25 6 0.20
26 7 0.23
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (25 bp):
CATTCATATCATTTATCATTTATCA
Found at i:3277844 original size:2 final size:2
Alignment explanation
Indices: 3277805--3277831 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3277795 TCATATAGTC
3277805 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
3277832 CAATAAAATA
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:3294010 original size:34 final size:34
Alignment explanation
Indices: 3293972--3294039 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
3293962 TTTATTATCG
* * *
3293972 AGGGTTAGAGTGTTATGTCTATCTTATGTTATTC
1 AGGGTTAGAATGTAATGTCTATCTTATGTAATTC
*
3294006 AGGGTTAGAATGTAATGTGTATCTTATGTAATTC
1 AGGGTTAGAATGTAATGTCTATCTTATGTAATTC
3294040 TGGTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (34 bp):
AGGGTTAGAATGTAATGTCTATCTTATGTAATTC
Found at i:3294649 original size:42 final size:42
Alignment explanation
Indices: 3294602--3294685 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
3294592 GGTTAGTTGT
3294602 GGTTCATTCATTACTTGCTAGTTAACCTTATATGTGGGCTGC
1 GGTTCATTCATTACTTGCTAGTTAACCTTATATGTGGGCTGC
3294644 GGTTCATTCATTACTTGCTAGTTAACCTTATATGTGGGCTGC
1 GGTTCATTCATTACTTGCTAGTTAACCTTATATGTGGGCTGC
3294686 CTTTTTCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (42 bp):
GGTTCATTCATTACTTGCTAGTTAACCTTATATGTGGGCTGC
Found at i:3301824 original size:2 final size:2
Alignment explanation
Indices: 3301817--3301878 Score: 60
Period size: 2 Copynumber: 33.0 Consensus size: 2
3301807 AATAATTATT
* *
3301817 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3301856 TA -A TT TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
3301879 CCCGGCTCGA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
1 4 0.08
2 44 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3301924 original size:12 final size:12
Alignment explanation
Indices: 3301876--3301941 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
3301866 ATATATATAT
* *
3301876 ATACCCGGCTCG
1 ATACCCGGCCCA
* *
3301888 ATTCCCTGCCCA
1 ATACCCGGCCCA
*
3301900 ATA-CCGACCCA
1 ATACCCGGCCCA
3301911 ATACCCGGCCCA
1 ATACCCGGCCCA
3301923 ATACCCGGCCCA
1 ATACCCGGCCCA
3301935 ATACCCG
1 ATACCCG
3301942 TTTAAATAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
11 9 0.20
12 36 0.80
ACGTcount: A:0.24, C:0.47, G:0.15, T:0.14
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:3301939 original size:24 final size:24
Alignment explanation
Indices: 3301876--3301941 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
3301866 ATATATATAT
* * * *
3301876 ATACCCGGCTCGATTCCCTGCCCA
1 ATACCCGGCCCAATACCCGGCCCA
*
3301900 ATA-CCGACCCAATACCCGGCCCA
1 ATACCCGGCCCAATACCCGGCCCA
3301923 ATACCCGGCCCAATACCCG
1 ATACCCGGCCCAATACCCG
3301942 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.24, C:0.47, G:0.15, T:0.14
Consensus pattern (24 bp):
ATACCCGGCCCAATACCCGGCCCA
Found at i:3303347 original size:23 final size:23
Alignment explanation
Indices: 3303321--3303389 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
3303311 CACCACAGCT
* * *
3303321 CGTATAATTGCACCGAAGTGTCA
1 CGTAGAATTGCACCGGAGTGCCA
*
3303344 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
3303367 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
3303390 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:3304064 original size:19 final size:19
Alignment explanation
Indices: 3304040--3304091 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
3304030 TTTATTAGAA
*
3304040 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCAT
*
3304059 ATGCATCGATGCACTTCAT
1 ATGCATCGATGCACTCCAT
*
3304078 GTGCATCGATGCAC
1 ATGCATCGATGCAC
3304092 CTTCAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCCAT
Found at i:3310221 original size:23 final size:23
Alignment explanation
Indices: 3310195--3310263 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3310185 CACCACAGCT
*
3310195 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * * *
3310218 CGTAGAATTACATCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
3310241 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
3310264 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:3310938 original size:44 final size:44
Alignment explanation
Indices: 3310870--3310972 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
3310860 TGCACTCCTG
* * *
3310870 ATGCATCGATGCACTGAGGGCATTCGATG-TTCATTTTATTAGAA
1 ATGCATCGATGCACTGACGACATTCGATGTTTCATTTTA-AAGAA
* **
3310914 ATGCATCGATGCACTGACGACATTCGATGTTTTATTTTAAATTA
1 ATGCATCGATGCACTGACGACATTCGATGTTTCATTTTAAAGAA
3310958 ATGCATCGATGCACT
1 ATGCATCGATGCACT
3310973 TCATGTGCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 44 0.85
45 8 0.15
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (44 bp):
ATGCATCGATGCACTGACGACATTCGATGTTTCATTTTAAAGAA
Found at i:3311836 original size:32 final size:32
Alignment explanation
Indices: 3311790--3311869 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
3311780 CTGTTGACCG
*
3311790 TTGACCGGCGTTGACCATTGTTGACCAGAACT
1 TTGACCGGCGTTGACCATTATTGACCAGAACT
* *
3311822 TTGATCGGCGTTGACCATTATTGACTAGAACT
1 TTGACCGGCGTTGACCATTATTGACCAGAACT
3311854 TTGACCGGCGTTGACC
1 TTGACCGGCGTTGACC
3311870 GGGAGTTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (32 bp):
TTGACCGGCGTTGACCATTATTGACCAGAACT
Found at i:3314160 original size:24 final size:24
Alignment explanation
Indices: 3314130--3314202 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
3314120 ATACATTACC
*
3314130 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
* * *
3314154 TGGATTCTGTTATGATATCTGATC
1 TGAATTCTGTTATGATTTCTGATA
* * *
3314178 TGAATTCTATTTTGATTTCGGATA
1 TGAATTCTGTTATGATTTCTGATA
3314202 T
1 T
3314203 CTCCGTTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:3314162 original size:48 final size:48
Alignment explanation
Indices: 3314109--3314202 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
3314099 TTCGACTTGA
* * * *
3314109 ATTCTGTTCTGATA-CATTACCTGAATTCTGTTCTGATTTCTGATATGG
1 ATTCTGTTATGATATC-TGACCTGAATTCTATTCTGATTTCGGATATGG
* *
3314157 ATTCTGTTATGATATCTGATCTGAATTCTATTTTGATTTCGGATAT
1 ATTCTGTTATGATATCTGACCTGAATTCTATTCTGATTTCGGATAT
3314203 CTCCGTTTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (48 bp):
ATTCTGTTATGATATCTGACCTGAATTCTATTCTGATTTCGGATATGG
