Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007029.1 Hibiscus syriacus cultivar Beakdansim tig00018197_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: 139753
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:83 original size:19 final size:20
Alignment explanation
Indices: 36--83 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
26 TGCAAATGGA
36 GATCGATCCTCGAGAGAAAT
1 GATCGATCCTCGAGAGAAAT
*
56 GATCAATCCTCGAGA-AAAT
1 GATCGATCCTCGAGAGAAAT
*
75 GATTGATCC
1 GATCGATCC
84 CTCTAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
GATCGATCCTCGAGAGAAAT
Found at i:13897 original size:119 final size:119
Alignment explanation
Indices: 13686--13923 Score: 467
Period size: 119 Copynumber: 2.0 Consensus size: 119
13676 CCTTTAGAAT
13686 ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
1 ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
*
13751 TGTTGATGTATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
66 TGTTGATATATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
13805 ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
1 ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
13870 TGTTGATATATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
66 TGTTGATATATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
13924 TGAATTTTGG
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 118 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (119 bp):
ATATAAGCTACCAGGATCGTCATCGAAAAAAGGTATTTTATTGTTGATTAGGCGGTTTCACCTAA
TGTTGATATATGTAAAAACTGTGGTGGTTGAAAATTGTGCATATAAGCCATTGA
Found at i:15615 original size:15 final size:15
Alignment explanation
Indices: 15595--15628 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
15585 CAATCAAATT
15595 CTTCCCTCTTGCCGA
1 CTTCCCTCTTGCCGA
15610 CTTCCCTCTTGCCGA
1 CTTCCCTCTTGCCGA
15625 CTTC
1 CTTC
15629 TGATACTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.47, G:0.12, T:0.35
Consensus pattern (15 bp):
CTTCCCTCTTGCCGA
Found at i:21452 original size:15 final size:15
Alignment explanation
Indices: 21428--21473 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
21418 TATATTAATT
*
21428 TTTTAAAATAATTTA
1 TTTTATAATAATTTA
*
21443 TTTTATAATAATATA
1 TTTTATAATAATTTA
*
21458 -TTTATAATTATTTA
1 TTTTATAATAATTTA
21472 TT
1 TT
21474 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTATAATAATTTA
Found at i:21496 original size:42 final size:41
Alignment explanation
Indices: 21449--21547 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 41
21439 TTTATTTTAT
*
21449 AATAATATATTTATAATTA-TTTATTATATTTTAAATTATTAA
1 AATAATATATTTATAATTACTTT-TTATATTTTAAATAATT-A
*
21491 AATAATATATTATATAA-TACTTTTTATATTTTTAATAATTA
1 AATAATATATT-TATAATTACTTTTTATATTTTAAATAATTA
*
21532 AAGAATATATTT-TAAT
1 AATAATATATTTATAAT
21548 AACCTAAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
39 3 0.06
40 1 0.02
41 11 0.22
42 28 0.55
43 8 0.16
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (41 bp):
AATAATATATTTATAATTACTTTTTATATTTTAAATAATTA
Found at i:21788 original size:20 final size:20
Alignment explanation
Indices: 21763--21930 Score: 139
Period size: 20 Copynumber: 8.2 Consensus size: 20
21753 AATGACCAAC
*
21763 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
21783 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
21803 AAAATCGCAA--CGATCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
21823 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
21844 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
