Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008919.1 Hibiscus syriacus cultivar Beakdansim tig00112223_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: 1453011
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 5
Found at i:747539 original size:19 final size:20
Alignment explanation
Indices: 747515--747565 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
747505 CGGCCAAGAG
* *
747515 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
747534 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
747554 CATGTATTTTCA
1 CATGTATTTTCA
747566 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:757372 original size:19 final size:20
Alignment explanation
Indices: 757348--757398 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
757338 CGGCCAAGAG
* *
757348 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
757367 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
757387 CATGTATTTTCA
1 CATGTATTTTCA
757399 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:766523 original size:13 final size:12
Alignment explanation
Indices: 766507--766548 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
766497 GTGCAAAAAG
766507 AAAGAAAATCAGA
1 AAAGAAAATCA-A
*
766520 AAAGAAAA-GAA
1 AAAGAAAATCAA
766531 AAAGAAAATTCAA
1 AAAGAAAA-TCAA
766544 AAAGA
1 AAAGA
766549 GAAAGCAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.74, C:0.05, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAGAAAATCAA
Found at i:766538 original size:24 final size:25
Alignment explanation
Indices: 766507--766553 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
766497 GTGCAAAAAG
766507 AAAGAAAA-TCAGAAAAGA-AAAGAA
1 AAAGAAAATTCA-AAAAGAGAAAGAA
766531 AAAGAAAATTCAAAAAGAGAAAG
1 AAAGAAAATTCAAAAAGAGAAAG
766554 CAAGCCAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.06
Consensus pattern (25 bp):
AAAGAAAATTCAAAAAGAGAAAGAA
Found at i:780998 original size:2 final size:2
Alignment explanation
Indices: 780987--781022 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
780977 TAACTATAGG
780987 TA TA -A 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 T
781023 GAAAATAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:781059 original size:23 final size:23
Alignment explanation
Indices: 781019--781063 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
781009 ATATATATAT
781019 ATATGAAAATAACTATCTTATAAC
1 ATATGAAAATAACTATC-TATAAC
781043 ATATG-AAATAAGC-ATCTATAA
1 ATATGAAAATAA-CTATCTATAA
781064 GTATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (23 bp):
ATATGAAAATAACTATCTATAAC
Found at i:781893 original size:15 final size:15
Alignment explanation
Indices: 781857--781886 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
781847 GTGCTTCAAC
781857 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
781871 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
781886 T
1 T
781887 CTTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:781909 original size:27 final size:27
Alignment explanation
Indices: 781879--781940 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
781869 CTTTTCTTTG
*
781879 CTTTTCTTCTTTTTGAATGC-CGAATTT
1 CTTTTCTTCTTTTAGAATGCTC-AATTT
*
781906 C-TTTCTTTCTTTTAGATTGCTTCAATTT
1 CTTTTC-TTCTTTTAGAATGC-TCAATTT
781934 CTTTTCT
1 CTTTTCT
781941 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 7 0.24
29 5 0.17
ACGTcount: A:0.13, C:0.19, G:0.08, T:0.60
Consensus pattern (27 bp):
CTTTTCTTCTTTTAGAATGCTCAATTT
Found at i:784241 original size:15 final size:15
Alignment explanation
Indices: 784206--784234 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
784196 GTGCTTCAAC
784206 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
784220 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
784235 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:789701 original size:13 final size:13
Alignment explanation
Indices: 789679--789708 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
789669 ACTAAACACC
789679 TTTC-ACATACCT
1 TTTCAACATACCT
789691 TTTCAACATACCT
1 TTTCAACATACCT
789704 TTTCA
1 TTTCA
789709 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:792475 original size:15 final size:15
Alignment explanation
Indices: 792440--792468 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
792430 ATGCTTCAAC
792440 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
792454 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
792469 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:796179 original size:20 final size:19
Alignment explanation
Indices: 796138--796179 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
796128 AGTGCTAGTG
*
796138 AAGAAATCCAGATTCAACA
1 AAGAAATCCAGACTCAACA
796157 AAGAAATTCCAGCACTCAA-A
1 AAGAAA-TCCAG-ACTCAACA
796177 AAG
1 AAG
796180 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 9 0.45
21 5 0.25
ACGTcount: A:0.52, C:0.21, G:0.12, T:0.14
Consensus pattern (19 bp):
AAGAAATCCAGACTCAACA
Found at i:798331 original size:12 final size:12
Alignment explanation
Indices: 798314--798338 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
798304 CAACAACAAC
798314 AAAAATACAAAA
1 AAAAATACAAAA
798326 AAAAATACAAAA
1 AAAAATACAAAA
798338 A
1 A
798339 GAAGTGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAATACAAAA
Found at i:804709 original size:11 final size:11
Alignment explanation
Indices: 804693--804748 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
804683 ATTGGAGTGC
804693 AAAAAGAAAAG
1 AAAAAGAAAAG
804704 AAAAAGACAAA-
1 AAAAAGA-AAAG
* *
804715 AAGAAGAATCAGAA
1 AAAAAGAA--A-AG
804729 AAAAAGAAAAG
1 AAAAAGAAAAG
804740 AAAAAGAAA
1 AAAAAGAAA
804749 TTCAAAAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.03
11 23 0.62
12 5 0.14
13 1 0.03
14 7 0.19
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:813743 original size:23 final size:23
Alignment explanation
Indices: 813716--813764 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
813706 TTCATTATCA
813716 TATGATGCATGAGTTGTTATTAT
1 TATGATGCATGAGTTGTTATTAT
813739 TATGATGCATGAGTTGTTATTAT
1 TATGATGCATGAGTTGTTATTAT
813762 TAT
1 TAT
813765 AACCTATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (23 bp):
TATGATGCATGAGTTGTTATTAT
Found at i:817971 original size:20 final size:20
Alignment explanation
Indices: 817932--818002 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
817922 CGGCCAAGAG
* *
817932 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
817951 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
817971 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
817991 CATGTATTTTCA
1 CATGTATTTTCA
818003 AAGGGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 12 0.24
20 37 0.76
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:818451 original size:20 final size:18
Alignment explanation
Indices: 818411--818452 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
818401 TCTCTATCCT
*
818411 TTATTTTTTTTTTCATTC
1 TTATTTTTATTTTCATTC
818429 TTATTATTTATTTTCATTAC
1 TTATT-TTTATTTTCATT-C
818449 TTAT
1 TTAT
818453 ATTATTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTTATTTTCATTC
Found at i:818739 original size:11 final size:11
Alignment explanation
Indices: 818717--818774 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
818707 ATTGGAGTGC
818717 AAAAGTAAAAAG
1 AAAAG-AAAAAG
818729 AAAAGAAAAAG
1 AAAAGAAAAAG
*
818740 ACAAA-AAGAAG
