Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002703.1 Hibiscus syriacus cultivar Beakdansim tig00005579_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: 102437
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:10562 original size:13 final size:13
Alignment explanation
Indices: 10546--10593 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
10536 CGCAATGTAA
10546 GTCATAAATGCGC
1 GTCATAAATGCGC
*
10559 GTCATAAATGCGT
1 GTCATAAATGCGC
10572 GTCATAAATGCGC
1 GTCATAAATGCGC
10585 GTCATAAAT
1 GTCATAAAT
10594 TTATGACGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:10563 original size:84 final size:85
Alignment explanation
Indices: 10403--10567 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 85
10393 ATACAATCAC
* * *
10403 GACACACGAATGTGTGTCATTTTCATTTATGACGGGGGTTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
*
10468 AATGCGTGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
*
10488 GACACACAAATGTGTGTCATCTTCATTTATGAC-GGGGCTTCAATGACGCGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
10552 AATGCGCGTCATAAAT
66 AATGCGCGTCATAAAT
10568 GCGTGTCATA
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 44 0.59
85 31 0.41
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCGCGTCATAAATTTAT
Found at i:10568 original size:26 final size:26
Alignment explanation
Indices: 10539--10593 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
10529 AATGACGCGC
*
10539 AATGTAAGTCATAAATGCGCGTCATA
1 AATGCAAGTCATAAATGCGCGTCATA
**
10565 AATGCGTGTCATAAATGCGCGTCATA
1 AATGCAAGTCATAAATGCGCGTCATA
10591 AAT
1 AAT
10594 TTATGACGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (26 bp):
AATGCAAGTCATAAATGCGCGTCATA
Found at i:13779 original size:20 final size:20
Alignment explanation
Indices: 13756--13819 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
13746 TAGTATTTAG
13756 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
13776 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
13796 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
13815 TTAAA
1 ATAAA
13820 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:13789 original size:19 final size:20
Alignment explanation
Indices: 13765--13814 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
13755 GATAAATTTA
*
13765 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
13784 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
13805 TT-ATAATTTT
1 TTAATAATTTT
13815 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:13817 original size:31 final size:30
Alignment explanation
Indices: 13732--13818 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
13722 TTTGATAATA
* *
13732 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
13763 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
13794 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
13819 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:16102 original size:29 final size:29
Alignment explanation
Indices: 16006--16091 Score: 154
Period size: 29 Copynumber: 3.0 Consensus size: 29
15996 ATGTAAAAAT
*
16006 AGAACAGGGAATTAATCCCATGTAGAATC
1 AGAATAGGGAATTAATCCCATGTAGAATC
16035 AGAATAGGGAATTAATCCCATGTAGAATC
1 AGAATAGGGAATTAATCCCATGTAGAATC
*
16064 AGAATAGGGAATTAATCCTATGTAGAAT
1 AGAATAGGGAATTAATCCCATGTAGAAT
16092 TAGGACGGGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (29 bp):
AGAATAGGGAATTAATCCCATGTAGAATC
Found at i:17909 original size:60 final size:60
Alignment explanation
Indices: 17813--17990 Score: 168
Period size: 60 Copynumber: 3.0 Consensus size: 60
17803 ATAATATGTC
* *