21865 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
21887 --AATCGTAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
21905 AAAATCGCAATGCGATTAAAG
1 AAAATCGCAACGCGATT-AAG
21926 AAAAT
1 AAAAT
21931 GAGTAAATTC
Statistics
Matches: 121, Mismatches: 15, Indels: 23
0.76 0.09 0.14
Matches are distributed among these distances:
17 2 0.02
18 3 0.02
20 80 0.66
21 16 0.13
22 20 0.17
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:21867 original size:42 final size:42
Alignment explanation
Indices: 21820--21920 Score: 161
Period size: 40 Copynumber: 2.5 Consensus size: 42
21810 CAACGATCAA
21820 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
* *
21862 CAGAAAATCGCAACGCG--ATTCCAAGAATCGTAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
*
21902 AAGAAAATCGCAATGCGAT
1 AAGAAAATCGCAACGCGAT
21921 TAAAGAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
40 37 0.70
42 16 0.30
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
Found at i:22037 original size:6 final size:6
Alignment explanation
Indices: 22026--22070 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
22016 GACACGTATT
22026 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
22071 CGAACCGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:22573 original size:6 final size:6
Alignment explanation
Indices: 22552--22594 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
22542 TCTCGTCTCG
22552 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
22595 AATACGTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:22722 original size:20 final size:20
Alignment explanation
Indices: 22697--22833 Score: 190
Period size: 20 Copynumber: 6.8 Consensus size: 20
22687 CTCATTTTCT
22697 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
22717 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
22737 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
22758 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
22777 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
22797 CAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
22817 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
22834 CTTCTTTTCA
Statistics
Matches: 105, Mismatches: 4, Indels: 14
0.85 0.03 0.11
Matches are distributed among these distances:
18 5 0.05
19 2 0.02
20 77 0.73
21 3 0.03
22 18 0.17
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.36
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:22868 original size:20 final size:20
Alignment explanation
Indices: 22690--22895 Score: 152
Period size: 20 Copynumber: 10.2 Consensus size: 20
22680 GAATTTACTC
*
22690 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
22710 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
**
22730 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
22750 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
22770 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
22790 ATTTTCTCAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
22810 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* ** *
22832 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
22852 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
22872 GTTTT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
22891 ATTTT
1 ATTTT
22896 GTTGGTCATT
Statistics
Matches: 153, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
19 22 0.14
20 107 0.70
21 11 0.07
22 13 0.08
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:28456 original size:16 final size:16