1 A-AAAGAAAAAG
*
818751 AAAA-AAAGCAG
1 AAAAGAAA-AAG
818762 AAAAG-AAAAG
1 AAAAGAAAAAG
818772 AAA
1 AAA
818775 TTCAAAAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 10 0.26
11 21 0.54
12 8 0.21
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:818745 original size:19 final size:18
Alignment explanation
Indices: 818717--818774 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 18
818707 ATTGGAGTGC
*
818717 AAAAGTAAAAAGAAAAGA
1 AAAAGCAAAAAGAAAAGA
818735 AAAAGACAAAAAGAAGAA-A
1 AAAAG-CAAAAAGAA-AAGA
818754 AAAAGCAGAAAAGAAAAGA
1 AAAAGCA-AAAAGAAAAGA
818773 AA
1 AA
818775 TTCAAAAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 9 0.26
19 24 0.69
20 2 0.06
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAGCAAAAAGAAAAGA
Found at i:819785 original size:21 final size:23
Alignment explanation
Indices: 819751--819793 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
819741 AAACACCTTG
819751 AAGAAGAACATTAAAG-CAATGA
1 AAGAAGAACATTAAAGACAATGA
*
819773 AAGAATAAC-TTAAAGACAATG
1 AAGAAGAACATTAAAGACAATG
819794 TAACTGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.16
Consensus pattern (23 bp):
AAGAAGAACATTAAAGACAATGA
Found at i:822151 original size:19 final size:20
Alignment explanation
Indices: 822127--822177 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
822117 CGTCCAAGAG
* *
822127 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
822146 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
822166 CATGTATTTTCA
1 CATGTATTTTCA
822178 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:824871 original size:20 final size:20
Alignment explanation
Indices: 824848--824885 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
824838 TAATTCATTT
824848 TATTAGATCATAAGCATTCA
1 TATTAGATCATAAGCATTCA
* *
824868 TATTAGCTCCTAAGCATT
1 TATTAGATCATAAGCATT
824886 ATACATTAGT
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:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (20 bp):
TATTAGATCATAAGCATTCA
Found at i:828089 original size:30 final size:33
Alignment explanation
Indices: 828030--828090 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 33
828020 TTGATAACAT
828030 TTCTATCCATTTCCTTTCTTATCATTTCCATTC
1 TTCTATCCATTTCCTTTCTTATCATTTCCATTC
828063 TTCT-TCCATTT-CTTAT-TTAT-ATTTCCAT
1 TTCTATCCATTTCCTT-TCTTATCATTTCCAT
828091 CTTAATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.30
31 7 0.26
32 8 0.30
33 4 0.15
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.57
Consensus pattern (33 bp):
TTCTATCCATTTCCTTTCTTATCATTTCCATTC
Found at i:834008 original size:8 final size:8
Alignment explanation
Indices: 833997--834021 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
833987 TCTTTTTCTT
833997 TTCTTTTC
1 TTCTTTTC
834005 TTCTTTTC
1 TTCTTTTC
834013 TTCTTTTC
1 TTCTTTTC
834021 T
1 T
834022 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:843133 original size:8 final size:8
Alignment explanation
Indices: 843120--843166 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
843110 CGTGCAAAGC
843120 AAAAGAAA
1 AAAAGAAA
843128 AAAAGAAA
1 AAAAGAAA
*
843136 AGAAG--A
1 AAAAGAAA
**
843142 ATCAGAAA
1 AAAAGAAA
843150 AAAAGAAA
1 AAAAGAAA
843158 AAAAGAAA
1 AAAAGAAA
843166 A
1 A
843167 GAAAAAGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
6 4 0.12
8 28 0.88
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAGAAA
Found at i:843148 original size:22 final size:21
Alignment explanation
Indices: 843115--843172 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
843105 ATTGGCGTGC
843115 AAAGCAAAAGAAAAAAAGAAAA
1 AAAG-AAAAGAAAAAAAGAAAA
* *
843137 GAAGAATCAGAAAAAAAGAAAA
1 AAAGAA-AAGAAAAAAAGAAAA
843159 AAAGAAAAGAAAAA
1 AAAGAAAAGAAAAA
843173 GAAATTCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 9 0.29
22 22 0.71
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (21 bp):
AAAGAAAAGAAAAAAAGAAAA
Found at i:843184 original size:30 final size:30
Alignment explanation
Indices: 843119--843185 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
843109 GCGTGCAAAG
843119 CAAAAGAAAAAAAGAAAAGAAGAATCAGAAA
1 CAAAAGAAAAAAAGAAAAGAAGAA-CAGAAA
843150 -AAAAGAAAAAAAGAAAAGAA-AA-AGAAA
1 CAAAAGAAAAAAAGAAAAGAAGAACAGAAA
843177 TTCAAAAGA
1 --CAAAAGA
843186 GAAAGCAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
27 5 0.15
29 2 0.06
30 26 0.79
ACGTcount: A:0.76, C:0.04, G:0.15, T:0.04
Consensus pattern (30 bp):
CAAAAGAAAAAAAGAAAAGAAGAACAGAAA
Found at i:856318 original size:36 final size:36
Alignment explanation
Indices: 856270--856378 Score: 157
Period size: 36 Copynumber: 3.1 Consensus size: 36
856260 CTATTTTCAC
*
856270 CACCATAATCCATCTCCATTATCACGCCTATATCAT
1 CACCATAATCCATCACCATTATCACGCCTATATCAT
*
856306 CACCATAGTCCATCACCATTATCACGCCTATATCAT
1 CACCATAATCCATCACCATTATCACGCCTATATCAT
* * * *
856342 CACCATATTCCATCAACA-TATCACGCCAATAACAT
1 CACCATAATCCATCACCATTATCACGCCTATATCAT
856377 CA
1 CA
856379 TCCTTCCATT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.25
36 50 0.75
ACGTcount: A:0.34, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
CACCATAATCCATCACCATTATCACGCCTATATCAT
Found at i:871214 original size:36 final size:36
Alignment explanation
Indices: 871166--871274 Score: 157
Period size: 36 Copynumber: 3.1 Consensus size: 36
871156 CTATTTTCAC
*
871166 CACCATAATCCATCTCCATTATCACGCCTATATCAT
1 CACCATAATCCATCACCATTATCACGCCTATATCAT
*
871202 CACCATAGTCCATCACCATTATCACGCCTATATCAT
1 CACCATAATCCATCACCATTATCACGCCTATATCAT
* * * *
871238 CACCATATTCCATCAACA-TATCACGCCAATAACAT
1 CACCATAATCCATCACCATTATCACGCCTATATCAT
871273 CA
1 CA
871275 TCCTTCCATT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 17 0.25
36 50 0.75
ACGTcount: A:0.34, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
CACCATAATCCATCACCATTATCACGCCTATATCAT
Found at i:871707 original size:12 final size:12
Alignment explanation
Indices: 871677--871711 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
871667 TATCTTTTAT
871677 TTATCTTGTTT-
1 TTATCTTGTTTC
*
871688 TAATCTTGTTTC
1 TTATCTTGTTTC
871700 TTATCTTGTTTC
1 TTATCTTGTTTC
871712 CAGCTCCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:872085 original size:26 final size:24
Alignment explanation
Indices: 872045--872103 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 24
872035 TAAAAAACCC
872045 AAAAAATAAAAAAAGGCAAAAATAACA
1 AAAAAAT-AAAAAA-GCAAAAATAA-A
* *
872072 AAAAAATAAAAAAGCTAAAATTAA
1 AAAAAATAAAAAAGCAAAAATAAA
872096 AAAAAATA
1 AAAAAATA
872104 GCAAACAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 9 0.30
25 8 0.27
26 6 0.20
27 7 0.23
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (24 bp):
AAAAAATAAAAAAGCAAAAATAAA
Found at i:872101 original size:27 final size:27
Alignment explanation
Indices: 872045--872101 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 27
872035 TAAAAAACCC
*
872045 AAAAAATAAAAAAAGGCAAAAATAACA
1 AAAAAATAAAAAAAGGCAAAAATAAAA
* *
872072 AAAAAAT-AAAAAA-GCTAAAATTAAA
1 AAAAAATAAAAAAAGGCAAAAATAAAA
872097 AAAAA
1 AAAAA
872102 TAGCAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 14 0.52
26 6 0.22
27 7 0.26
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (27 bp):
AAAAAATAAAAAAAGGCAAAAATAAAA
Found at i:875711 original size:24 final size:24
Alignment explanation
Indices: 875684--875735 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
875674 TTAAAATATC
875684 AAGAGACATGTCTTG-TGAATCACA