17813 CCTAAACTCTGACTATCATT-TCAAATTAGTCCTTAAACTTTTAAATATTTTGATTTCATT
1 CCTAAACTATGACTCTCATTCT-AAATTAGTCCTTAAACTTTTAAATATTTTGATTTCATT
* * * * * *
17873 CTTAAACTATGACTCTCATTCTAAATTAGTCATTAAAATTTTGAACA-TTCGAATTTCA-T
1 CCTAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTTG-ATTTCATT
* * * * *
17932 CCCAAACTATGAATCTTATTCTAAATT-GATCCCTAAACTTTTAGATATTTAT-ATTTCAT
1 CCTAAACTATGACTCTCATTCTAAATTAG-TCCTTAAACTTTTAAATATTT-TGATTTCAT
17991 CATCGAATTC
Statistics
Matches: 93, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
58 1 0.01
59 45 0.48
60 46 0.49
61 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.43
Consensus pattern (60 bp):
CCTAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTTGATTTCATT
Found at i:18242 original size:61 final size:61
Alignment explanation
Indices: 18126--18302 Score: 150
Period size: 60 Copynumber: 2.9 Consensus size: 61
18116 TGAATAATTT
* * * *
18126 AGGAT-AAAATTGAAATATTCAAAAAGTTTG-GGCACCAATTTAGGATGA-AGATCATAACTTG
1 AGGATGAAAATTGAAATGTTC-AAAAGTTTGAGG-ACCAATTTAGAATAATAG-TCATAACTTA
* * * **
18187 TGGATGAAAAATGAAATGTTCAAAAGTTTGAGGACGAATTTAGAATAATAGTCATAGTTTA
1 AGGATGAAAATTGAAATGTTCAAAAGTTTGAGGACCAATTTAGAATAATAGTCATAACTTA
* * * *
18248 AGGATG-AAATTGAAATGTTTAAAA-TTTTAGGGACTAATTT-GAAATAATGGTCATA
1 AGGATGAAAATTGAAATGTTCAAAAGTTTGA-GGACCAATTTAG-AATAATAGTCATA
18303 GATTAGGGAC
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
59 5 0.05
60 37 0.39
61 37 0.39
62 17 0.18
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.31
Consensus pattern (61 bp):
AGGATGAAAATTGAAATGTTCAAAAGTTTGAGGACCAATTTAGAATAATAGTCATAACTTA
Found at i:18500 original size:16 final size:16
Alignment explanation
Indices: 18481--18513 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18471 TTTCGATTCA
18481 GGTTA-TTTTCGGTTTG
1 GGTTACTTTT-GGTTTG
18497 GGTTACTTTTGGTTTG
1 GGTTACTTTTGGTTTG
18513 G
1 G
18514 CTAAAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.06, C:0.06, G:0.33, T:0.55
Consensus pattern (16 bp):
GGTTACTTTTGGTTTG
Found at i:26192 original size:23 final size:23
Alignment explanation
Indices: 26142--26186 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
26132 AATAAGTTCG
* *
26142 CAAACGCTAAATGAATATGTTAA
1 CAAACACTAAATAAATATGTTAA
26165 CAAACACTAAATAAATATGTTA
1 CAAACACTAAATAAATATGTTA
26187 GTAAACTCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (23 bp):
CAAACACTAAATAAATATGTTAA
Found at i:27574 original size:24 final size:24
Alignment explanation
Indices: 27546--27598 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
27536 ACCGGAAGTC
*
27546 ATGTTAGCGAACATATAATTGAGT
1 ATGTTAGCGAACATATAATTGAAT
*
27570 ATGTTGGCGAACATATAATTGAAT
1 ATGTTAGCGAACATATAATTGAAT
27594 ATGTT
1 ATGTT
27599 TGTAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (24 bp):
ATGTTAGCGAACATATAATTGAAT
Found at i:27939 original size:6 final size:6
Alignment explanation
Indices: 27928--27954 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27918 TTGTCTTGTA
27928 TATATC TATATC TATATC TATATC TAT
1 TATATC TATATC TATATC TATATC TAT
27955 CATAAGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TATATC
Found at i:28461 original size:6 final size:6
Alignment explanation
Indices: 28453--28554 Score: 69
Period size: 6 Copynumber: 17.0 Consensus size: 6
28443 GTCAGTCTCT
* * * * * * * *
28453 TCTTCT TCTTCT TCTTCT TCTTCC TCCTCC TCCTCC TCCTCC TCCTCT
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
* * * * * * *
28501 TCTTCT TCTTCC TCCTCC TCCTCC TCCTCC TCCTCC TCTTCT TCTTCT
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
28549 TCTTCC
1 TCTTCC
28555 GACATGTGGG