Alignment explanation
Indices: 28435--28467 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28425 CCTAGCAATA
28435 GAATCATAACATGAAG
1 GAATCATAACATGAAG
28451 GAATCATAACATGAAG
1 GAATCATAACATGAAG
28467 G
1 G
28468 GCAAGAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.18
Consensus pattern (16 bp):
GAATCATAACATGAAG
Found at i:30861 original size:20 final size:20
Alignment explanation
Indices: 30832--30877 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
30822 AGTTGGGTTG
*
30832 TTACCCTGTCCAAAAGTTTT
1 TTACCTTGTCCAAAAGTTTT
30852 TTACCTTGTCCAAAAGTTTT
1 TTACCTTGTCCAAAAGTTTT
30872 TTACCT
1 TTACCT
30878 GTTAATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (20 bp):
TTACCTTGTCCAAAAGTTTT
Found at i:35124 original size:39 final size:39
Alignment explanation
Indices: 35070--35144 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
35060 ACTGGGACTT
*
35070 CGGCTTCTGCTCCTGTAATGCCTACTGTCATCAATGTCC
1 CGGCTTCTGCTCCTGTAACGCCTACTGTCATCAATGTCC
*
35109 CGGCTTCTTCTCCTGTAACGCCTACTGTCATCAATG
1 CGGCTTCTGCTCCTGTAACGCCTACTGTCATCAATG
35145 ACCCTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.33
Consensus pattern (39 bp):
CGGCTTCTGCTCCTGTAACGCCTACTGTCATCAATGTCC
Found at i:41168 original size:61 final size:60
Alignment explanation
Indices: 41099--41234 Score: 168
Period size: 60 Copynumber: 2.2 Consensus size: 60
41089 TTAATGGTAG
**
41099 AGTTAATAATCAAGAC-CAATAAATTTATTTTCTTTCAATTAGGTCCTTAGT-TCATTAAATT
1 AGTTAATAATCAAG-CTCAATAAATTTA-TTTCTTTCAATTAAATCCTTA-TCTCATTAAATT
* * * **
41160 GGTTAATAAACAAGCTTAATACGTTTATTTCTTTCAATTAAATCCTTATCTCATTAAATT
1 AGTTAATAATCAAGCTCAATAAATTTATTTCTTTCAATTAAATCCTTATCTCATTAAATT
41220 AGTTAATAATCAAGC
1 AGTTAATAATCAAGC
41235 CAGGTTAATT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
59 1 0.02
60 43 0.67
61 20 0.31
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (60 bp):
AGTTAATAATCAAGCTCAATAAATTTATTTCTTTCAATTAAATCCTTATCTCATTAAATT
Found at i:42374 original size:17 final size:16
Alignment explanation
Indices: 42352--42384 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
42342 CGAACTACAA
42352 ATAATGTTTATATCTGC
1 ATAATGTTTAT-TCTGC
42369 ATAATGTTTATTCTGC
1 ATAATGTTTATTCTGC
42385 TTCTAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (16 bp):
ATAATGTTTATTCTGC
Found at i:48782 original size:18 final size:17
Alignment explanation
Indices: 48754--48804 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
48744 AGATTAATAT
48754 ATTTCATATTTAATTTAA
1 ATTT-ATATTTAATTTAA
*
48772 ATTATATATTTAACTTAA
1 ATT-TATATTTAATTTAA
*
48790 ATTTA-ATTAAATTTA
1 ATTTATATTTAATTTA
48805 TATAATACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.28
17 2 0.07
18 18 0.62
19 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATATTTAATTTAA
Found at i:53542 original size:27 final size:28
Alignment explanation
Indices: 53476--53542 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 28
53466 TATGTCCACT
*
53476 TAAAATTATT-TTATTATTATTTCAATA
1 TAAAATAATTATTATTATTATTTCAATA
* *
53503 TGATATGATATTATTATTATTATTT-AATA
1 TAAAAT-A-ATTATTATTATTATTTCAATA
53532 TAAAATAATTA
1 TAAAATAATTA
53543 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 8 0.25
28 1 0.03
29 11 0.34
30 12 0.38
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (28 bp):
TAAAATAATTATTATTATTATTTCAATA
Found at i:54461 original size:15 final size:16
Alignment explanation
Indices: 54435--54465 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
54425 TAAGAGAGAC