1 AAGAGACATGTCTTGTTG-ATCACA
875708 AAGAGACATGTCTTGTTGATCACA
1 AAGAGACATGTCTTGTTGATCACA
875732 AAGA
1 AAGA
875736 TTCACGCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (24 bp):
AAGAGACATGTCTTGTTGATCACA
Found at i:877730 original size:79 final size:80
Alignment explanation
Indices: 877621--877831 Score: 219
Period size: 79 Copynumber: 2.6 Consensus size: 80
877611 CATCATGTAG
* * * * *
877621 CACGTCTTGCACTCATATTAAACAAAACAACATGTTTATCCTTTATTTTAATTA-ACTCATGTGT
1 CACGTCTTGCACTCTTATTCAACATAACAACATGTTTATCATTTATTTTAATTACACTCATGTGC
* *
877685 ATTCCCATTGTTAAA
66 ATTCACATTGATAAA
* * * *
877700 CACGTCTTGCACTCTTATTCAACATGACAACATGTTTTTCATTTAATTATAATTACCATTCATGT
1 CACGTCTTGCACTCTTATTCAACATAACAACATGTTTATCATTT-ATTTTAATTA-CACTCATGT
* *
877765 GCATTCATATTGATAAG
64 GCATTCACATTGATAAA
* * * *
877782 CACGTTTTTGCA-TTTATATTCAACATAACAGCATGTTTATCATTTGTTTT
1 CACG-TCTTGCACTCT-TATTCAACATAACAACATGTTTATCATTTATTTT
877832 GTTAAATTCA
Statistics
Matches: 107, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
79 38 0.36
80 9 0.08
82 28 0.26
83 32 0.30
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (80 bp):
CACGTCTTGCACTCTTATTCAACATAACAACATGTTTATCATTTATTTTAATTACACTCATGTGC
ATTCACATTGATAAA
Found at i:877898 original size:28 final size:28
Alignment explanation
Indices: 877858--877913 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
877848 CTCACATTCA
*
877858 CATAACATCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
877886 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
877914 TTAATTCACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:881804 original size:79 final size:80
Alignment explanation
Indices: 881695--881905 Score: 219
Period size: 79 Copynumber: 2.6 Consensus size: 80
881685 CATCATGTAG
* * * * *
881695 CACGTCTTGCACTCATATTAAACAAAACAACATGTTTATCCTTTATTTTAATTA-ACTCATGTGT
1 CACGTCTTGCACTCTTATTCAACATAACAACATGTTTATCATTTATTTTAATTACACTCATGTGC
* *
881759 ATTCCCATTGTTAAA
66 ATTCACATTGATAAA
* * * *
881774 CACGTCTTGCACTCTTATTCAACATGACAACATGTTTTTCATTTAATTATAATTACCATTCATGT
1 CACGTCTTGCACTCTTATTCAACATAACAACATGTTTATCATTT-ATTTTAATTA-CACTCATGT
* *
881839 GCATTCATATTGATAAG
64 GCATTCACATTGATAAA
* * * *
881856 CACGTTTTTGCA-TTTATATTCAACATAACAGCATGTTTATCATTTGTTTT
1 CACG-TCTTGCACTCT-TATTCAACATAACAACATGTTTATCATTTATTTT
881906 GTTAAATTCA
Statistics
Matches: 107, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
79 38 0.36
80 9 0.08
82 28 0.26
83 32 0.30
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (80 bp):
CACGTCTTGCACTCTTATTCAACATAACAACATGTTTATCATTTATTTTAATTACACTCATGTGC
ATTCACATTGATAAA
Found at i:881986 original size:28 final size:28
Alignment explanation
Indices: 881932--881987 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
881922 CTCACATTCA
**
881932 CATAACAACATGTTCATCATTTGTTTTG
1 CATAACAACATGTTCATCATTCATTTTG
* *
881960 CATAACAGCATGTTCGTCATTCATTTTG
1 CATAACAACATGTTCATCATTCATTTTG
881988 TTAATTCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (28 bp):
CATAACAACATGTTCATCATTCATTTTG
Found at i:883636 original size:19 final size:21
Alignment explanation
Indices: 883612--883663 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
883602 CGGCCAAGAA
*
883612 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
883631 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
883652 CATGTATTTTCA
1 CATGTATTTTCA
883664 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:884401 original size:17 final size:17
Alignment explanation
Indices: 884369--884401 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
884359 AAATTGGAGT
*
884369 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAAAAAAG
884386 ACAAAAAGAAAAAAAA
1 ACAAAAAGAAAAAAAA
884402 TCAGAATAGA
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:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAAAAAAG
Found at i:884407 original size:25 final size:25
Alignment explanation
Indices: 884379--884426 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
884369 ACAAAAAGAA
884379 AGAAAAGACA-AAAAGAAAAAAAATC
1 AGAAAAGA-ATAAAAGAAAAAAAATC
*
884404 AGAATAGAATAAAAGAAAAAAAA
1 AGAAAAGAATAAAAGAAAAAAAA
884427 AGAATTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.06
Consensus pattern (25 bp):
AGAAAAGAATAAAAGAAAAAAAATC
Found at i:886761 original size:17 final size:17
Alignment explanation
Indices: 886739--886790 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
886729 AAATTGGAGT
886739 GCAAAAAGAAAGAAAAG
1 GCAAAAAGAAAGAAAAG
*
886756 GCAAAAAGAAGAGAAAAA
1 GCAAAAAGAA-AGAAAAG
*
886774 TCAGAAAAG-AAGAAAAG
1 GCA-AAAAGAAAGAAAAG
886791 AAGAAAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 16 0.53
18 9 0.30
19 5 0.17
ACGTcount: A:0.69, C:0.06, G:0.23, T:0.02
Consensus pattern (17 bp):
GCAAAAAGAAAGAAAAG
Found at i:886787 original size:8 final size:8
Alignment explanation
Indices: 886776--886800 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
886766 GAGAAAAATC
886776 AGAAAAGA
1 AGAAAAGA
886784 AGAAAAGA
1 AGAAAAGA
886792 AGAAAAGA
1 AGAAAAGA
886800 A
1 A
886801 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:892689 original size:19 final size:20
Alignment explanation
Indices: 892665--892715 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
892655 CGGCCAAGAG
* *
892665 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
892684 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
892704 CATGTATTTTCA
1 CATGTATTTTCA
892716 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:896120 original size:36 final size:36
Alignment explanation
Indices: 896061--896162 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
896051 GATGTTATTG
896061 GCGTGAT-ATGGTGATGGAATATGGTGATGATATAA
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
896096 GCGTGATAATGGTGATGGACTATGGTGATGATATAG
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
896132 GCGTGATAATGGAGATGGATTATGGTGATGA
1 GCGTGATAATGGTGATGGAATATGGTGATGA
896163 AAATAGTATC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 7 0.11
36 55 0.89
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
GCGTGATAATGGTGATGGAATATGGTGATGATATAA
Found at i:898396 original size:36 final size:36
Alignment explanation
Indices: 898349--898448 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
898339 GATACTATTT
*
898349 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
898385 TCATCACCATAATCCATCACCATTATCGCGCTTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
898421 TCATCACCATATTCCATCACCA-TATCAC
1 TCATCACCATAATCCATCACCATTATCAC
898449 ACCAATAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 5 0.08
36 54 0.92
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:898404 original size:13 final size:12
Alignment explanation
Indices: 898349--898461 Score: 53
Period size: 13 Copynumber: 9.5 Consensus size: 12
898339 GATACTATTT
898349 TCATCACCATAA
1 TCATCACCATAA
* *
898361 TCCATCTCCATTA
1 T-CATCACCATAA
*
898374 TCA-CGCC-TATA
1 TCATCACCATA-A
898385 TCATCACCATAA
1 TCATCACCATAA
898397 TCCATCACCAT--
1 T-CATCACCATAA
* *
898408 T-ATCGCGCTTATA
1 TCATCAC-CATA-A
*
898421 TCATCACCATAT
1 TCATCACCATAA
898433 TCCATCACCAT-A
1 T-CATCACCATAA
898445 TCA-CACCAATAA
1 TCATCACC-ATAA
898457 -CATCA
1 TCATCA
898462 TCCTTCCATT
Statistics
Matches: 76, Mismatches: 11, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
9 4 0.05
10 7 0.09
11 14 0.18
12 13 0.17
13 34 0.45
14 4 0.05
ACGTcount: A:0.34, C:0.35, G:0.03, T:0.28