Found at i:3318744 original size:12 final size:12
Alignment explanation
Indices: 3318723--3318785 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
3318713 TCGACTTGAA
3318723 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
3318735 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
*
3318747 TTCTGTTATGAT
1 TTCTGTTCTGAT
* * *
3318759 ATCTGATCTGAA
1 TTCTGTTCTGAT
*
3318771 TTCTGTTTTGAT
1 TTCTGTTCTGAT
3318783 TTC
1 TTC
3318786 GGATATCTCC
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.52
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:3318749 original size:24 final size:24
Alignment explanation
Indices: 3318719--3318785 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
3318709 ATTTTCGACT
*
3318719 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTATGATTTCTGATC
* *
3318743 TGGATTCTGTTATGATATCTGATC
1 TGAATTCTGTTATGATTTCTGATC
*
3318767 TGAATTCTGTTTTGATTTC
1 TGAATTCTGTTATGATTTC
3318786 GGATATCTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATC
Found at i:3320408 original size:26 final size:24
Alignment explanation
Indices: 3320379--3320459 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 24
3320369 AATATATTAT
3320379 TTTAATTACATTTAAATTTATAACA
1 TTTAATT-CATTTAAATTTATAACA
*
3320404 GTTTAAGTT-TTCTTAAATTTATAACA
1 -TTTAA-TTCAT-TTAAATTTATAACA
3320430 ---AATTCATTTAAATTTATAACAA
1 TTTAATTCATTTAAATTTATAAC-A
3320452 TTTTAATT
1 -TTTAATT
3320460 TCTCCAAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
21 15 0.33
22 4 0.09
25 1 0.02
26 23 0.51
27 2 0.04
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTAATTCATTTAAATTTATAACA
Found at i:3320474 original size:47 final size:48
Alignment explanation
Indices: 3320382--3320474 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 48
3320372 ATATTATTTT
* *
3320382 AATTACATTTAAATTTATAACAGTTTAAGTTTTCTTAAATTTATAACA
1 AATTACATTTAAATTTATAACAGTTTAAGTTTTCTCAAATCTATAACA
*
3320430 AATT-CATTTAAATTTATAACAATTTTAA--TTTCTCCAAATCTATAA
1 AATTACATTTAAATTTATAAC-AGTTTAAGTTTTCT-CAAATCTATAA
3320475 TGAATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
46 5 0.12
47 25 0.62
48 10 0.25
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (48 bp):
AATTACATTTAAATTTATAACAGTTTAAGTTTTCTCAAATCTATAACA
Found at i:3326574 original size:16 final size:15
Alignment explanation
Indices: 3326532--3326574 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
3326522 CTCAAAGTTA
3326532 AATATTATTTTAAAT
1 AATATTATTTTAAAT
*
3326547 AATTATTTTTTTACAAT
1 AA-TATTATTTTA-AAT
*
3326564 AATATCATTTT
1 AATATTATTTT
3326575 CATCTCATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 2 0.09
16 16 0.70
17 5 0.22
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (15 bp):
AATATTATTTTAAAT
Found at i:3327888 original size:14 final size:16
Alignment explanation
Indices: 3327855--3327888 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3327845 GAATTAAAAT
3327855 TAAATGAAATTTTGAA
1 TAAATGAAATTTTGAA
3327871 TAAAT-AAATTTT-AA
1 TAAATGAAATTTTGAA
3327885 TAAA
1 TAAA
3327889 ATATTGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 7 0.39
16 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
TAAATGAAATTTTGAA
Found at i:3329539 original size:14 final size:14
Alignment explanation
Indices: 3329516--3329546 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3329506 TGAACAGTAA
*
3329516 AATACGGTATGAAC
1 AATACCGTATGAAC
3329530 AATACCGTATGAAC
1 AATACCGTATGAAC
3329544 AAT
1 AAT
3329547 GATGAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (14 bp):
AATACCGTATGAAC
Found at i:3329627 original size:22 final size:21
Alignment explanation
Indices: 3329602--3329644 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3329592 ATTATCAAAG
*
3329602 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGA-TACCCTGCTACA
*
3329624 GGGAATCGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
3329645 ATATTGCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.19
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:3330290 original size:31 final size:31
Alignment explanation
Indices: 3330236--3330363 Score: 118
Period size: 31 Copynumber: 4.1 Consensus size: 31
3330226 GAACCTCGAC
* * *
3330236 AACTGTCCATAGGTCCCG-AAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAA-AACATAGGTA
* * *
3330267 AACTGTCCATATGTTCCTTAGAACATATGTA
1 AACTGTCCATATGTTCCGTAAAACATAGGTA
* * *
3330298 TATTGTCCATATGTCCCG-AAAGACATAGGTA
1 AACTGTCCATATGTTCCGTAAA-ACATAGGTA
3330329 ATTA-TGTCCATATGTTCCGTAAAACATAGGTA
1 A--ACTGTCCATATGTTCCGTAAAACATAGGTA
3330361 AAC
1 AAC
3330364 CCTTGACTCT
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
30 3 0.04
31 45 0.58
32 25 0.32
33 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAAAACATAGGTA
Found at i:3330314 original size:62 final size:62
Alignment explanation
Indices: 3330239--3330356 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
3330229 CCTCGACAAC
* * *
3330239 TGTCCATAGGTCCCG-AAGAACCTAGGTAA-ACTGTCCATATGTTCCTTAGAACATATGTATAT
1 TGTCCATAGGTCCCGAAAG-ACATAGGTAATA-TGTCCATATGTTCCGTAAAACATATGTATAT
*
3330301 TGTCCATATGTCCCGAAAGACATAGGTAATTATGTCCATATGTTCCGTAAAACATA
1 TGTCCATAGGTCCCGAAAGACATAGGTAA-TATGTCCATATGTTCCGTAAAACATA
3330357 GGTAAACCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
62 23 0.47
63 25 0.51
64 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (62 bp):
TGTCCATAGGTCCCGAAAGACATAGGTAATATGTCCATATGTTCCGTAAAACATATGTATAT
Found at i:3330918 original size:16 final size:16
Alignment explanation
Indices: 3330897--3330927 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3330887 CTCTTATGTC
3330897 TTCTCACATACATATA
1 TTCTCACATACATATA
*
3330913 TTCTCATATACATAT
1 TTCTCACATACATAT
3330928 CAATAACACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TTCTCACATACATATA
Found at i:3332490 original size:3 final size:3
Alignment explanation
Indices: 3332482--3332509 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3332472 TAGCTAGTTG
3332482 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3332510 ATTTGCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3332707 original size:19 final size:19
Alignment explanation
Indices: 3332683--3332724 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
3332673 TATTGTCAGT
3332683 AGCATTTGAGCAAGCTAAG
1 AGCATTTGAGCAAGCTAAG