54435 CTAAAGAATATTTAAA
1 CTAAAGAATATTTAAA
54451 CTAAA-AATATTTAAA
1 CTAAAGAATATTTAAA
54466 TCAACTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
CTAAAGAATATTTAAA
Found at i:60975 original size:21 final size:21
Alignment explanation
Indices: 60949--60988 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
60939 GCTTTAAAAG
60949 ATGGGAACGCGCCTCCAGAGT
1 ATGGGAACGCGCCTCCAGAGT
60970 ATGGGAACGCGCCTCCAGA
1 ATGGGAACGCGCCTCCAGA
60989 ATATTATCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.30, G:0.33, T:0.12
Consensus pattern (21 bp):
ATGGGAACGCGCCTCCAGAGT
Found at i:61379 original size:58 final size:59
Alignment explanation
Indices: 61283--61403 Score: 199
Period size: 58 Copynumber: 2.1 Consensus size: 59
61273 TTTTTAGATT
* * *
61283 TTAAATGAATGATTATGATTCAATCAGAATCATTAAAATATTACCTTAAAATTCAAATG
1 TTAAATGAATGATTATGAGTAAATCAGAATAATTAAAATATTACCTTAAAATTCAAATG
*
61342 TTAAATGAATGATTATG-GTAAATCAGAATAATTAAAATATTATCTTAAAATTCAAATG
1 TTAAATGAATGATTATGAGTAAATCAGAATAATTAAAATATTACCTTAAAATTCAAATG
61400 TTAA
1 TTAA
61404 GTAAGTTATC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 41 0.71
59 17 0.29
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.36
Consensus pattern (59 bp):
TTAAATGAATGATTATGAGTAAATCAGAATAATTAAAATATTACCTTAAAATTCAAATG
Found at i:61564 original size:12 final size:12
Alignment explanation
Indices: 61547--61622 Score: 53
Period size: 12 Copynumber: 5.9 Consensus size: 12
61537 TATTTTATCT
*
61547 TTTTAAAATTAC
1 TTTTAAAATTAA
*
61559 TTTTAAACAATAA
1 TTTTAAA-ATTAA
*
61572 TCTTAAACAATTAAA
1 T-TTTAA-AATT-AA
* *
61587 TTTTAAACTGTAT
1 TTTTAAAAT-TAA
*
61600 TTTTAAAATTAC
1 TTTTAAAATTAA
61612 TTTTAAAATTA
1 TTTTAAAATTA
61623 TATATATATA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
12 20 0.40
13 15 0.30
14 11 0.22
15 4 0.08
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (12 bp):
TTTTAAAATTAA
Found at i:61628 original size:2 final size:2
Alignment explanation
Indices: 61621--61690 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
61611 CTTTTAAAAT
61621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61691 ATTAAGTAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:68146 original size:36 final size:35
Alignment explanation
Indices: 68106--68175 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
68096 TAAAGCGTCC
* **
68106 TGAATAGAAATAAGTATATCGATTATGATCCTTTTT
1 TGAATAGAAATAAGCATAGAGATTATGAT-CTTTTT
*
68142 TGAATAGAGATAAGCATAGAGATTATGATCTTTT
1 TGAATAGAAATAAGCATAGAGATTATGATCTTTT
68176 GATGACTCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 5 0.17
36 25 0.83
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (35 bp):
TGAATAGAAATAAGCATAGAGATTATGATCTTTTT
Found at i:74994 original size:23 final size:24
Alignment explanation
Indices: 74968--75031 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
74958 TATATTCCAT
*
74968 ATATATATTTTAAAAT-ATAATTA
1 ATATATATTTTAAAATAATAATAA
*
74991 ATATA-AGATTTAAAATAATAATAA
1 ATATATA-TTTTAAAATAATAATAA
*
75015 ATTTAATATTTTAAAAT
1 ATAT-ATATTTTAAAAT
75032 TGAATTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.03
23 13 0.39
24 9 0.27
25 9 0.27
26 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATATATTTTAAAATAATAATAA
Found at i:75001 original size:24 final size:25
Alignment explanation
Indices: 74974--75031 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
74964 CCATATATAT
*
74974 ATTTTAAAAT-ATAATTAATATAAG
1 ATTTTAAAATAATAATAAATATAAG
* *
74998 A-TTTAAAATAATAATAAATTTAAT