Consensus pattern (12 bp):
TCATCACCATAA
Found at i:898476 original size:33 final size:33
Alignment explanation
Indices: 898432--898500 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
898422 CATCACCATA
898432 TTCCATCACCATATCA-CACCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
898465 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
898498 TTC
1 TTC
898501 ATTCATCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:904125 original size:36 final size:36
Alignment explanation
Indices: 904074--904185 Score: 163
Period size: 36 Copynumber: 3.1 Consensus size: 36
904064 ATACTATTTC
*
904074 CATCACCATAATCCATCTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCACCATTATCACGCCTATAT
* *
904110 CATCACCATAGTCCATCACCATTATCACGCTTATAT
1 CATCACCATAATCCATCACCATTATCACGCCTATAT
* * *
904146 CATCACCATATTCCATCACCA-TATCACGCCAATAA
1 CATCACCATAATCCATCACCATTATCACGCCTATAT
904181 CATCA
1 CATCA
904186 TCCTTCCATT
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 53 0.77
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
CATCACCATAATCCATCACCATTATCACGCCTATAT
Found at i:904219 original size:33 final size:33
Alignment explanation
Indices: 904156--904220 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
904146 CATCACCATA
*
904156 TTCCATCACCATATCACGCCAATAACATCATCC
1 TTCCATCACCATATCACACCAATAACATCATCC
* * *
904189 TTCCATTACCATTTCATCACCATTAA-ATCATC
1 TTCCATCACCATATCA-CACCAATAACATCATC
904221 ATTCATTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.32, C:0.35, G:0.02, T:0.31
Consensus pattern (33 bp):
TTCCATCACCATATCACACCAATAACATCATCC
Found at i:911505 original size:36 final size:36
Alignment explanation
Indices: 911453--911565 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
911443 GATACTATTT
* *
911453 TCATCACCATAATCCATCTCCATTATCATGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
911489 TCATCACCATAGTCCATCACCATTATCACGCTTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
911525 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
911560 ACATCA
1 TCATCA
911566 TCCTTCCATT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 16 0.23
36 53 0.77
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:911580 original size:33 final size:33
Alignment explanation
Indices: 911536--911604 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
911526 CATCACCATA
*
911536 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
911569 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
911602 TTC
1 TTC
911605 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:913881 original size:25 final size:24
Alignment explanation
Indices: 913849--913896 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
913839 GTAGGAGTCT
913849 TTTCTTTTCTCTTTTGT-TTTCTTC
1 TTTCTTTTCTCTTTT-TATTTCTTC
*
913873 TTTCTTTTTTTCTTTTTATTTCTT
1 TTTC-TTTTCTCTTTTTATTTCTT
913897 TTGTTGCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (24 bp):
TTTCTTTTCTCTTTTTATTTCTTC
Found at i:914352 original size:36 final size:36
Alignment explanation
Indices: 914278--914390 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
914268 AATGGAAGGA
* * *
914278 TGATGTTATTGGCGTGAT-ATGGTGAAGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
914313 TGATGATATAGGCGTGATAATGCTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
914349 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
914385 TGATGA
1 TGATGA
914391 AAATAGTATC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 16 0.23
36 53 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:919136 original size:36 final size:36
Alignment explanation
Indices: 919084--919182 Score: 146
Period size: 36 Copynumber: 2.8 Consensus size: 36
919074 AATACTATTT
*
919084 TCATCACCATAATCCATCTCCATTATCACACCTATA
1 TCATCACCATAATCCATCACCATTATCACACCTATA
* * *
919120 TCATCACCATAGTCCATCACCATTATCACGCTTATA
1 TCATCACCATAATCCATCACCATTATCACACCTATA
*
919156 TCATCACCATATTCCATCACCA-TATCA
1 TCATCACCATAATCCATCACCATTATCA
919183 TGCCAATAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 5 0.09
36 53 0.91
ACGTcount: A:0.32, C:0.35, G:0.02, T:0.30
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACACCTATA
Found at i:919139 original size:13 final size:11
Alignment explanation
Indices: 919084--919183 Score: 71
Period size: 13 Copynumber: 8.4 Consensus size: 11
919074 AATACTATTT
919084 TCATCACCATAA
1 TCATCACCAT-A
*
919096 TCCATCTCCATTA
1 T-CATCACCA-TA
919109 TCA-CACCTATA
1 TCATCACC-ATA
919120 TCATCACCATA
1 TCATCACCATA
919131 GTCCATCACCAT-
1 -T-CATCACCATA
919143 T-ATCACGCTTATA
1 TCATCAC-C--ATA
919156 TCATCACCATA
1 TCATCACCATA
919167 TTCCATCACCATA
1 -T-CATCACCATA
919180 TCAT
1 TCAT
919184 GCCAATAACA
Statistics
Matches: 73, Mismatches: 2, Indels: 27
0.72 0.02 0.26
Matches are distributed among these distances:
9 5 0.07
10 1 0.01
11 18 0.25
12 13 0.18
13 30 0.41
14 6 0.08
ACGTcount: A:0.32, C:0.35, G:0.02, T:0.31
Consensus pattern (11 bp):
TCATCACCATA
Found at i:919211 original size:33 final size:33
Alignment explanation
Indices: 919167--919235 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
919157 CATCACCATA
*
919167 TTCCATCACCATATCAT-GCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
919200 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
919233 TTC
1 TTC
919236 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:919610 original size:18 final size:19
Alignment explanation
Indices: 919589--919624 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
919579 AAGCAACAAA
919589 AAGAAAA-AAAAAAGAAAG
1 AAGAAAACAAAAAAGAAAG
*
919607 AAGAAAACAAAAGAGAAA
1 AAGAAAACAAAAAAGAAA
919625 AGACTCCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (19 bp):
AAGAAAACAAAAAAGAAAG
Found at i:924058 original size:20 final size:19
Alignment explanation
Indices: 924015--924063 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
924005 CGGCCAAGAG
* *
924015 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
*
924034 AATGTATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAT
924054 CATGTATTTT
1 CATGTATTTT
924064 TCAACCTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:926319 original size:19 final size:21
Alignment explanation
Indices: 926295--926346 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
926285 CGGCCAAGAG
*
926295 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
926314 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
926335 CATGTATTTTCA
1 CATGTATTTTCA
926347 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:927812 original size:19 final size:21
Alignment explanation
Indices: 927788--927839 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
927778 CGGCCAAGAG
*
927788 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
927807 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
927828 CATGTATTTTCA
1 CATGTATTTTCA
927840 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:931769 original size:19 final size:21
Alignment explanation
Indices: 931745--931795 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
931735 TTCCAAGAGT
*
931745 ATGTATCTTCA-TTAAAA-TC
1 ATGTATTTTCATTTAAAAGTC
931764 ATGTATTTTCATTTAAAAGTC
1 ATGTATTTTCATTTAAAAGTC
931785 ATGTATTTTCA
1 ATGTATTTTCA
931796 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 10 0.34
20 6 0.21
21 13 0.45
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (21 bp):
ATGTATTTTCATTTAAAAGTC