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (6 bp):
TCTTCC
Found at i:28464 original size:9 final size:9
Alignment explanation
Indices: 28449--28554 Score: 59
Period size: 9 Copynumber: 11.8 Consensus size: 9
28439 CTCGGTCAGT
*
28449 CTCTTCTTC
1 CTCTTCCTC
* *
28458 TTCTTCTTC
1 CTCTTCCTC
* *
28467 TTCTTCTTC
1 CTCTTCCTC
*
28476 CTCCTCCTC
1 CTCTTCCTC
*
28485 CTCCTCCTC
1 CTCTTCCTC
* *
28494 CTCCTCTTC
1 CTCTTCCTC
* *
28503 TTCTTCTTC
1 CTCTTCCTC
*
28512 CTCCTCCTC
1 CTCTTCCTC
*
28521 CTCCTCCTC
1 CTCTTCCTC
*
28530 CTCCTCCTC
1 CTCTTCCTC
* *
28539 TTCTTCTTC
1 CTCTTCCTC
*
28548 TTCTTCC
1 CTCTTCC
28555 GACATGTGGG
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 83 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (9 bp):
CTCTTCCTC
Found at i:28473 original size:3 final size:3
Alignment explanation
Indices: 28474--28538 Score: 94
Period size: 3 Copynumber: 21.7 Consensus size: 3
28464 TTCTTCTTCT
* * * *
28474 TCC TCC TCC TCC TCC TCC TCC TCC TCT TCT TCT TCT TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
28522 TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TC
28539 TTCTTCTTCT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (3 bp):
TCC
Found at i:28502 original size:36 final size:36
Alignment explanation
Indices: 28462--28547 Score: 163
Period size: 36 Copynumber: 2.4 Consensus size: 36
28452 TTCTTCTTCT
28462 TCTTCTTCTTCTTCCTCCTCCTCCTCCTCCTCCTCC
1 TCTTCTTCTTCTTCCTCCTCCTCCTCCTCCTCCTCC
28498 TCTTCTTCTTCTTCCTCCTCCTCCTCCTCCTCCTCC
1 TCTTCTTCTTCTTCCTCCTCCTCCTCCTCCTCCTCC
*
28534 TCCTCTTCTTCTTC
1 TCTTCTTCTTCTTC
28548 TTCTTCCGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (36 bp):
TCTTCTTCTTCTTCCTCCTCCTCCTCCTCCTCCTCC
Found at i:30609 original size:29 final size:29
Alignment explanation
Indices: 30575--30633 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
30565 CCTAAATTAA
*
30575 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
30604 TTTGATGTAATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
30633 T
1 T
30634 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTAATTGCTTACATCAATTTAGT
Found at i:30644 original size:29 final size:29
Alignment explanation
Indices: 30584--30641 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
30574 ATTTGATGTC
* *
30584 ATTGCTTACATCAATTTAGTTTTGATGTA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
*
30613 ATTGCTTACATCAATTTAG-TTAGGTGAA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
30641 A
1 A
30642 ATTAAGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (29 bp):
ATTGCTTACATCAATTTAGTTTAGATGAA
Found at i:35296 original size:29 final size:29
Alignment explanation
Indices: 35262--35349 Score: 167
Period size: 29 Copynumber: 3.0 Consensus size: 29
35252 CCTAAATTAA
35262 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
35291 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
35320 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
35349 T
1 T
35350 ATGTGAAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:39952 original size:11 final size:11
Alignment explanation
Indices: 39919--39957 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
39909 ATGAGACTCC
39919 AAAAGAATAAG
1 AAAAGAATAAG
39930 AAAGAGGAATAAG
1 AAA-A-GAATAAG
*
39943 AAAAGAATAAC
1 AAAAGAATAAG
39954 AAAA
1 AAAA
39958 AGAAGGGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 13 0.52
12 2 0.08
13 10 0.40
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.08
Consensus pattern (11 bp):
AAAAGAATAAG
Found at i:41426 original size:25 final size:25
Alignment explanation