1 ATTTTAAAATAATAATAAATATAAG
75022 ATTTTAAAAT
1 ATTTTAAAAT
75032 TGAATTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.28
24 13 0.45
25 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTTTAAAATAATAATAAATATAAG
Found at i:75639 original size:2 final size:2
Alignment explanation
Indices: 75632--75719 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
75622 TCCTAACTTT
75632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75716 TA TA
1 TA TA
75720 GTTAAAATAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75850 original size:21 final size:20
Alignment explanation
Indices: 75799--75857 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
75789 AGTTTTAGAA
*
75799 TTTTAAGGTTTAAGATTTAG
1 TTTTAAGGTTTAAGATTGAG
* * *
75819 TGTTCATGGTTTATGATGTGAG
1 T-TTTAAGGTTTAAGAT-TGAG
*
75841 TTTTAAGGTTTGAGATT
1 TTTTAAGGTTTAAGATT
75858 TTGAGGTTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
20 2 0.07
21 23 0.79
22 4 0.14
ACGTcount: A:0.24, C:0.02, G:0.25, T:0.49
Consensus pattern (20 bp):
TTTTAAGGTTTAAGATTGAG
Found at i:79900 original size:21 final size:22
Alignment explanation
Indices: 79876--79922 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
79866 GTTTACGTCG
79876 TTGACATGACAATCCACGAT-A
1 TTGACATGACAATCCACGATGA
** *
79897 TTGATGTGACAGTCCACGATGA
1 TTGACATGACAATCCACGATGA
79919 TTGA
1 TTGA
79923 TAATGTAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (22 bp):
TTGACATGACAATCCACGATGA
Found at i:82460 original size:20 final size:20
Alignment explanation
Indices: 82435--82475 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
82425 AAACTAGTAT
82435 AACTAAAAGTTATA-AAAAAA
1 AACT-AAAGTTATAGAAAAAA
*
82455 AACTAAATTTATAGAAAAAA
1 AACTAAAGTTATAGAAAAAA
82475 A
1 A
82476 TACATAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (20 bp):
AACTAAAGTTATAGAAAAAA
Found at i:83392 original size:70 final size:69
Alignment explanation
Indices: 83310--83448 Score: 224
Period size: 70 Copynumber: 2.0 Consensus size: 69
83300 AGATAATAAT
* * *
83310 ATAATTTTTATATTTATTTAGAGATAGTTGTTATAAAATTGTTCTATACTTTATTATTCAATTAG
1 ATAATTTTTATATTTATTTAGAGATAATTGTTATAAAATTGTACCATACTTTATTATTCAATTAG
83375 ATTC
66 ATTC
* *
83379 ATAATTTTTTATATTTATTTTGAGATAATTGTTATAATATTGTACCATACTTTATTATTCAATTA
1 ATAA-TTTTTATATTTATTTAGAGATAATTGTTATAAAATTGTACCATACTTTATTATTCAATTA
83444 GATTC
65 GATTC
83449 TTATTTTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
69 4 0.06
70 60 0.94
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (69 bp):
ATAATTTTTATATTTATTTAGAGATAATTGTTATAAAATTGTACCATACTTTATTATTCAATTAG
ATTC
Found at i:84706 original size:11 final size:11
Alignment explanation
Indices: 84665--84724 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
84655 ATTAGATATT
*
84665 AGATAAAACAA
1 AGATAAAAAAA
84676 AGA-AAAAAATA
1 AGATAAAAAA-A
*
84687 AAAT-AAAAAA
1 AGATAAAAAAA
84697 AGATAAAAAAA
1 AGATAAAAAAA
* *
84708 ATATAAGGAAAA
1 AGATAA-AAAAA
84720 AGATA
1 AGATA
84725 TAAGAATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
10 9 0.23
11 22 0.56
12 8 0.21
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.12
Consensus pattern (11 bp):
AGATAAAAAAA
Found at i:84719 original size:24 final size:23
Alignment explanation
Indices: 84678--84724 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
84668 TAAAACAAAG
*
84678 AAAAAAATAAAATAAAAAAAGATA
1 AAAAAAATAAAA-GAAAAAAGATA
* *
84702 AAAAAAATATAAGGAAAAAGATA
1 AAAAAAATAAAAGAAAAAAGATA
84725 TAAGAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.13