Found at i:932717 original size:329 final size:323
Alignment explanation
Indices: 932082--932733 Score: 978
Period size: 329 Copynumber: 2.0 Consensus size: 323
932072 TGTGAAGACC
* *
932082 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCGAGTTTGAGATACAACATAACCACCATCTT
1 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGAAACAACATAACCACCATCTT
* *
932147 CATTTCATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGTAGCCATCTCTCT
66 CATTTCATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGCCATCTCTAT
* *
932212 TTCATTTCTTTCTATTTCATTTCCTTTATTATATATTCATTTCTTAAGACCATTATTAATATCAT
131 TTCATTTCTTTCTATTCCATTTACTTTATTATATATTCATTTCTTAAGACCATTATTAATATCAT
*
932277 TTCTTTCTTATATTATTTTGCAGCCCAAGCTTATTAATTCAAGGAAATCAGTACTTTTCAATCCT
196 TTCTTTCTTATATTATTTTGCAGCCCAAGCTTATTAATTCAAGGAAATCAGTACTTATCAATCCT
* *
932342 AGATCGGGACACAATAAGTCTATATACTCTTTTCACCAATGCGTGTAGATTCGCCTTACATCA
261 AGATCGGGACACAATAAGGCTATATACTCTTTTCACCAAAGCGTGTAGATTCGCCTTACATCA
* *
932405 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGAAATAACATCACCACCATCTT
1 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGAAACAACATAACCACCATCTT
932470 CATTTCATCATCAACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGC
66 CA--T--T--T---CATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGC
*
932535 CATCTCTA-TTCTTATTCTTTC-ATTCCA-TTACTTATATTAT-TATTCATTTCTTAA-ACCCAT
122 CATCTCTATTTCAT-TTCTTTCTATTCCATTTACTT-TATTATATATTCATTTCTTAAGA-CCAT
* *
932595 TATTAATCAT-ATTTCTTTCTTATTATT-TTTT-TAGCCCAAGCTTATTAATTCAAGGACATCAG
184 TATTAAT-ATCATTTCTTTCTTA-TATTATTTTGCAGCCCAAGCTTATTAATTCAAGGAAATCAG
* *
932657 TACTTATCAATCCTAGATCGGGACACAATAAGGCTATCTACTCTTTTCATCAAAGCGTGTAGATT
247 TACTTATCAATCCTAGATCGGGACACAATAAGGCTATATACTCTTTTCACCAAAGCGTGTAGATT
932722 CGCCTTACATCA
312 CGCCTTACATCA
932734 ACACAAGACA
Statistics
Matches: 299, Mismatches: 16, Indels: 22
0.89 0.05 0.07
Matches are distributed among these distances:
323 63 0.21
325 1 0.00
327 1 0.00
329 103 0.34
330 46 0.15
331 21 0.07
332 64 0.21
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (323 bp):
GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGAAACAACATAACCACCATCTT
CATTTCATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGCCATCTCTAT
TTCATTTCTTTCTATTCCATTTACTTTATTATATATTCATTTCTTAAGACCATTATTAATATCAT
TTCTTTCTTATATTATTTTGCAGCCCAAGCTTATTAATTCAAGGAAATCAGTACTTATCAATCCT
AGATCGGGACACAATAAGGCTATATACTCTTTTCACCAAAGCGTGTAGATTCGCCTTACATCA
Found at i:933469 original size:16 final size:17
Alignment explanation
Indices: 933443--933483 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
933433 TATCAAAAAG
*
933443 TCTTTTCTTTTCTT-TT
1 TCTTTTTTTTTCTTCTT
*
933459 TGTTTTTTTTTCTTCTT
1 TCTTTTTTTTTCTTCTT
933476 TCTTTTTT
1 TCTTTTTT
933484 CCTTTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (17 bp):
TCTTTTTTTTTCTTCTT
Found at i:936114 original size:24 final size:22
Alignment explanation
Indices: 936082--936126 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
936072 TTGGCTCATT
* *
936082 CTTTTAAATTTCAAGAGGTACATC
1 CTTTGAAATGTCAA-AGG-ACATC
936106 CTTTGAAATGTCAAAGGACAT
1 CTTTGAAATGTCAAAGGACAT
936127 ATCGTGTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
CTTTGAAATGTCAAAGGACATC
Found at i:944512 original size:16 final size:16
Alignment explanation
Indices: 944491--944522 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
944481 ATTTCCATCC
944491 TATGCTTAGTTGAATA
1 TATGCTTAGTTGAATA
944507 TATGCTTAGTTGAATA
1 TATGCTTAGTTGAATA
944523 ACTAGCTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (16 bp):
TATGCTTAGTTGAATA
Found at i:949287 original size:25 final size:26
Alignment explanation
Indices: 949257--949316 Score: 113
Period size: 25 Copynumber: 2.3 Consensus size: 26
949247 CCCTAGAACA
949257 CCCATGTGCATGCCATATGACCA-CC
1 CCCATGTGCATGCCATATGACCAGCC
949282 CCCATGTGCATGCCATATGACCAGCC
1 CCCATGTGCATGCCATATGACCAGCC
949308 CCCATGTGC
1 CCCATGTGC
949317 CTTGCATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 23 0.68
26 11 0.32
ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20
Consensus pattern (26 bp):
CCCATGTGCATGCCATATGACCAGCC
Found at i:953938 original size:15 final size:16
Alignment explanation
Indices: 953911--953947 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
953901 CTTTATTATC
953911 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
953927 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
953942 TTATTT
1 TTATTT
953948 TAGTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:954327 original size:11 final size:10
Alignment explanation
Indices: 954299--954326 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
954289 TATTTTTTTC
954299 AAAAAAAACA
1 AAAAAAAACA
954309 AAAAAAAACA
1 AAAAAAAACA
954319 AAAAAAAA
1 AAAAAAAA
954327 AGCCAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:964159 original size:24 final size:24
Alignment explanation
Indices: 964109--964156 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
964099 GCCTATTTTT
* * *
964109 GATGAAGAACCTGAAACAATGCAA
1 GATGAAGAAACTGAAAAAATACAA
964133 GATGAAGAAACTGAAGAAAATACA
1 GATGAAGAAACTGAA-AAAATACA
964157 GATCATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.54, C:0.12, G:0.21, T:0.12
Consensus pattern (24 bp):
GATGAAGAAACTGAAAAAATACAA
Found at i:969253 original size:1 final size:1
Alignment explanation
Indices: 969249--969295 Score: 58
Period size: 1 Copynumber: 47.0 Consensus size: 1
969239 AAATTTTGGC
* * * *
969249 TTTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
969296 AAAATAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:969264 original size:12 final size:12
Alignment explanation
Indices: 969256--969295 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
969246 GGCTTTTTTG
969256 TTTTTTTTTG--
1 TTTTTTTTTGTT
969266 TTTTTTTTTGTT
1 TTTTTTTTTGTT
969278 TTTTTTTTTGTT
1 TTTTTTTTTGTT
969290 TTTTTT
1 TTTTTT
969296 AAAATAGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.36
12 18 0.64
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:969274 original size:22 final size:22
Alignment explanation
Indices: 969249--969295 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
969239 AAATTTTGGC
969249 TTTTTTG--TTTTTTTTTGTTT
1 TTTTTTGTTTTTTTTTTTGTTT
969269 TTTTTTGTTTTTTTTTTTGTTT
1 TTTTTTGTTTTTTTTTTTGTTT
969291 TTTTT
1 TTTTT
969296 AAAATAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.28
22 18 0.72
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (22 bp):
TTTTTTGTTTTTTTTTTTGTTT
Found at i:969295 original size:10 final size:10
Alignment explanation
Indices: 969249--969294 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
969239 AAATTTTGGC
969249 TTTTTTGTTT
1 TTTTTTGTTT
969259 TTTTTTGTTT
1 TTTTTTGTTT
969269 TTTTTTGTTT
1 TTTTTTGTTT
969279 TTTTTT-TTGT
1 TTTTTTGTT-T
969289 TTTTTT
1 TTTTTT
969295 TAAAATAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 2 0.06
10 33 0.94
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:970588 original size:26 final size:26
Alignment explanation
Indices: 970558--970625 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
970548 CCCTAGAACA
*
970558 CCCATGTGCTTTGCATATGAT-AAGCC
1 CCCATGTGCCTTGCATATGATCAA-CC
970584 CCCATGTGCCTTGCATATGATCAACC
1 CCCATGTGCCTTGCATATGATCAACC
*
970610 CCCATATGCCTTGCAT
1 CCCATGTGCCTTGCAT
970626 GTGGTTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 37 0.95
27 2 0.05