3332702 AGCATTTGAGCAAGCTAAG
1 AGCATTTGAGCAAGCTAAG
3332721 AGCA
1 AGCA
3332725 AGCGATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (19 bp):
AGCATTTGAGCAAGCTAAG
Found at i:3334759 original size:29 final size:31
Alignment explanation
Indices: 3334683--3334791 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 31
3334673 ATATTTAACC
* *
3334683 AAACTTGAAGGGCTAAAATAGCT-AAAATAG
1 AAACTTAAAGGGCTAAAATAGGTAAAAATAG
* *
3334713 AAA-TTTAAGGACTAAAAT-GGTAAAAATAG
1 AAACTTAAAGGGCTAAAATAGGTAAAAATAG
* * *
3334742 AAACTTAAAGGGCT-AAATAAGTAAAAACAT
1 AAACTTAAAGGGCTAAAATAGGTAAAAATAG
*
3334772 AAA-TTGAAGGGGCTAAAATA
1 AAACTT-AAAGGGCTAAAATA
3334792 TAAATAAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.03
29 29 0.45
30 29 0.45
31 5 0.08
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.21
Consensus pattern (31 bp):
AAACTTAAAGGGCTAAAATAGGTAAAAATAG
Found at i:3336281 original size:3 final size:3
Alignment explanation
Indices: 3336273--3336311 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
3336263 AAATTGTTAT
3336273 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
3336312 TTTATATAGA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3336944 original size:125 final size:126
Alignment explanation
Indices: 3336691--3337028 Score: 462
Period size: 125 Copynumber: 2.7 Consensus size: 126
3336681 TGATAACACT
* * * * * * *
3336691 TGGTTATCTAGGATTGACACGGCTCCTACGTGACGAGGAGATCTGGTCATGTGATGAAACTGCTC
1 TGGTTATCTAAG-TTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACACTGCTC
* * * * * *
3336756 ATCTGTTCATGAGTCATGGCCATCTAAAGGTGATAACAAGGTTCCTCTCTGCTAGGGATGAC
65 ATCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACAAGGTTCCACTATGATAGGGACGAC
* **
3336818 TGGTTATCTAAGTTGACACAACTCCTACATAATGAGGAGATCTATTCAGGTGATGACAC-GCTCA
1 TGGTTATCTAAGTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACACTGCTCA
* *
3336882 TCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACACGGTTCCACTATGATGGGGACGAC
66 TCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACAAGGTTCCACTATGATAGGGACGAC
* * * *
3336943 TGGTTATCTAAATTGACACAGCTCATACATAATAAGGATATCTGGTCAGGTGATGACACTGCTCA
1 TGGTTATCTAAGTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACACTGCTCA
3337008 TCTGTTCATGAGTCTTGGTCA
66 TCTGTTCATGAGTCTTGGTCA
3337029 GGGAATTTTA
Statistics
Matches: 185, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
125 110 0.59
126 64 0.35
127 11 0.06
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (126 bp):
TGGTTATCTAAGTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGGTGATGACACTGCTCA
TCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACAAGGTTCCACTATGATAGGGACGAC
Found at i:3337312 original size:32 final size:32
Alignment explanation
Indices: 3337264--3337386 Score: 174
Period size: 32 Copynumber: 3.8 Consensus size: 32
3337254 TTCACATCAG
* * * *
3337264 GATGTTAAATCCCCAAAGATGCCCCAATATTT
1 GATGTTGAATCTCCAAAGATGCCTCAACATTT
3337296 GATGTTGAATCTCCAAAGATGCCTCAACATTT
1 GATGTTGAATCTCCAAAGATGCCTCAACATTT
* *
3337328 GATGTTGAATCTTCAAAGATGCCTCAGCATTT
1 GATGTTGAATCTCCAAAGATGCCTCAACATTT
*
3337360 GATGTTGAATCTTCAAAGATGTCCTCA
1 GATGTTGAATCTCCAAAGATG-CCTCA
3337387 TTGTTCATTG
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 79 0.94
33 5 0.06
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCTCAACATTT
Found at i:3338443 original size:22 final size:22
Alignment explanation
Indices: 3338391--3338456 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
3338381 TCTTTACATG
* * *
3338391 TGCTTATTGTCCCTTT-TTCTT
1 TGCTTATTTTCTCTTTGCTCTT
*
3338412 TGTTTATTTTCTCTTTGCTCTT
1 TGCTTATTTTCTCTTTGCTCTT
* * *
3338434 TGCTTCTTTTCTTTTTTCTCTT
1 TGCTTATTTTCTCTTTGCTCTT
3338456 T
1 T
3338457 CTTTGCTTCT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 13 0.36
22 23 0.64
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.68
Consensus pattern (22 bp):
TGCTTATTTTCTCTTTGCTCTT
Found at i:3338470 original size:13 final size:13
Alignment explanation
Indices: 3338430--3338470 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3338420 TTCTCTTTGC
3338430 TCTTTGCTTCTTT
1 TCTTTGCTTCTTT
*
3338443 TCTTT-TTTCTCTT
1 TCTTTGCTTCT-TT
3338456 TCTTTGCTTCTTT
1 TCTTTGCTTCTTT
3338469 TC
1 TC
3338471 CCTTCGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 16 0.67
14 4 0.17
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (13 bp):
TCTTTGCTTCTTT
Found at i:3340224 original size:64 final size:65
Alignment explanation
Indices: 3340080--3340235 Score: 190
Period size: 64 Copynumber: 2.4 Consensus size: 65
3340070 CCAAGTGTGA
* * ***
3340080 ATCGATGCATAAAATGCATTCGATG-TTTGAAAAAATAGCCTGGTGCATCGATGCATGGCTTGTG
1 ATCGATGCATAAAATGCATTCGATGTTTTCAAAAAATA-CCTAGTGCATCGATGCATGGAGAGTG
3340144 C
65 C
* * * *
3340145 GTCGATACATCAAATGCATTCGATGTTTTCATAAAAT-CCTAGTGCATCGATGCATGGAGAGTGC
1 ATCGATGCATAAAATGCATTCGATGTTTTCAAAAAATACCTAGTGCATCGATGCATGGAGAGTGC
* *
3340209 ATCGGTGCATGAAATGCATTCGATGTT
1 ATCGATGCATAAAATGCATTCGATGTT
3340236 CAATTTATTC
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 46 0.60
65 22 0.29
66 9 0.12
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (65 bp):
ATCGATGCATAAAATGCATTCGATGTTTTCAAAAAATACCTAGTGCATCGATGCATGGAGAGTGC
Found at i:3340665 original size:18 final size:18
Alignment explanation
Indices: 3340627--3340666 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3340617 TTTACTCCCC
*
3340627 CTTACTATAGCACATCTT
1 CTTACTATAGCACATCAT
3340645 CTTACTATAGCACCAT-AT
1 CTTACTATAGCA-CATCAT
3340663 CTTA
1 CTTA
3340667 AACCTTCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.38
Consensus pattern (18 bp):
CTTACTATAGCACATCAT
Found at i:3342208 original size:21 final size:21
Alignment explanation
Indices: 3342182--3342221 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3342172 TCAATAGGCC
3342182 ATTAGGAGATTGAGGAACGAG
1 ATTAGGAGATTGAGGAACGAG
*
3342203 ATTAGGAGGTTGAGGAACG
1 ATTAGGAGATTGAGGAACG
3342222 GGAGGACGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.40, T:0.20
Consensus pattern (21 bp):
ATTAGGAGATTGAGGAACGAG
Found at i:3346239 original size:21 final size:21
Alignment explanation
Indices: 3346213--3346252 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3346203 AAGACTATTC
3346213 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTGAAACA
**
3346234 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
3346253 ATAAGTCTTA
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:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAACA
Found at i:3348346 original size:64 final size:65
Alignment explanation
Indices: 3348171--3348357 Score: 191
Period size: 64 Copynumber: 2.9 Consensus size: 65
3348161 TGACCGTTGG
* * ** * * * *
3348171 AATACTTAGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAATGCATTCAATG-TTTGAAAA
1 AATACCTAGTGCATCGATGCATGACGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAA
* ** * * *
3348235 AATAGCCTGGTGCATCGATGCATGACTTGTGCATCGATTCATCAAATGCATTCGATGTTTTCATA
1 AATA-CCTAGTGCATCGATGCATGACGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAA
3348300 A
65 A
* *
3348301 AAT-CCTAGTGCATCGATGCATGGA-GAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AATACCTAGTGCATCGATGCAT-GACGAGTGCATCGATGCATAAAATGCATTCGATGTT
3348358 CAATTTATTC
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
64 49 0.48
65 44 0.43
66 9 0.09
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (65 bp):
AATACCTAGTGCATCGATGCATGACGAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAA
Found at i:3349857 original size:63 final size:63
Alignment explanation
Indices: 3349756--3349981 Score: 328
Period size: 63 Copynumber: 3.6 Consensus size: 63
3349746 ATTTATGATG
* * * *
3349756 ATCATGCAGAATGCGAAGATGCAAATACAGATGTAAAATTGATGATCCTCTTAAATACAATGC
1 ATCATGCAGAATGCGAAGATGCAAATACAGATGCAAAATTGATGATCGTCTAAAATGCAATGC
* * *
3349819 ATCATGCAAAATGCGAAGCTGCAAATGCAGATGCAAAATTGATGATCGTCTAAAATGCAATGC
1 ATCATGCAGAATGCGAAGATGCAAATACAGATGCAAAATTGATGATCGTCTAAAATGCAATGC
** * *
3349882 ATCATGCAGAATGTAAAGATGCAAATATAGATGCTAAATTGATGATCGTCTAAAATGCAATGC
1 ATCATGCAGAATGCGAAGATGCAAATACAGATGCAAAATTGATGATCGTCTAAAATGCAATGC
*
3349945 ATCATGCAGAATGCGACA-ATGCAAATGCAGATGCAAA
1 ATCATGCAGAATGCGA-AGATGCAAATACAGATGCAAA
3349982 TATGCAAATG
Statistics
Matches: 143, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
63 142 0.99
64 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.23
Consensus pattern (63 bp):
ATCATGCAGAATGCGAAGATGCAAATACAGATGCAAAATTGATGATCGTCTAAAATGCAATGC
Found at i:3349889 original size:36 final size:36
Alignment explanation
Indices: 3349849--3349952 Score: 84
Period size: 36 Copynumber: 3.1 Consensus size: 36
3349839 GCAAATGCAG
3349849 ATGCAAAATTGATGATCGTCTAAAATGCAATGCATC
1 ATGCAAAATTGATGATCGTCTAAAATGCAATGCATC
* * * *
3349885 ATGCAGAATGTAAAGAT-G-C--AAAT---AT--A-G
1 ATGCAAAAT-TGATGATCGTCTAAAATGCAATGCATC
*
3349912 ATGCTAAATTGATGATCGTCTAAAATGCAATGCATC
1 ATGCAAAATTGATGATCGTCTAAAATGCAATGCATC
3349948 ATGCA
1 ATGCA
3349953 GAATGCGACA
Statistics
Matches: 47, Mismatches: 10, Indels: 22
0.59 0.13 0.28
Matches are distributed among these distances:
26 5 0.11
27 8 0.17
28 2 0.04
30 6 0.13
33 6 0.13
35 2 0.04
36 13 0.28
37 5 0.11
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (36 bp):
ATGCAAAATTGATGATCGTCTAAAATGCAATGCATC
Found at i:3349986 original size:20 final size:20
Alignment explanation
Indices: 3349963--3350001 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3349953 GAATGCGACA
3349963 ATGCAAATGCAGATGCAAAT
1 ATGCAAATGCAGATGCAAAT
*
3349983 ATGCAAATGCAGTTGCAAA
1 ATGCAAATGCAGATGCAAA
3350002 AATGTAGATC
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:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (20 bp):
ATGCAAATGCAGATGCAAAT
Found at i:3351854 original size:32 final size:32
Alignment explanation
Indices: 3351818--3351879 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
3351808 ATGAAAAATG
*
3351818 ACACAATCAAAAGAAAAGAAA-TAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATTAA-TTAGTGT
3351850 ACACAAACAAAAGAAAAGAAATTAATTAGT
1 ACACAAACAAAAGAAAAGAAATTAATTAGT
3351880 ACAGATAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.18
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATTAATTAGTGT
Found at i:3353719 original size:29 final size:29
Alignment explanation
Indices: 3353682--3353787 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 29
3353672 ACCAAACTTG
*
3353682 AAGGGCTAAAATAGCT-AAAATAGAAATTT
1 AAGGGCTAAAATAG-TAAAAATAGAAATTA
* * *
3353711 AAGGACTAAAATGGTAAAAATAGACACTTA
1 AAGGGCTAAAATAGTAAAAATAGA-AATTA
*
3353741 AAGGTCT-AAATAAGTAAAAATAGAAATTGA
1 AAGGGCTAAAAT-AGTAAAAATAGAAATT-A
*
3353771 AGGGGCTAAAATA-TAAA
1 AAGGGCTAAAATAGTAAA
3353788 TAAAATAAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
28 1 0.02
29 31 0.49
30 27 0.43
31 4 0.06
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.22
Consensus pattern (29 bp):
AAGGGCTAAAATAGTAAAAATAGAAATTA
Found at i:3355202 original size:3 final size:3
Alignment explanation
Indices: 3355194--3355242 Score: 80
Period size: 3 Copynumber: 15.7 Consensus size: 3
3355184 CCAAAATTCT
3355194 TAA TAA TAA TAA TAA TAA TTAA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA
3355241 TA
1 TA
3355243 TTTATATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3355215 original size:19 final size:19
Alignment explanation
Indices: 3355193--3355242 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
3355183 ACCAAAATTC
3355193 TTAATAATAATAATAATAA
1 TTAATAATAATAATAATAA
3355212 TTAATAATAATAATAATAA
1 TTAATAATAATAATAATAA
3355231 -TAATATATAATA
1 TTAATA-ATAATA
3355243 TTTATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.17
19 25 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAATAATAATAATAATAA
Found at i:3355228 original size:22 final size:22
Alignment explanation
Indices: 3355194--3355242 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
3355184 CCAAAATTCT
3355194 TAATAATAATAATAATAAT-TAA
1 TAATAATAATAATAATAATAT-A
3355216 TAATAATAATAATAATAATATA
1 TAATAATAATAATAATAATATA
3355238 TAATA
1 TAATA
3355243 TTTATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATAATAATAATAATAATATA
Found at i:3360648 original size:16 final size:15
Alignment explanation
Indices: 3360606--3360648 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
3360596 CTCAAAGTTA
3360606 AATATTATTTTAAAT
1 AATATTATTTTAAAT
*
3360621 AATTATTTTTTTACAAT
1 AA-TATTATTTTA-AAT
*
3360638 AATATCATTTT
1 AATATTATTTT
3360649 CATCTCATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 2 0.09
16 16 0.70
17 5 0.22
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (15 bp):
AATATTATTTTAAAT