Consensus pattern (23 bp):
AAAAAAATAAAAGAAAAAAGATA
Found at i:84848 original size:51 final size:51
Alignment explanation
Indices: 84735--84833 Score: 132
Period size: 52 Copynumber: 2.0 Consensus size: 51
84725 TAAGAATATA
* *
84735 AAAATATTAAATAAATTAAAGGAAGAAAAAATAAGAAAAAACATAAAAAAGT
1 AAAATATTAAATAAATAAAAGG-AGAAAAAAGAAGAAAAAACATAAAAAAGT
*
84787 AAAATATTAAATAAATCAAAAGG-GAAAAAAGAA-AGAAAAC-TAAAAAA
1 AAAATATTAAATAAAT-AAAAGGAGAAAAAAGAAGAAAAAACATAAAAAA
84834 ATGTTAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 7 0.16
50 6 0.14
51 9 0.21
52 16 0.37
53 5 0.12
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (51 bp):
AAAATATTAAATAAATAAAAGGAGAAAAAAGAAGAAAAAACATAAAAAAGT
Found at i:85105 original size:14 final size:14
Alignment explanation
Indices: 85086--85124 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
85076 GAATCAATTG
85086 AAAATTTAGAGTTA
1 AAAATTTAGAGTTA
*
85100 AAAATTTAGAGTTG
1 AAAATTTAGAGTTA
*
85114 AAAATTCAGAG
1 AAAATTTAGAG
85125 ACAAAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.31
Consensus pattern (14 bp):
AAAATTTAGAGTTA
Found at i:85813 original size:9 final size:9
Alignment explanation
Indices: 85799--85850 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
85789 CAAAAGAAAG
85799 AAATAAA-A
1 AAATAAATA
85807 TAAATAAATA
1 -AAATAAATA
*
85817 AAA-ACATA
1 AAATAAATA
85825 AAATAAATA
1 AAATAAATA
*
85834 AAATTAAATT
1 AAA-TAAATA
85844 AAATAAA
1 AAATAAA
85851 AAACAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 7 0.19
9 21 0.57
10 9 0.24
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAAATA
Found at i:85828 original size:13 final size:13
Alignment explanation
Indices: 85799--85851 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 13
85789 CAAAAGAAAG
85799 AAATAAAATAAAT
1 AAATAAAATAAAT
85812 AAATAAAAACATAAAAT
1 AAAT--AAA-AT-AAAT
85829 AAATAAAATTAAATT
1 AAATAAAA-TAAA-T
85844 AAATAAAA
1 AAATAAAA
85852 AACAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 16 0.47
16 2 0.06
17 8 0.24
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:86046 original size:2 final size:2
Alignment explanation
Indices: 86035--86064 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
86025 TTTTCAAAAT
86035 TA TA TA -A 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 T
86065 TCGAAAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:86048 original size:34 final size:34
Alignment explanation
Indices: 85858--86048 Score: 247
Period size: 34 Copynumber: 5.4 Consensus size: 34
85848 AAAAAACAAA
* *
85858 TATATATTATATATATTCTAAAATGTTTTCAAAAC
1 TATATAATATATATTTTC-AAAATGTTTTCAAAAC
* * * *
85893 TATATATTATATAATTTAAAAATGTTTTCAAAAAAT
1 TATATAATATATATTTTCAAAATGTTTTC--AAAAC
*
85929 TATATATTATATATATGTTTTCAAAGTGTTTTCAAAAC
1 TATATA--ATATATA--TTTTCAAAATGTTTTCAAAAC
85967 TATATAATATATATTTTCAAAATGTTTTCAAAAC
1 TATATAATATATATTTTCAAAATGTTTTCAAAAC
*
86001 TATATAATATATATTTTCAAAATGTTTTCAAAAT
1 TATATAATATATATTTTCAAAATGTTTTCAAAAC
86035 TATATAATATATAT
1 TATATAATATATAT
86049 ATATATATAT
Statistics
Matches: 139, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
34 78 0.56
35 15 0.11
36 17 0.12
38 16 0.12
40 13 0.09
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (34 bp):
TATATAATATATATTTTCAAAATGTTTTCAAAAC
Found at i:87291 original size:9 final size:9
Alignment explanation
Indices: 87277--87345 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
87267 AGGGCTGGAA
87277 ACCGGTTTG
1 ACCGGTTTG
*
87286 ACCGGTTTTCT
1 ACCGG-TTT-G
*
87297 ACCGGTTCG