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.29
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGATCAACC
Found at i:979382 original size:14 final size:14
Alignment explanation
Indices: 979365--979419 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
979355 AAGATACTAC
*
979365 CTTTCCATCACTAT
1 CTTTCCATCACCAT
*
979379 CTTTCCAACACCAT
1 CTTTCCATCACCAT
*
979393 TTTTCCATCACCAT
1 CTTTCCATCACCAT
*
979407 C-TTCTATCACCAT
1 CTTTCCATCACCAT
979420 TCACGCCTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
13 11 0.31
14 24 0.69
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (14 bp):
CTTTCCATCACCAT
Found at i:981655 original size:40 final size:40
Alignment explanation
Indices: 981595--981675 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
981585 CCAAAGAATA
* ***
981595 TGATGTAAGGTAATTCTACCTTATCGTTTGATTGTGGATC
1 TGATGTAAGGCAATTCTACCTTATCAAATGATTGTGGATC
* * *
981635 TGATGTAAGGCACTTGTACCTTTTCAAATGATTGTGGATC
1 TGATGTAAGGCAATTCTACCTTATCAAATGATTGTGGATC
981675 T
1 T
981676 AGGAAGGAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (40 bp):
TGATGTAAGGCAATTCTACCTTATCAAATGATTGTGGATC
Found at i:984263 original size:13 final size:13
Alignment explanation
Indices: 984241--984270 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
984231 ACTAAACACC
984241 TTTC-ACATACCT
1 TTTCAACATACCT
984253 TTTCAACATACCT
1 TTTCAACATACCT
984266 TTTCA
1 TTTCA
984271 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:989575 original size:89 final size:91
Alignment explanation
Indices: 989469--989646 Score: 234
Period size: 89 Copynumber: 2.0 Consensus size: 91
989459 AAATGATGCA
* * *
989469 TGGCCAAATAGGGAGAGAGCTCTTCATCTTGGCGTCTAAA-AAACCACATGCAAGGCACAT-GGG
1 TGGCCAAATAGGGAGAGAACTATTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATGGGG
*
989532 GCTGTTCACATGCAAAACACATGGCT
66 GCTGGTCACATGCAAAACACATGGCT
* * * * *
989558 TGGCCGAATAGGGAGAGAACTATTCATCTTGGTGCCTAAATGATCCTCATGCAAGGCACATGGGG
1 TGGCCAAATAGGGAGAGAACTATTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATGGGG
* **
989623 GCTGGTCATATGCAAGGCACATGG
66 GCTGGTCACATGCAAAACACATGG
989647 GTGTTATAAG
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
89 35 0.47
90 17 0.23
91 23 0.31
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (91 bp):
TGGCCAAATAGGGAGAGAACTATTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATGGGG
GCTGGTCACATGCAAAACACATGGCT
Found at i:992735 original size:23 final size:24
Alignment explanation
Indices: 992693--992745 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
992683 TTTCTTTCTT
992693 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
992717 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
992740 TTTCTT
1 TTTCTT
992746 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:996527 original size:14 final size:14
Alignment explanation
Indices: 996508--996562 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
996498 AAGATACTAC
996508 CTTTCCATCACCAT
1 CTTTCCATCACCAT
*
996522 CTTTCCAACACCAT
1 CTTTCCATCACCAT
996536 -TTTGCCATCACCAT
1 CTTT-CCATCACCAT
*
996550 C-TTCTATCACCAT
1 CTTTCCATCACCAT
996563 TCACGCCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
13 12 0.33
14 24 0.67
ACGTcount: A:0.24, C:0.40, G:0.02, T:0.35
Consensus pattern (14 bp):
CTTTCCATCACCAT
Found at i:999165 original size:14 final size:14
Alignment explanation
Indices: 999146--999200 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
999136 AAGATACTAC
999146 CTTTCCATCACCAT
1 CTTTCCATCACCAT
*
999160 CTTTCCAACACCAT
1 CTTTCCATCACCAT
*
999174 TTTTCCATCACCAT
1 CTTTCCATCACCAT
*
999188 C-TTCTATCACCAT
1 CTTTCCATCACCAT
999201 TCACACCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
13 11 0.31
14 25 0.69
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (14 bp):
CTTTCCATCACCAT
Found at i:1003192 original size:14 final size:14
Alignment explanation
Indices: 1003173--1003227 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
1003163 AAGATACTAC
1003173 CTTTCCATCACCAT
1 CTTTCCATCACCAT
*
1003187 CTTTCCAACACCAT
1 CTTTCCATCACCAT
*
1003201 TTTTCCATCACCAT
1 CTTTCCATCACCAT
*
1003215 C-TTCTATCACCAT
1 CTTTCCATCACCAT
1003228 TCACACCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
13 11 0.31
14 25 0.69
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (14 bp):
CTTTCCATCACCAT
Found at i:1005807 original size:35 final size:36
Alignment explanation
Indices: 1005768--1005843 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
1005758 TTGGTGGTTA
*
1005768 TATAGGCGTG-CAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAAATGGTAATGGAAGATGGTGATGT
* *
1005803 TATAGGTGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGAAAATGGTAATGGAAGATGGTGATGT
1005839 T-TAGG
1 TATAGG
1005844 TAGTATCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 13 0.35
36 24 0.65
ACGTcount: A:0.29, C:0.03, G:0.38, T:0.30
Consensus pattern (36 bp):
TATAGGCGTGAAAATGGTAATGGAAGATGGTGATGT
Found at i:1005834 original size:13 final size:13
Alignment explanation
Indices: 1005780--1005837 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
1005770 TAGGCGTGCA
*
1005780 ATGGTAATGGAAG
1 ATGGTGATGGAAG
** *
1005793 ATGGTGATGTTAT
1 ATGGTGATGGAAG
*
1005806 A-GGTG-T-GAAA
1 ATGGTGATGGAAG
1005816 ATGGTGATGGAAG
1 ATGGTGATGGAAG
1005829 ATGGTGATG
1 ATGGTGATG
1005838 TTTAGGTAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.15
12 5 0.15
13 22 0.65
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:1006925 original size:17 final size:17
Alignment explanation
Indices: 1006903--1006935 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1006893 CTCTTGGACT
*
1006903 CCAATTCTAGCTTTACG
1 CCAATTATAGCTTTACG
1006920 CCAATTATAGCTTTAC
1 CCAATTATAGCTTTAC
1006936 ATCAGCTCCC
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:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (17 bp):
CCAATTATAGCTTTACG
Found at i:1008981 original size:90 final size:91
Alignment explanation
Indices: 1008827--1009000 Score: 260
Period size: 90 Copynumber: 1.9 Consensus size: 91
1008817 CCTAGAACAC
* *
1008827 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATTATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGAGCCTTGCATGAGGATTATTTAGGCACCAAGATG
*
1008892 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * *
1008918 CCATGTGTTTTGCATGTGAACAG-CCCCATGAGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGAGCCTTGCATGAGGATTATTTAGGCACCAAGATG
1008982 AAGAGCTCTCTCCCTATTC
66 AAGAGCTCTCTCCCTATTC
1009001 AGACAAGCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 55 0.74
91 19 0.26
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGAGCCTTGCATGAGGATTATTTAGGCACCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:1012721 original size:24 final size:24
Alignment explanation
Indices: 1012667--1012721 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1012657 AAAAAATCAG
*
1012667 AAAAG-AAGCACTCAAAATGAAGA
1 AAAAGAAAACACTCAAAATGAAGA
**
1012690 AATTGAAAACACTCAAAA-GAAGAA
1 AAAAGAAAACACTCAAAATGAAG-A
1012714 AAAAGAAA
1 AAAAGAAA
1012722 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.65, C:0.11, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAATGAAGA
Found at i:1016636 original size:24 final size:24
Alignment explanation
Indices: 1016582--1016636 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1016572 GAAAAATCAG
*
1016582 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