Indices: 41398--41456 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
41388 CTATGTTAAG
*
41398 TTTTTCTACTCACTCACCATTGTTA
1 TTTTTCCACTCACTCACCATTGTTA
*
41423 TTTTTCCACTCACTCTCCATTGTTA
1 TTTTTCCACTCACTCACCATTGTTA
41448 TTTTTCCAC
1 TTTTTCCAC
41457 CTTAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.17, C:0.31, G:0.03, T:0.49
Consensus pattern (25 bp):
TTTTTCCACTCACTCACCATTGTTA
Found at i:43176 original size:18 final size:18
Alignment explanation
Indices: 43155--43189 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43145 CATACATTTA
43155 AATGACAACATGTTCCAT
1 AATGACAACATGTTCCAT
43173 AATGACAACATGTTCCA
1 AATGACAACATGTTCCA
43190 CATAACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (18 bp):
AATGACAACATGTTCCAT
Found at i:43966 original size:37 final size:37
Alignment explanation
Indices: 43907--44136 Score: 174
Period size: 37 Copynumber: 6.2 Consensus size: 37
43897 AAAATACGGG
*
43907 TATAGTATATAG-TTTTTGAAAACATTTTTGAAAATTA
1 TATAATATATAGATTTTT-AAAACATTTTTGAAAATTA
*
43944 TATAATATATAGATTTTTAAAACATTTTAGAAAATATA
1 TATAATATATAGATTTTTAAAACATTTTTGAAAAT-TA
* * * * *
43982 TATAATATATATAGTTTTGAAAATAATTTTGAAAGTTTA
1 TATAATATATAGA-TTTTTAAAACATTTTTGAAA-ATTA
*
44021 TATAATATATA-ATTTTTGAAAAAAAACATTTTTGAAAA-CA
1 TATAATATATAGATTTTT-----AAAACATTTTTGAAAATTA
* * *
44061 TCT-A-ATATAG--TTTTAAAACGTTTTTGAAAACTA
1 TATAATATATAGATTTTTAAAACATTTTTGAAAATTA
* **
44094 TATAACATATA-A-TTCGAAAACATCTTTT-AAAATTA
1 TATAATATATAGATTTTTAAAACAT-TTTTGAAAATTA
44129 TATAATAT
1 TATAATAT
44137 TGTTTTGAAA
Statistics
Matches: 156, Mismatches: 22, Indels: 32
0.74 0.10 0.15
Matches are distributed among these distances:
32 15 0.10
33 3 0.02
34 1 0.01
35 26 0.17
36 4 0.03
37 35 0.22
38 25 0.16
39 30 0.19
40 4 0.03
42 13 0.08
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (37 bp):
TATAATATATAGATTTTTAAAACATTTTTGAAAATTA
Found at i:44172 original size:17 final size:17
Alignment explanation
Indices: 44128--44172 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
44118 TTTTAAAATT
*
44128 ATATAATATTGTTTTGAA
1 ATAT-ATATTATTTTGAA
*
44146 A-ATATTTTATTTTGAA
1 ATATATATTATTTTGAA
44162 ATATATATTAT
1 ATATATATTAT
44173 ATATAGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 12 0.52
17 10 0.43
18 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
ATATATATTATTTTGAA
Found at i:45549 original size:13 final size:11
Alignment explanation
Indices: 45488--45545 Score: 55
Period size: 12 Copynumber: 5.0 Consensus size: 11
45478 AACTTTAACC
*
45488 ATTTCTTATTT
1 ATTTCTTTTTT
45499 ATTTACCTTTTTT
1 ATTT--CTTTTTT
*
45512 ATTATTTTTTTT
1 ATT-TCTTTTTT
45524 ATTTC-TTTTT
1 ATTTCTTTTTT
45534 ATTTCCTTTTTT
1 ATTT-CTTTTTT
45546 TATTATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 9 0.23
11 6 0.15
12 14 0.36
13 9 0.23
14 1 0.03
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTCTTTTTT
Found at i:45589 original size:3 final size:3
Alignment explanation
Indices: 45581--45612 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
45571 AAATATTGGC
45581 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
45613 TATCTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:46632 original size:17 final size:17
Alignment explanation
Indices: 46612--46644 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46602 CTCACTAACC
*
46612 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
46629 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
46645 ATCGTTTGCA
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:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:50968 original size:84 final size:84