Found at i:3361949 original size:15 final size:15
Alignment explanation
Indices: 3361915--3361947 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3361905 GAATTAAAAT
3361915 TAAATGAAATTTGAA
1 TAAATGAAATTTGAA
*
3361930 TAAAT-AAATTTTAA
1 TAAATGAAATTTGAA
3361944 TAAA
1 TAAA
3361948 ATTTGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (15 bp):
TAAATGAAATTTGAA
Found at i:3363583 original size:14 final size:14
Alignment explanation
Indices: 3363560--3363590 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3363550 ATGAACAGTA
*
3363560 AATACGGTATGAAC
1 AATACCGTATGAAC
3363574 AATACCGTATGAAC
1 AATACCGTATGAAC
3363588 AAT
1 AAT
3363591 GATGAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (14 bp):
AATACCGTATGAAC
Found at i:3364294 original size:30 final size:30
Alignment explanation
Indices: 3364222--3364305 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
3364212 CCCGAAGGAC
* **
3364222 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGACAA
*
3364252 CTATCCAGAGGTCATAAAGAACCTCGACAA
1 CTATCCAGAGGTCACAAAGAACCTCGACAA
* * * *
3364282 CTGTCCATAGGTCCCGAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
3364306 AGGTAAACTG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGACAA
Found at i:3364318 original size:31 final size:31
Alignment explanation
Indices: 3364280--3364407 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
3364270 GAACCTCGAC
* *
3364280 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* ** *
3364311 AACTGTCCATATGTTCCTTAGAACATATGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
*
3364342 TACTGTCCATATGTCCCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
* * *
3364373 ATTCTGTCCATATGTTCC-ATAAAACATAGGTA
1 A-ACTGTCCATATGTCCCGA-AGAACATAGGTA
3364405 AAC
1 AAC
3364408 CCTCGATTCT
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
30 1 0.01
31 51 0.65
32 25 0.32
33 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:3364358 original size:62 final size:63
Alignment explanation
Indices: 3364281--3364400 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
3364271 AACCTCGACA
* * *
3364281 ACTGTCCATAGGTCCCG-AAGAACCTAGGTAA-ACTGTCCATATGTTCCTTAGAACATATGTAT
1 ACTGTCCATAGGTCCCGAAAG-ACATAGGTAATACTGTCCATATGTTCCATAAAACATATGTAT
* *
3364343 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCATAAAACATA
1 ACTGTCCATAGGTCCCGAAAGACATAGGTAATACTGTCCATATGTTCCATAAAACATA
3364401 GGTAAACCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
62 25 0.49
63 26 0.51
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (63 bp):
ACTGTCCATAGGTCCCGAAAGACATAGGTAATACTGTCCATATGTTCCATAAAACATATGTAT
Found at i:3364959 original size:16 final size:16
Alignment explanation
Indices: 3364938--3364968 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3364928 CTCTTATGTC
3364938 TTCTCATATACATATA
1 TTCTCATATACATATA
3364954 TTCTCATATACATAT
1 TTCTCATATACATAT
3364969 CAATAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCTCATATACATATA
Found at i:3366125 original size:19 final size:19
Alignment explanation
Indices: 3366093--3366144 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
3366083 ATAATTATCT
*
3366093 GGAATGCTCCACACACTCTA
1 GGAA-GCTCTACACACTCTA
3366113 GGAAGCTCTACACACTCTA
1 GGAAGCTCTACACACTCTA
3366132 GGAAGCTCTACAC
1 GGAAGCTCTACAC
3366145 TCTTCCACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 27 0.87
20 4 0.13
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (19 bp):
GGAAGCTCTACACACTCTA
Found at i:3366532 original size:3 final size:3
Alignment explanation
Indices: 3366524--3366554 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3366514 TAGCTAGTTG
3366524 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3366555 ATTTGCTTTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3368784 original size:29 final size:31
Alignment explanation
Indices: 3368708--3368793 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 31
3368698 ATATTTAACC
* *
3368708 AAACTTGAAGGGCTAAAATAGCT-AAAATAG
1 AAACTTAAAGGGCTAAAATAGGTAAAAATAG
* *
3368738 AAA-TTTAAGGACTAAAAT-GGTAAAAATAG
1 AAACTTAAAGGGCTAAAATAGGTAAAAATAG
*
3368767 AAACTTAAAGGGCT-AAATAAGTAAAAA
1 AAACTTAAAGGGCTAAAATAGGTAAAAA
3368794 CGTAAATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.04
29 27 0.57
30 18 0.38
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.21
Consensus pattern (31 bp):
AAACTTAAAGGGCTAAAATAGGTAAAAATAG
Found at i:3370309 original size:3 final size:3
Alignment explanation
Indices: 3370303--3370332 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3370293 AATAATAATA
3370303 ATT ATT ATT ATT ATT ATT ATT ATT AATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT
3370333 AAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3370969 original size:126 final size:126
Alignment explanation
Indices: 3370720--3371058 Score: 489
Period size: 126 Copynumber: 2.7 Consensus size: 126
3370710 TGATAACACT
*** * * * *
3370720 TGGTTATCTAGAATTGACACGGGTCCTACGTGACGAGGAGATCTAGTCATGTGATGACACTGCTC
1 TGGTTATCTA-AATTGACACAACTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACTGCTC
* * * *
3370785 ATCTGTTCATGAGTCTTGGCCATCTAAAGGTGATAACACGATTCCTCTCTGCTAGGGACGAC
65 ATCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACACGATTCCACTATGATAGGGACGAC
* * *
3370847 TGGTTATCTAAGTTGACATAACTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACTGCTTA
1 TGGTTATCTAAATTGACACAACTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACTGCTCA
* * *
3370912 TCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACACGGTTCCACTATGATGGGGACGGC
66 TCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACACGATTCCACTATGATAGGGACGAC
* * *
3370973 TGGTTATCTAAATTGACACAGCTCCTACATAATGAGGATATCTGGTCAGGTGATGACACTGCTCA
1 TGGTTATCTAAATTGACACAACTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACTGCTCA
3371038 TCTGTTCATGAGTCTTGGTCA
66 TCTGTTCATGAGTCTTGGTCA
3371059 GGGAATTTTA
Statistics
Matches: 189, Mismatches: 23, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
126 179 0.95
127 10 0.05
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (126 bp):
TGGTTATCTAAATTGACACAACTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACTGCTCA
TCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACACGATTCCACTATGATAGGGACGAC
Found at i:3372094 original size:32 final size:32