1016605 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
1016629 AAAAGAAA
1 AAAAGAAA
1016637 GAAAGAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:1020270 original size:33 final size:33
Alignment explanation
Indices: 1020233--1020296 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
1020223 CTTGGCTTTG
*
1020233 CTTCT-TTTTGAAATTCTTCTTTTTCTTTCTTGT
1 CTTCTATTCTGAAATTCTTC-TTTTCTTTCTTGT
** *
1020266 CTTCTATTCTGATTTTTTTCTTTTCTTTCTT
1 CTTCTATTCTGAAATTCTTCTTTTCTTTCTT
1020297 TTTGCACTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 16 0.62
34 10 0.38
ACGTcount: A:0.08, C:0.19, G:0.05, T:0.69
Consensus pattern (33 bp):
CTTCTATTCTGAAATTCTTCTTTTCTTTCTTGT
Found at i:1020659 original size:20 final size:21
Alignment explanation
Indices: 1020622--1020660 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1020612 GATGGTCTTG
*
1020622 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
1020643 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
1020661 TTATATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:1022630 original size:20 final size:20
Alignment explanation
Indices: 1022605--1022653 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1022595 AACATTTCAT
1022605 TATTTGAGCCACTTTCCATG
1 TATTTGAGCCACTTTCCATG
*
1022625 TATTTGAGCCACTTTCTATG
1 TATTTGAGCCACTTTCCATG
*
1022645 TGTTTGAGC
1 TATTTGAGC
1022654 TAAAGATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (20 bp):
TATTTGAGCCACTTTCCATG
Found at i:1024101 original size:20 final size:19
Alignment explanation
Indices: 1024078--1024144 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 19
1024068 TTCAAAAAAA
1024078 CAAAAAAAAAACAAAAAAGG
1 CAAAAAAAAAA-AAAAAAGG
*
1024098 CAAAAAAAACAAAAAAAAAG
1 CAAAAAAAA-AAAAAAAAGG
*
1024118 CAAAAAAACAAAAAAAAAGC
1 CAAAAAAA-AAAAAAAAAGG
1024138 CAAAAAA
1 CAAAAAA
1024145 GCCAAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 39 0.93
21 3 0.07
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAAAAAAGG
Found at i:1024135 original size:29 final size:29
Alignment explanation
Indices: 1024071--1024134 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
1024061 TTTATTTTTC
*
1024071 AAAAAAACAAAAAAAAAACAAAAAAGGCA
1 AAAAAAACAAAAAAAAAACAAAAAAGACA
*
1024100 AAAAAAACAAAAAAAAAGCAAAAAA-ACA
1 AAAAAAACAAAAAAAAAACAAAAAAGACA
1024128 AAAAAAA
1 AAAAAAA
1024135 AGCCAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 9 0.27
29 24 0.73
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (29 bp):
AAAAAAACAAAAAAAAAACAAAAAAGACA
Found at i:1024151 original size:19 final size:19
Alignment explanation
Indices: 1024071--1024144 Score: 98
Period size: 19 Copynumber: 3.8 Consensus size: 19
1024061 TTTATTTTTC
1024071 AAAAAAA-CAAAAAAA-AA
1 AAAAAAAGCAAAAAAACAA
1024088 ACAAAAAAGGCAAAAAAAACAA
1 A-AAAAAA-GC-AAAAAAACAA
1024110 AAAAAAAGCAAAAAAACAA
1 AAAAAAAGCAAAAAAACAA
1024129 AAAAAAAGCCAAAAAA
1 AAAAAAAG-CAAAAAA
1024145 GCCAAAATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.02
18 6 0.12
19 18 0.35
20 10 0.20
21 13 0.25
22 3 0.06
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAAAGCAAAAAAACAA
Found at i:1029657 original size:18 final size:18
Alignment explanation
Indices: 1029636--1029680 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1029626 TTCTCAAATC
1029636 GTGCCTTTTTACGAATAT
1 GTGCCTTTTTACGAATAT
1029654 GTGCCTTTTTACGAATAT
1 GTGCCTTTTTACGAATAT
1029672 GTGCCTTTT
1 GTGCCTTTT
1029681 CGGGTCGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (18 bp):
GTGCCTTTTTACGAATAT
Found at i:1030481 original size:15 final size:16
Alignment explanation
Indices: 1030444--1030481 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1030434 CCTTTGATAA
1030444 CATTTC-TATCCATTT
1 CATTTCTTATCCATTT
1030459 CATTTCTTATCC-TTT
1 CATTTCTTATCCATTT
*
1030474 CGTTTCTT
1 CATTTCTT
1030482 TCTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.58
Consensus pattern (16 bp):
CATTTCTTATCCATTT
Found at i:1030664 original size:10 final size:10
Alignment explanation
Indices: 1030646--1030684 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
1030636 AAGTGCCAGG
1030646 AAAAAAGAAA
1 AAAAAAGAAA
*
1030656 AAGAAAGAAGA
1 AAAAAAGAA-A
1030667 AAAAAAGAAA
1 AAAAAAGAAA
1030677 AAAAAAGA
1 AAAAAAGA
1030685 CTCCTACATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1040780 original size:15 final size:15
Alignment explanation
Indices: 1040769--1040797 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1040759 ACTCAAAAAG
1040769 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
1040784 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
1040798 TTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:1042273 original size:39 final size:39
Alignment explanation
Indices: 1042210--1042302 Score: 159
Period size: 39 Copynumber: 2.4 Consensus size: 39
1042200 TAAGAGTGGA
*
1042210 AAGATACAATGTTTTGAAAGGATACAACCTTTGGAGTAC
1 AAGACACAATGTTTTGAAAGGATACAACCTTTGGAGTAC
*
1042249 AAGACACAATGTTTTGAAATGATACAACCTTTGGAGTAC
1 AAGACACAATGTTTTGAAAGGATACAACCTTTGGAGTAC
*
1042288 AAGACACAATTTTTT
1 AAGACACAATGTTTT
1042303 AATCAAAGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (39 bp):
AAGACACAATGTTTTGAAAGGATACAACCTTTGGAGTAC
Found at i:1044172 original size:36 final size:36
Alignment explanation
Indices: 1044120--1044232 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
1044110 GATACTATTT
*
1044120 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
1044156 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
1044192 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
1044227 ACATCA
1 TCATCA
1044233 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:1044175 original size:13 final size:11
Alignment explanation
Indices: 1044120--1044218 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
1044110 GATACTATTT
1044120 TCATCACCATAA
1 TCATCACCAT-A
*
1044132 TCCATCTCCATTA
1 T-CATCACCA-TA
*
1044145 TCA-CGCCTATA
1 TCATCACC-ATA
1044156 TCATCACCATA
1 TCATCACCATA
1044167 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
1044181 TCA-CGCCTATA
1 TCATCACC-ATA
1044192 TCATCACCATA
1 TCATCACCATA
1044203 TTCCATCACCATA
1 -T-CATCACCATA
1044216 TCA
1 TCA
1044219 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:1044247 original size:33 final size:33
Alignment explanation
Indices: 1044132--1044271 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
1044122 ATCACCATAA
* * *
1044132 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
1044166 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
1044204 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1044237 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1044270 TC
1 TC
1044272 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:1049745 original size:36 final size:36
Alignment explanation
Indices: 1049693--1049805 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
1049683 GATACTATTT
*
1049693 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
1049729 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
1049765 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
1049800 ACATCA
1 TCATCA
1049806 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:1049748 original size:13 final size:11
Alignment explanation
Indices: 1049693--1049791 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
1049683 GATACTATTT
1049693 TCATCACCATAA