Alignment explanation
Indices: 50696--51853 Score: 1397
Period size: 84 Copynumber: 13.9 Consensus size: 84
50686 GCTCAAGACA
* * * * **
50696 AGAAGGGCTATTTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAACTTAAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
50761 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCT
* * * * * * *
50780 AGAAGGGCTATCTG-C--C-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
** *
50841 TCACAGCATAACTCAAGTCT
65 TTGCAGCATAACTTAAGTCT
* * * *
50861 AGAAGAGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
50925 TGCAGCACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCT
* * * *
50944 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTATGCTCAGCT-CAACGACACATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
*
51008 TTGCAGCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCT
* * *
51028 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
51093 TGCAGTACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCT
* * *
51112 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGTCACATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* * *
51176 TTGCAGTATAACGTAAGTCG
65 TTGCAGCATAACTTAAGTCT
* * * *
51196 ATAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
51261 TGCAGCACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCT
* * *
51280 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGTCACATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* *
51344 TTGCAGTATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCT
* * *
51364 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
51429 TGCAGCACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCT
* * *
51448 AGAAGGGTTGTCTGCCAACACAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
51513 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCT
* ** * * ** * * *
51532 AGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTTGATTATACTCAGCTTCGAGGGCACGTCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
*
51593 TTGCAGCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCT
* *
51613 AGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
51678 TACAGCATAACTCAAGGCT
66 TGCAGCATAACTTAAGTCT
* * * * *
51697 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTATGTTTAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
** *
51762 TGCAGCATAACGCAAGGCT
66 TGCAGCATAACTTAAGTCT
* * **
51781 AGAAGGGTTATCTGCCAAC-AAAGACCTTCAAGTTCGACTACGCTCATCTCTTAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
51845 TACAGCATA
66 TGCAGCATA
51854 GCCCAAGGCA
Statistics
Matches: 920, Mismatches: 138, Indels: 33
0.84 0.13 0.03
Matches are distributed among these distances:
80 46 0.05
81 84 0.09
82 2 0.00
83 100 0.11
84 657 0.71
85 31 0.03
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTTAAGTCT
Found at i:52495 original size:39 final size:37
Alignment explanation
Indices: 52427--52776 Score: 226
Period size: 37 Copynumber: 9.4 Consensus size: 37
52417 TATATATATC
* * *
52427 TATATATTATATAG-TTTGCAAATAGTTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACA-TTTTTGAAAATA
* *
52464 TGGGTATAATATATAGTTTTCGAAAACTTTTTTGAAAAT-
1 T--ATATAATATATAGTTTT-GAAAACATTTTTGAAAATA
* *
52503 TATATAATATATAGATTTTTAAAACATTTTAGAAAATA
1 TATATAATATATAG-TTTTGAAAACATTTTTGAAAATA
* * *
52541 TATATAATATATATAGTTTTGAAAATAATTTTGAAAGTA
1 TATAT-A-ATATATAGTTTTGAAAACATTTTTGAAAATA
*
52580 TATATAATATATAATTTTTGAAAAAAACATTTTTG-AAA-A
1 TATATAATATAT-AGTTTTG---AAAACATTTTTGAAAATA
* * *
52619 CATAT-A-ATATAGTTTT-AAAACGTTTTTGAAAA-C
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
* *