Alignment explanation
Indices: 3372058--3372119 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
3372048 ATGAAAAATG
*
3372058 ACACAATCAAAAGAAAAGAAA-TAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATTAA-TTAGTGT
3372090 ACACAAACAAAAGAAAAGAAATTAATTAGT
1 ACACAAACAAAAGAAAAGAAATTAATTAGT
3372120 ACAGGTAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.18
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATTAATTAGTGT
Found at i:3372551 original size:20 final size:20
Alignment explanation
Indices: 3372526--3372576 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3372516 CCATTACAGG
3372526 TTCGTGAGGATCAAGTTCAA
1 TTCGTGAGGATCAAGTTCAA
*
3372546 TTCGTGAGGATCGAGTTCAA
1 TTCGTGAGGATCAAGTTCAA
*
3372566 TTCGAGAGGAT
1 TTCGTGAGGAT
3372577 GTAACACCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29
Consensus pattern (20 bp):
TTCGTGAGGATCAAGTTCAA
Found at i:3373023 original size:18 final size:18
Alignment explanation
Indices: 3373000--3373084 Score: 80
Period size: 18 Copynumber: 4.7 Consensus size: 18
3372990 TACATATACC
**
3373000 ATCATTATCATGATCTCT
1 ATCATTATCATGATCAAT
* **
3373018 ATCATTCTCAACATCAAT
1 ATCATTATCATGATCAAT
**
3373036 ATCATTATCATGATCTCT
1 ATCATTATCATGATCAAT
* **
3373054 ATCATGATCAACATCAAT
1 ATCATTATCATGATCAAT
3373072 ATCATTATCATGA
1 ATCATTATCATGA
3373085 ACCCATTTAA
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (18 bp):
ATCATTATCATGATCAAT
Found at i:3373047 original size:36 final size:36
Alignment explanation
Indices: 3373000--3373084 Score: 152
Period size: 36 Copynumber: 2.4 Consensus size: 36
3372990 TACATATACC
**
3373000 ATCATTATCATGATCTCTATCATTCTCAACATCAAT
1 ATCATTATCATGATCTCTATCATGATCAACATCAAT
3373036 ATCATTATCATGATCTCTATCATGATCAACATCAAT
1 ATCATTATCATGATCTCTATCATGATCAACATCAAT
3373072 ATCATTATCATGA
1 ATCATTATCATGA
3373085 ACCCATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (36 bp):
ATCATTATCATGATCTCTATCATGATCAACATCAAT
Found at i:3373335 original size:12 final size:12
Alignment explanation
Indices: 3373320--3373372 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
3373310 TTTATAATAT
3373320 CATGTATTAACC
1 CATGTATTAACC
*
3373332 CATGTATTGACC
1 CATGTATTAACC
*
3373344 CATGTATT-AGC
1 CATGTATTAACC
* *
3373355 TATGTATTATCC
1 CATGTATTAACC
3373367 CATGTA
1 CATGTA
3373373 CAGTACTGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 9 0.26
12 25 0.74
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (12 bp):
CATGTATTAACC
Found at i:3373494 original size:21 final size:20
Alignment explanation
Indices: 3373468--3373574 Score: 72
Period size: 21 Copynumber: 5.5 Consensus size: 20
3373458 GGACCTATCA
3373468 TCCCGAAGGATGTCATTTGTG
1 TCCCGAAGGATGTCA-TTGTG
3373489 TCCCGAAGGACCTGTCA-----
1 TCCCGAAGGA--TGTCATTGTG
3373506 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCAT-TGTG
3373527 TCCCGAAGGACCTGTCA-----
1 TCCCGAAGGA--TGTCATTGTG
*
3373544 TCCCGAAGGATGTAATATGTG
1 TCCCGAAGGATGTCAT-TGTG
3373565 TCCCGAAGGA
1 TCCCGAAGGA
3373575 CCTGTCATCC
Statistics
Matches: 69, Mismatches: 1, Indels: 32
0.68 0.01 0.31
Matches are distributed among these distances:
15 9 0.13
17 20 0.29
21 30 0.43
23 10 0.14
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.24
Consensus pattern (20 bp):
TCCCGAAGGATGTCATTGTG
Found at i:3373498 original size:38 final size:38
Alignment explanation
Indices: 3373446--3373620 Score: 296
Period size: 38 Copynumber: 4.6 Consensus size: 38
3373436 GCTCGTATAA
* *
3373446 CTGTGTCCCGAAGGACCTATCATCCCGAAGGATGTCAT
1 CTGTGTCCCGAAGGACCTGTCATCCCGAAGGATGTAAT
* *
3373484 TTGTGTCCCGAAGGACCTGTCATCCCGAAGGATGTCAT
1 CTGTGTCCCGAAGGACCTGTCATCCCGAAGGATGTAAT
3373522 CTGTGTCCCGAAGGACCTGTCATCCCGAAGGATGTAAT
1 CTGTGTCCCGAAGGACCTGTCATCCCGAAGGATGTAAT
* *
3373560 ATGTGTCCCGAAGGACCTGTCATCCCAAAGGATGTAAT
1 CTGTGTCCCGAAGGACCTGTCATCCCGAAGGATGTAAT
3373598 CTGTGTCCCGAAGGACCTGTCAT
1 CTGTGTCCCGAAGGACCTGTCAT
3373621 ATATCCCGAA
Statistics
Matches: 130, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 130 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (38 bp):
CTGTGTCCCGAAGGACCTGTCATCCCGAAGGATGTAAT
Found at i:3373511 original size:17 final size:17
Alignment explanation
Indices: 3373489--3373553 Score: 69
Period size: 17 Copynumber: 3.6 Consensus size: 17
3373479 GTCATTTGTG
3373489 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTGTCA
*
3373506 TCCCGAAGGATGTCATCTGT-G
1 TCCCGAAGGA---C--CTGTCA
3373527 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTGTCA
3373544 TCCCGAAGGA
1 TCCCGAAGGA
3373554 TGTAATATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
16 4 0.10
17 20 0.50
18 1 0.03
20 1 0.03
21 10 0.25
22 4 0.10
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTGTCA
Found at i:3373813 original size:33 final size:33
Alignment explanation
Indices: 3373771--3373868 Score: 187
Period size: 33 Copynumber: 3.0 Consensus size: 33
3373761 ATCATATAGC
*
3373771 TTGTATAACATTCTTGTATGATCTCATAGATCA
1 TTGTGTAACATTCTTGTATGATCTCATAGATCA
3373804 TTGTGTAACATTCTTGTATGATCTCATAGATCA
1 TTGTGTAACATTCTTGTATGATCTCATAGATCA
3373837 TTGTGTAACATTCTTGTATGATCTCATAGATC
1 TTGTGTAACATTCTTGTATGATCTCATAGATC
3373869 CCTTTTCATA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TTGTGTAACATTCTTGTATGATCTCATAGATCA
Found at i:3374788 original size:27 final size:27
Alignment explanation
Indices: 3374758--3374811 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3374748 CTTAAATTTT
* *
3374758 AAATACCATAAATTCCAGTAATTCCAG
1 AAATACCATAAATTCAAGAAATTCCAG
*
3374785 AAATTCCATAAATTCAAGAAATTCCAG
1 AAATACCATAAATTCAAGAAATTCCAG
3374812 TACTGGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.26
Consensus pattern (27 bp):
AAATACCATAAATTCAAGAAATTCCAG
Found at i:3374790 original size:18 final size:18
Alignment explanation
Indices: 3374767--3374813 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
3374757 TAAATACCAT
*
3374767 AAATTCCAGTAATTCCAG
1 AAATTCCAGTAATTCAAG
3374785 AAATTCCA-TAAATTCAAG
1 AAATTCCAGT-AATTCAAG
3374803 AAATTCCAGTA
1 AAATTCCAGTA
3374814 CTGGAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.28
Consensus pattern (18 bp):
AAATTCCAGTAATTCAAG
Found at i:3375050 original size:31 final size:30
Alignment explanation
Indices: 3375013--3375084 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
3375003 TACAATCAAT
* * *