1 ACCGGTTTG
*
87306 AACCAGTTTG
1 -ACCGGTTTG
*
87316 ACCGGTCTG
1 ACCGGTTTG
87325 AACC-GTTTG
1 -ACCGGTTTG
*
87334 ACCGGTCTG
1 ACCGGTTTG
87343 ACC
1 ACC
87346 CGACCCGACC
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
8 3 0.07
9 23 0.50
10 15 0.33
11 5 0.11
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:87321 original size:19 final size:19
Alignment explanation
Indices: 87297--87343 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
87287 CCGGTTTTCT
87297 ACCGGTTC-GAACCAGTTTG
1 ACCGGTTCTGAACC-GTTTG
87316 ACCGG-TCTGAACCGTTTG
1 ACCGGTTCTGAACCGTTTG
87334 ACCGG-TCTGA
1 ACCGGTTCTGA
87344 CCCGACCCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.26
Consensus pattern (19 bp):
ACCGGTTCTGAACCGTTTG
Found at i:87334 original size:18 final size:19
Alignment explanation
Indices: 87305--87343 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
87295 CTACCGGTTC
87305 GAACCAGTTTGACCGGTCT
1 GAACCAGTTTGACCGGTCT
87324 GAACC-GTTTGACCGGTCT
1 GAACCAGTTTGACCGGTCT
87342 GA
1 GA
87344 CCCGACCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (19 bp):
GAACCAGTTTGACCGGTCT
Found at i:87374 original size:6 final size:7
Alignment explanation
Indices: 87357--87386 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
87347 GACCCGACCC
87357 GACCGTT
1 GACCGTT
87364 GACCG-T
1 GACCGTT
87370 GACCGTT
1 GACCGTT
87377 GACCGTT
1 GACCGTT
87384 GAC
1 GAC
87387 TTCATTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:87375 original size:13 final size:13
Alignment explanation
Indices: 87357--87382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
87347 GACCCGACCC
87357 GACCGTTGACCGT
1 GACCGTTGACCGT
87370 GACCGTTGACCGT
1 GACCGTTGACCGT
87383 TGACTTCATT
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:89905 original size:25 final size:25
Alignment explanation
Indices: 89854--89900 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
89844 ATTAATAATT
89854 AATTTTATTAATGGTTTTATTTTAA
1 AATTTTATTAATGGTTTTATTTTAA
*
89879 AATTTTATTTAT-G-TTTATTTTA
1 AATTTTATTAATGGTTTTATTTTA
89901 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 1 0.05
25 11 0.52
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (25 bp):
AATTTTATTAATGGTTTTATTTTAA
Found at i:94076 original size:33 final size:34
Alignment explanation
Indices: 94007--94089 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
93997 TTTGACTCAA
* * *
94007 ATATATTA-AATATTTTAAAATAGTTAAAATATT
1 ATATTTTATAATATTTTAAAAGAGTTAAAATAAT
*
94040 ATATTTTATAATATTTTAAACGA-TTAAAATAAT
1 ATATTTTATAATATTTTAAAAGAGTTAAAATAAT
*
94073 ATATTTTATAATTTTTT
1 ATATTTTATAATATTTT
94090 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (34 bp):
ATATTTTATAATATTTTAAAAGAGTTAAAATAAT
Found at i:94436 original size:30 final size:32
Alignment explanation
Indices: 94386--94449 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 32
94376 TAGTCTCTGA
* *
94386 GATCATTTGAATTCTTAAGATACTTTTATTTT
1 GATCATTTCAATTCTTAAGATACTTTTAATTT
94418 GATCA-TTCAATT-TTAAGATACTTTTAATTT
1 GATCATTTCAATTCTTAAGATACTTTTAATTT
94448 GA
1 GA
94450 AATTACAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 19 0.63
31 6 0.20
32 5 0.17
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.50
Consensus pattern (32 bp):
GATCATTTCAATTCTTAAGATACTTTTAATTT
Found at i:95429 original size:40 final size:39
Alignment explanation
Indices: 95367--95489 Score: 149
Period size: 39 Copynumber: 3.1 Consensus size: 39
95357 CGTGCACTCC
* * ** *
95367 TGGAGTATT-TTCAATTTTCCTGAAGACGTCATTACAATCG