52652 TATATAACATATAG-TTCGAAAACATCTTTT-AAAAT-
1 TATATAATATATAGTTTTGAAAACAT-TTTTGAAAATA
**
52687 TATATAATAT-T-GTTTTGGAAATATTTTATTTTG-AAATA
1 TATATAATATATAGTTTT-GAAA-A-CAT-TTTTGAAAATA
* * * *
52725 TATATTATATATAATTTT-AAAACAATATTTTTAATATA
1 TATATAATATATAGTTTTGAAAAC-AT-TTTTGAAAATA
52763 TATATATATATATA
1 TATATA-ATATATA
52777 TATTATATAG
Statistics
Matches: 247, Mismatches: 37, Indels: 56
0.73 0.11 0.16
Matches are distributed among these distances:
32 11 0.04
33 8 0.03
34 6 0.02
35 29 0.12
36 10 0.04
37 54 0.22
38 38 0.15
39 49 0.20
40 28 0.11
41 14 0.06
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAATA
Found at i:52674 original size:35 final size:34
Alignment explanation
Indices: 52603--52693 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 34
52593 ATTTTTGAAA
**
52603 AAAACATTTTTGAAAAC-ATAT-AATATAGTTTT
1 AAAACATTTTTGAAAACTATATAAATATAGTTCG
*
52635 AAAACGTTTTTGAAAACTATATAACATATAGTTCG
1 AAAACATTTTTGAAAACTATATAA-ATATAGTTCG
*
52670 AAAACATCTTTT-AAAATTATATAA
1 AAAACAT-TTTTGAAAACTATATAA
52694 TATTGTTTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
32 16 0.32
33 4 0.08
34 1 0.02
35 25 0.50
36 4 0.08
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (34 bp):
AAAACATTTTTGAAAACTATATAAATATAGTTCG
Found at i:52732 original size:17 final size:18
Alignment explanation
Indices: 52688--52732 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 18
52678 TTTTAAAATT
*
52688 ATATAATATTGTTTTGGAA
1 ATAT-ATATTATTTTGGAA
52707 ATAT-T-TTATTTT-GAA
1 ATATATATTATTTTGGAA
52722 ATATATATTAT
1 ATATATATTAT
52733 ATATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 7 0.30
16 7 0.30
17 5 0.22
19 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
ATATATATTATTTTGGAA
Found at i:54084 original size:11 final size:11
Alignment explanation
Indices: 54070--54133 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 11
54060 TTTATTTACC
54070 TTTTTTATTATT
1 TTTTTTATTA-T
54082 TTTTTTATT-T
1 TTTTTTATTAT
*
54092 CTTTTTATT-T
1 TTTTTTATTAT
54102 CCTTTTTTATTAT
1 --TTTTTTATTAT
54115 TTTATTACTATTAT
1 TTT-TT--TATTAT
54129 TTTTT
1 TTTTT
54134 AAATATTGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
10 10 0.23
11 3 0.07
12 19 0.43
13 3 0.07
14 9 0.20
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:54099 original size:22 final size:22
Alignment explanation
Indices: 54070--54134 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
54060 TTTATTTACC
54070 TTTTTTATTATTTTTTTTATT-
1 TTTTTTATTATTTTTTTTATTA
*
54091 TCTTTTTATT-TCCTTTTTTATTA
1 T-TTTTTATTAT-TTTTTTTATTA
*
54114 TTTTATTACTATTATTTTTTA
1 TTTT-TTATTATT-TTTTTTA
54135 AATATTGGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
21 2 0.06
22 20 0.57
23 5 0.14
24 8 0.23
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTTATTATTTTTTTTATTA
Found at i:54152 original size:3 final size:3
Alignment explanation
Indices: 54144--54172 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54134 AAATATTGGC
54144 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54173 TATCTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55438 original size:3 final size:3
Alignment explanation
Indices: 55432--55492 Score: 70
Period size: 3 Copynumber: 19.0 Consensus size: 3
55422 TACAAAAAAA
55432 TAT TATT TATT TATT TAT TTAT TTAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TA-T TA-T TA-T TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT
55478 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
55493 CACATTTTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 35 0.64
4 18 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:55443 original size:4 final size:4