1 TCATCACCAT-A
*
1049705 TCCATCTCCATTA
1 T-CATCACCA-TA
*
1049718 TCA-CGCCTATA
1 TCATCACC-ATA
1049729 TCATCACCATA
1 TCATCACCATA
1049740 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
1049754 TCA-CGCCTATA
1 TCATCACC-ATA
1049765 TCATCACCATA
1 TCATCACCATA
1049776 TTCCATCACCATA
1 -T-CATCACCATA
1049789 TCA
1 TCA
1049792 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:1049820 original size:33 final size:33
Alignment explanation
Indices: 1049705--1049844 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
1049695 ATCACCATAA
* * *
1049705 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
1049739 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
1049777 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1049810 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1049843 TC
1 TC
1049845 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:1053030 original size:15 final size:14
Alignment explanation
Indices: 1053010--1053079 Score: 67
Period size: 13 Copynumber: 5.1 Consensus size: 14
1053000 CCTTTGATAA
1053010 CATTTCTATCCATTT
1 CATTTCTAT-CATTT
1053025 CATTTCTTATCATTT
1 CATTTC-TATCATTT
*
1053040 CATTTCT-TTATTT
1 CATTTCTATCATTT
1053053 CATTTCT-T-ATTT
1 CATTTCTATCATTT
*
1053065 CAATTT-AATCATTT
1 C-ATTTCTATCATTT
1053079 C
1 C
1053080 TTCCTTTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.10
13 18 0.37
14 6 0.12
15 17 0.35
16 3 0.06
ACGTcount: A:0.21, C:0.20, G:0.00, T:0.59
Consensus pattern (14 bp):
CATTTCTATCATTT
Found at i:1053070 original size:13 final size:13
Alignment explanation
Indices: 1053021--1053066 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 13
1053011 ATTTCTATCC
1053021 ATTTCATTTCTTAT
1 ATTTCATTTCTT-T
1053035 CATTTCATTTCTTT
1 -ATTTCATTTCTTT
1053049 ATTTCATTTC-TT
1 ATTTCATTTCTTT
1053061 ATTTCA
1 ATTTCA
1053067 ATTTAATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.26
13 10 0.32
14 1 0.03
15 12 0.39
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTCATTTCTTT
Found at i:1056812 original size:19 final size:20
Alignment explanation
Indices: 1056788--1056836 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1056778 TATCCTTTAT
1056788 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
1056807 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
1056827 -TATTATTATT
1 TTATT-TTATT
1056837 CCCTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:1061547 original size:16 final size:17
Alignment explanation
Indices: 1061526--1061558 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1061516 AGCTTCCATC
1061526 TCTCATTTA-TAAATAG
1 TCTCATTTATTAAATAG
1061542 TCTCATTTATTAAATAG
1 TCTCATTTATTAAATAG
1061559 CCTACCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (17 bp):
TCTCATTTATTAAATAG
Found at i:1061838 original size:23 final size:24
Alignment explanation
Indices: 1061810--1061863 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
1061800 AAAATCAGCA
1061810 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
1061833 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
1061857 AAGAAAA
1 AAGAAAA
1061864 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:1061868 original size:24 final size:23
Alignment explanation
Indices: 1061810--1061869 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
1061800 AAAATCAGCA
1061810 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
1061833 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
1061857 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
1061870 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:1062200 original size:19 final size:19
Alignment explanation
Indices: 1062176--1062215 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1062166 ACCTATAGTT
*
1062176 CACATCTTTATATAATATG
1 CACATCATTATATAATATG
*
1062195 CACATCATTATATTATATG
1 CACATCATTATATAATATG
1062214 CA
1 CA
1062216 TTATATAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (19 bp):
CACATCATTATATAATATG
Found at i:1063046 original size:19 final size:21
Alignment explanation
Indices: 1063022--1063073 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1063012 CGGCCAAGAG
*
1063022 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
*
1063041 CATGTATTTTTATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
1063062 CATGTATTTTCA
1 CATGTATTTTCA
1063074 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:1063497 original size:15 final size:14
Alignment explanation
Indices: 1063477--1063507 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1063467 GCCATCTCTC
1063477 TTTCATTTCTTTCTA
1 TTTCATTTCTTT-TA
1063492 TTTCATTTCTTTTA
1 TTTCATTTCTTTTA
1063506 TT
1 TT
1063508 ATATATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTCATTTCTTTTA
Found at i:1065198 original size:19 final size:20
Alignment explanation
Indices: 1065174--1065224 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1065164 CGGCCAAGAG
* *
1065174 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
1065193 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
1065213 CATGTATTTTCA
1 CATGTATTTTCA
1065225 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:1067342 original size:24 final size:24
Alignment explanation
Indices: 1067275--1067336 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
1067265 TTCCAACAGT
* * * *
1067275 TATGCCACTTGAAATTCAAAAAGA
1 TATGTCACTTGAAGTGCCAAAAGA
*
1067299 TATGTCACTTGAAGTGCCAAAAGT
1 TATGTCACTTGAAGTGCCAAAAGA
1067323 TATGATCA-TTGAAG
1 TATG-TCACTTGAAG
1067337 CTCCAAGTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (24 bp):
TATGTCACTTGAAGTGCCAAAAGA
Found at i:1068997 original size:19 final size:20
Alignment explanation
Indices: 1068973--1069023 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1068963 CGGCCAAGAG
* *
1068973 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
1068992 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
1069012 CATGTATTTTCA
1 CATGTATTTTCA
1069024 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:1069961 original size:13 final size:13
Alignment explanation
Indices: 1069943--1069976 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1069933 AGATACTATT
*
1069943 TCCATCACCATCC
1 TCCATCACCATAC
1069956 TCCATCACCATAC
1 TCCATCACCATAC
1069969 TCCATCAC
1 TCCATCAC
1069977 TATTCACACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.50, G:0.00, T:0.24
Consensus pattern (13 bp):
TCCATCACCATAC
Found at i:1070215 original size:30 final size:30
Alignment explanation
Indices: 1070181--1070239 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1070171 TCATTTTTAT
*
1070181 TTCTTACTTAT-CATATTACTTAATCAATTG
1 TTCTTACTTATACAGATTACTT-ATCAATTG
* *
1070211 TTCTTATTTTTACAGATTACTTATCAATT
1 TTCTTACTTATACAGATTACTTATCAATT
1070240 CAAAGTGTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.53
Consensus pattern (30 bp):
TTCTTACTTATACAGATTACTTATCAATTG
Found at i:1075074 original size:13 final size:13
Alignment explanation
Indices: 1075056--1075108 Score: 65
Period size: 12 Copynumber: 4.2 Consensus size: 13
1075046 CCTTACATCA
1075056 ATTTCATTTCTTT
1 ATTTCATTTCTTT
1075069 ATTTCATTTC-TT
1 ATTTCATTTCTTT
**
1075081 ATTTCAATTTAATT
1 ATTTC-ATTTCTTT
1075095 ATTTC-TTTCTTT
1 ATTTCATTTCTTT
1075107 AT
1 AT
1075109 ATTGTACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 14 0.40
13 14 0.40
14 7 0.20
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTTCATTTCTTT
Done.