3375013 CCCAACTTTTTCCAAAATTACGAATTGGTC
1 CCCAACTTTTTCAAAAATTACAAAATGGTC
3375043 CCTCAAC-TTTTCAAAAATTACAAAATGGTC
1 CC-CAACTTTTTCAAAAATTACAAAATGGTC
*
3375073 CCCAAATTTTTC
1 CCCAACTTTTTC
3375085 TAAAGCTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.08
30 29 0.81
31 4 0.11
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (30 bp):
CCCAACTTTTTCAAAAATTACAAAATGGTC
Found at i:3376122 original size:17 final size:17
Alignment explanation
Indices: 3376100--3376150 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
3376090 TTGGTCACTA
3376100 AATAAATCTATTTATGG
1 AATAAATCTATTTATGG
*
3376117 AATAAAAT-TATTTTTGG
1 AAT-AAATCTATTTATGG
* *
3376134 AAAAAATACCATTTATG
1 AATAAAT-CTATTTATG
3376151 TCTTTAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 4 0.15
17 13 0.48
18 10 0.37
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (17 bp):
AATAAATCTATTTATGG
Found at i:3377518 original size:20 final size:21
Alignment explanation
Indices: 3377481--3377520 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3377471 ACCATAACAA
3377481 ATAAATATATACACACATAAT
1 ATAAATATATACACACATAAT
* *
3377502 ATAAA-ATATTCATACATAA
1 ATAAATATATACACACATAA
3377521 ATGACTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAATATATACACACATAAT
Found at i:3381230 original size:24 final size:24
Alignment explanation
Indices: 3381193--3381257 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
3381183 GCTTTCTGGT
*
3381193 CTGAATTCTATTTTGATACTTGAC
1 CTGAATTCTGTTTTGATACTTGAC
* *
3381217 CTGGATTCTGTTTTGATATTTGAC
1 CTGAATTCTGTTTTGATACTTGAC
*
3381241 CTGAATTATGTTTTGAT
1 CTGAATTCTGTTTTGAT
3381258 TTCTGATATC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (24 bp):
CTGAATTCTGTTTTGATACTTGAC
Found at i:3383536 original size:17 final size:17
Alignment explanation
Indices: 3383514--3383553 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3383504 ACATTTGATT
*
3383514 GTTGACCATTGACCTGC
1 GTTGACCATTGACCGGC
**
3383531 GTTGACTGTTGACCGGC
1 GTTGACCATTGACCGGC
3383548 GTTGAC
1 GTTGAC
3383554 TACTGTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.25, G:0.30, T:0.30
Consensus pattern (17 bp):
GTTGACCATTGACCGGC
Found at i:3383554 original size:17 final size:17
Alignment explanation
Indices: 3383522--3383554 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3383512 TTGTTGACCA
*
3383522 TTGACCTGCGTTGACTG
1 TTGACCGGCGTTGACTG
3383539 TTGACCGGCGTTGACT
1 TTGACCGGCGTTGACT
3383555 ACTGTTGACC
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:0.12, C:0.24, G:0.30, T:0.33
Consensus pattern (17 bp):
TTGACCGGCGTTGACTG
Found at i:3385856 original size:24 final size:24
Alignment explanation
Indices: 3385829--3385899 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
3385819 ATCTTATTTA
* *
3385829 TATTCTGATTTTTGATCTGAATTC
1 TATTCTGATATTTGACCTGAATTC
* ** *
3385853 TATTTTGATACCTGACCTGGATTC
1 TATTCTGATATTTGACCTGAATTC
*
3385877 TGTTCTGATATTTGACCTGAATT
1 TATTCTGATATTTGACCTGAATT
3385900 ATGTTTTGAT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.48
Consensus pattern (24 bp):
TATTCTGATATTTGACCTGAATTC
Found at i:3385904 original size:24 final size:24
Alignment explanation
Indices: 3385826--3385915 Score: 72
Period size: 24 Copynumber: 3.8 Consensus size: 24
3385816 TTTATCTTAT
* *
3385826 TTATATTCTGATTTTTGATCTGAA
1 TTATATTCTGATATTTGACCTGAA
* * ** *
3385850 TTCTATTTTGATACCTGACCTGGA
1 TTATATTCTGATATTTGACCTGAA
* *
3385874 TTCTGTTCTGATATTTGACCTGAA
1 TTATATTCTGATATTTGACCTGAA
* * *
3385898 TTATGTTTTGATTTTTGA
1 TTATATTCTGATATTTGA
3385916 TATCTCCGTT
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (24 bp):
TTATATTCTGATATTTGACCTGAA
Found at i:3387865 original size:3 final size:3
Alignment explanation
Indices: 3387857--3387905 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
3387847 CTAAAATTCT
* *
3387857 TAA TAA TAA TAA TAA TTAA TAT TAT TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
3387904 TA
1 TA
3387906 TTTATATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:3387885 original size:19 final size:19
Alignment explanation
Indices: 3387859--3387905 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 19
3387849 AAAATTCTTA
3387859 ATAATAATAATAATTAATATT
1 ATAATAATAATAA-TAATA-T
3387880 ATTAATAATAATAATAATAT
1 A-TAATAATAATAATAATAT
3387900 ATAATA
1 ATAATA
3387906 TTTATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.20
20 2 0.08
21 6 0.24
22 12 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATAATAATAATAATAT
Found at i:3387907 original size:25 final size:25
Alignment explanation
Indices: 3387856--3387907 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
3387846 ACTAAAATTC
*
3387856 TTAATAATAATAATAATTAATATTA
1 TTAATAATAATAATAATTAATAATA
3387881 TTAATAATAATAATAA-TATATAATA
1 TTAATAATAATAATAATTA-ATAATA
3387906 TT
1 TT
3387908 TATATATACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTAATAATAATAATAATTAATAATA
Found at i:3390359 original size:17 final size:17
Alignment explanation
Indices: 3390337--3390372 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3390327 TTGCCTAGGG
3390337 CCCTTAAAATGTCAGGA
1 CCCTTAAAATGTCAGGA
3390354 CCCTTAAAATGTCAGGA
1 CCCTTAAAATGTCAGGA
3390371 CC
1 CC
3390373 GGCACTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (17 bp):
CCCTTAAAATGTCAGGA
Found at i:3394726 original size:16 final size:15
Alignment explanation
Indices: 3394684--3394726 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
3394674 CTCAAAGTTA
3394684 AATATTATTTTACAT
1 AATATTATTTTACAT
*
3394699 AATTATTTTTTTACAAT
1 AA-TATTATTTTAC-AT
*
3394716 AATATCATTTT
1 AATATTATTTT
3394727 CACCTCATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 2 0.09
16 17 0.74
17 4 0.17
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (15 bp):
AATATTATTTTACAT
Found at i:3395598 original size:27 final size:25
Alignment explanation
Indices: 3395568--3395620 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
3395558 TTTTTATTAT
*
3395568 TAAATTAAAATTAAATAAGATTTTGAA
1 TAAA-TAAAATTAAATAA-ATATTGAA
* *
3395595 TAAATAAATTTTAATAAATATTGAA
1 TAAATAAAATTAAATAAATATTGAA
3395620 T
1 T
3395621 TATAATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.35
26 11 0.48
27 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
TAAATAAAATTAAATAAATATTGAA
Found at i:3395612 original size:14 final size:16