1 TGGAGTCTTCTTC-ATTTGCCTGAAGACACCA-TACAATCA
*
95407 TGGAGTCTTCTTCATTTGCCTGAAGATACCATACAATCA
1 TGGAGTCTTCTTCATTTGCCTGAAGACACCATACAATCA
* *
95446 TGGAGTCTTCTTCATTTGTCTGAAGATACCATACAATCA
1 TGGAGTCTTCTTCATTTGCCTGAAGACACCATACAATCA
95485 TGGAG
1 TGGAG
95490 CATTCATATT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 50 0.67
40 22 0.29
41 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (39 bp):
TGGAGTCTTCTTCATTTGCCTGAAGACACCATACAATCA
Found at i:95452 original size:39 final size:39
Alignment explanation
Indices: 95399--95489 Score: 164
Period size: 39 Copynumber: 2.3 Consensus size: 39
95389 AAGACGTCAT
*
95399 TACAATCGTGGAGTCTTCTTCATTTGCCTGAAGATACCA
1 TACAATCATGGAGTCTTCTTCATTTGCCTGAAGATACCA
*
95438 TACAATCATGGAGTCTTCTTCATTTGTCTGAAGATACCA
1 TACAATCATGGAGTCTTCTTCATTTGCCTGAAGATACCA
95477 TACAATCATGGAG
1 TACAATCATGGAG
95490 CATTCATATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (39 bp):
TACAATCATGGAGTCTTCTTCATTTGCCTGAAGATACCA
Found at i:104120 original size:65 final size:65
Alignment explanation
Indices: 104016--104184 Score: 275
Period size: 65 Copynumber: 2.6 Consensus size: 65
104006 ATAATTAATT
* * *
104016 TTAACTCTCTCGGTCTTATACTTTATATAAGTTGTATCTCATAATTAATTTTAACTCTTATAAAA
1 TTAACTCCCTCGGTCTTATAATTTATATAATTTGTATCTCATAATTAATTTTAACTCTTATAAAA
* * *
104081 TTAACTCCCGCGGTCTTATAATTTATAGAATTTGTATCTCATAATTAATTTTAACTCTTATAAAT
1 TTAACTCCCTCGGTCTTATAATTTATATAATTTGTATCTCATAATTAATTTTAACTCTTATAAAA
*
104146 TTAACTTCCTCGGTCTTATAATTTATATAATTTGTATCT
1 TTAACTCCCTCGGTCTTATAATTTATATAATTTGTATCT
104185 TGTGTTGACT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 95 1.00
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (65 bp):
TTAACTCCCTCGGTCTTATAATTTATATAATTTGTATCTCATAATTAATTTTAACTCTTATAAAA
Found at i:105379 original size:5 final size:5
Alignment explanation
Indices: 105369--105395 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
105359 CCCACCCTTA
105369 TATAC TATAC TATAC TATAC TATAC TA
1 TATAC TATAC TATAC TATAC TATAC TA
105396 ACCTGTCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAC
Found at i:110671 original size:5 final size:5
Alignment explanation
Indices: 110661--110686 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
110651 TTAAACTCTT
110661 CACCA CACCA CACCA CACCA CACCA C
1 CACCA CACCA CACCA CACCA CACCA C
110687 CAATTTATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.62, G:0.00, T:0.00
Consensus pattern (5 bp):
CACCA
Found at i:112140 original size:18 final size:17
Alignment explanation
Indices: 112117--112150 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
112107 TGAGATAAAG
112117 TCCGAATTCGAATCCGAA
1 TCCGAATTCG-ATCCGAA
112135 TCCGAATTCGATCCGA
1 TCCGAATTCGATCCGA
112151 CCCGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (17 bp):
TCCGAATTCGATCCGAA
Found at i:113806 original size:62 final size:59
Alignment explanation
Indices: 113693--113812 Score: 143
Period size: 62 Copynumber: 2.0 Consensus size: 59
113683 ATAGTTGAAT
* *
113693 GATCATTTTGTAACTTTAATAGTCGAGAGACTTAAAAAAGCAACATTCTATAGTCGGAC
1 GATCATTTTGTAACTTTAATAGTAGAGAGACTTAAAAAAGCAACATACTATAGTCGGAC
* * **
113752 GATCATTTTGTAAAACTTTTAATAGTAGA-ATGACTTAATAAAGTAGTATACTATAGTCGGA
1 GATCATTTTGT--AAC-TTTAATAGTAGAGA-GACTTAAAAAAGCAACATACTATAGTCGGA
113813 GGACTATTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 11 0.22
61 4 0.08
62 36 0.71
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (59 bp):
GATCATTTTGTAACTTTAATAGTAGAGAGACTTAAAAAAGCAACATACTATAGTCGGAC
Done.