Alignment explanation
Indices: 3395579--3395614 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
3395569 AAATTAAAAT
3395579 TAAATAAGATTTTGAA
1 TAAATAAGATTTTGAA
3395595 TAAATAA-ATTTT-AA
1 TAAATAAGATTTTGAA
3395609 TAAATA
1 TAAATA
3395615 TTGAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 5 0.25
16 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
TAAATAAGATTTTGAA
Found at i:3397596 original size:23 final size:23
Alignment explanation
Indices: 3397570--3397614 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3397560 CACCACAGCT
*
3397570 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
3397593 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
3397615 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:3397852 original size:149 final size:149
Alignment explanation
Indices: 3397582--3398045 Score: 885
Period size: 149 Copynumber: 3.1 Consensus size: 149
3397572 TATAATTGCA
*
3397582 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
3397646 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
3397711 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
3397731 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
* *
3397796 TCCTTGAGAATCATATACATATGCTAGGGATCATATATGTTTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
3397861 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
3397880 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
3397945 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
3398010 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
3398029 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
3398046 CCCTCGACTC
Statistics
Matches: 309, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
148 1 0.00
149 308 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:3399572 original size:21 final size:21
Alignment explanation
Indices: 3399548--3399592 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3399538 TGTTGTTCGT
* *
3399548 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3399569 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3399590 TTG
1 TTG
3399593 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3400504 original size:19 final size:19
Alignment explanation
Indices: 3400472--3400523 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
3400462 TTAATTATCT
*
3400472 GGAATGCTCCACACACTCTA
1 GGAA-GCTCTACACACTCTA
3400492 GGAAGCTCTACACACTCTA
1 GGAAGCTCTACACACTCTA
3400511 GGAAGCTCTACAC
1 GGAAGCTCTACAC
3400524 TTTTCCACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 27 0.87
20 4 0.13
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (19 bp):
GGAAGCTCTACACACTCTA
Found at i:3400910 original size:3 final size:3
Alignment explanation
Indices: 3400902--3400941 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3400892 TAGCTAGTTG
3400902 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3400942 ATTTGCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3401139 original size:19 final size:19
Alignment explanation
Indices: 3401115--3401156 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
3401105 TATTGTCAGT
3401115 AGCATTTGAGCAAGCTAAG
1 AGCATTTGAGCAAGCTAAG
3401134 AGCATTTGAGCAAGCTAAG
1 AGCATTTGAGCAAGCTAAG
3401153 AGCA
1 AGCA
3401157 AGCGATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (19 bp):
AGCATTTGAGCAAGCTAAG
Found at i:3403010 original size:20 final size:19
Alignment explanation
Indices: 3402981--3403021 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3402971 ACACATAACA
3402981 AATAAAAATATACACACAT
1 AATAAAAATATACACACAT
* *
3403000 AATATAAAATATTCATACAT
1 AATA-AAAATATACACACAT
3403020 AA
1 AA
3403022 ATGACTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAAAAATATACACACAT
Found at i:3403191 original size:29 final size:30
Alignment explanation
Indices: 3403119--3403223 Score: 117
Period size: 29 Copynumber: 3.5 Consensus size: 30
3403109 TTAACCAAAC
* *
3403119 TTGAAGGGCTAAAATAGCT-AAAATATAAA
1 TTGAAGGGCTAAAATAGGTAAAAATAGAAA
* *
3403148 TTTAAGGACTAAAAT-GGTAAAAATAGAAA
1 TTGAAGGGCTAAAATAGGTAAAAATAGAAA
* *
3403177 CTTGAAGGGCT-AAATAAGTAAAAACAGAAA
1 -TTGAAGGGCTAAAATAGGTAAAAATAGAAA
3403207 TTGAAGGGGCTAAAATA
1 TTGAA-GGGCTAAAATA
3403224 TAAATAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.03
29 31 0.49
30 25 0.40
31 5 0.08
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (30 bp):
TTGAAGGGCTAAAATAGGTAAAAATAGAAA
Found at i:3404741 original size:16 final size:16
Alignment explanation
Indices: 3404699--3404741 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
3404689 TTGTAACCAA
*
3404699 AATTGTTATTAATAAT
1 AATTATTATTAATAAT
* *
3404715 AATAATAATTAATAAT
1 AATTATTATTAATAAT
3404731 AATTATTATTA
1 AATTATTATTA
3404742 TTATTATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
AATTATTATTAATAAT
Found at i:3405390 original size:126 final size:126
Alignment explanation
Indices: 3405136--3405474 Score: 480
Period size: 126 Copynumber: 2.7 Consensus size: 126
3405126 TGATAACACT
*** * * *
3405136 TGGTTATCTAGAATTGACACGGGTCCTACGTGATGAGGAGATCTAGTCATGTGATGACACTGCTC
1 TGGTTATCTA-AATTGACACAACTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACTGCTC
* * * * *
3405201 ATCTATTCATGAGTCTTGGCCATCTAAAGGTGATAACACGATTCCTCTCTGCTAGGGACGAC
65 ATCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACACGATTCCACTATGATAGGGACGAC
* * *
3405263 TGGTTATCTAAGTTGACATAACTCCTATATAATGAGGAGATCTAGTCAGGTGATGACACTGCTCA
1 TGGTTATCTAAATTGACACAACTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACTGCTCA
* * *
3405328 TCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACACGGTTCCACTATGATGGGGATGAC
66 TCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACACGATTCCACTATGATAGGGACGAC
* * *
3405389 TGGTTATCTAAATTGACACAACTCCTACATAATGAGGATATCTGGTCAGGTGATGAAACTGCTCA
1 TGGTTATCTAAATTGACACAACTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACTGCTCA
*
3405454 TCTGTTCTTGAGTCTTGGTCA
66 TCTGTTCATGAGTCTTGGTCA
3405475 GGGAATTTTA
Statistics
Matches: 188, Mismatches: 24, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
126 178 0.95
127 10 0.05
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (126 bp):
TGGTTATCTAAATTGACACAACTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACTGCTCA
TCTGTTCATGAGTCTTGGTCATCTAAAGGTGATAACACGATTCCACTATGATAGGGACGAC
Done.