Alignment explanation
Indices: 55434--55458 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55424 CAAAAAAATA
55434 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
55459 ATTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:55482 original size:23 final size:24
Alignment explanation
Indices: 55433--55492 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
55423 ACAAAAAAAT
55433 ATTATTTATTTATTTATTTATTTATT
1 ATTA-TTA-TTATTTATTTATTTATT
55459 ATTATTATTA-TTATATTA-TTATT
1 ATTATTATTATTTAT-TTATTTATT
55482 ATTATTATTAT
1 ATTATTATTAT
55493 CACATTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 19 0.59
24 6 0.19
25 3 0.09
26 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTATTATTATTTATTTATTTATT
Found at i:55491 original size:20 final size:21
Alignment explanation
Indices: 55432--55492 Score: 81
Period size: 20 Copynumber: 2.9 Consensus size: 21
55422 TACAAAAAAA
55432 TATTATTTATTTATTTATT-TATT
1 TATTA-TTA-TTA-TTATTATATT
55455 TATTATTATTATTATTATA-T
1 TATTATTATTATTATTATATT
55475 TATTATTATTATTATTAT
1 TATTATTATTATTATTAT
55493 CACATTTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 24 0.65
21 5 0.14
22 3 0.08
23 5 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTATTATTATTATTATATT
Found at i:62526 original size:28 final size:27
Alignment explanation
Indices: 62460--62522 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
62450 TTGCTTTGAT
* *
62460 TATTATTATTGGTTTAGGGTTTTTAAC
1 TATTATTATTAGTTTAGGGTTATTAAC
62487 T-TTATGTTATTAGTTTAGGGATTATT-AC
1 TATTA--TTATTAGTTTAGGG-TTATTAAC
62515 TATTATTA
1 TATTATTA
62523 ATTAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
26 3 0.10
27 4 0.13
28 16 0.53
29 7 0.23
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (27 bp):
TATTATTATTAGTTTAGGGTTATTAAC
Found at i:62677 original size:25 final size:25
Alignment explanation
Indices: 62633--62697 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
62623 AAACAAGCCA
*
62633 ACAACCCAAACAACATGCCCAACTTG
1 ACAACCC-AACAACAGGCCCAACTTG
62659 ACAACCCAACAACAGGCCCAACTTG
1 ACAACCCAACAACAGGCCCAACTTG
*
62684 ACAACCCAATAACA
1 ACAACCCAACAACA
62698 ATTAGGGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
25 30 0.81
26 7 0.19
ACGTcount: A:0.45, C:0.38, G:0.08, T:0.09
Consensus pattern (25 bp):
ACAACCCAACAACAGGCCCAACTTG
Found at i:75788 original size:16 final size:16
Alignment explanation
Indices: 75767--75804 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
75757 TTTGAAGATG
75767 TTTACTGCTTTGGGCA
1 TTTACTGCTTTGGGCA
*
75783 TTTACTGCTTTGGGTA
1 TTTACTGCTTTGGGCA
75799 TTTACT
1 TTTACT
75805 CAGTTAGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (16 bp):
TTTACTGCTTTGGGCA
Found at i:76291 original size:2 final size:2
Alignment explanation
Indices: 76284--76334 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
76274 TCAATCTACA
*
76284 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76326 AT AT AT AT A
1 AT AT AT AT A
76335 ATTCATGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:76497 original size:85 final size:85
Alignment explanation
Indices: 76354--76510 Score: 269
Period size: 85 Copynumber: 1.8 Consensus size: 85
76344 ATACAACATT
* **
76354 TTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAATGCGTGTCATAAATTTATG
1 TTCATTTATGAAGGGGGCTTCAATGACACGCAATGTAAGTCATAAATGCACGTCATAAATTTATG
76419 ACACACAAATGTGTGTCATC
66 ACACACAAATGTGTGTCATC
*
76439 TTCATTTATGAAGGGGGCTTCAATGACGCGCAATGTAAGTCATAAATGCACGTCATAAATTTATG
1 TTCATTTATGAAGGGGGCTTCAATGACACGCAATGTAAGTCATAAATGCACGTCATAAATTTATG
*
76504 ACGCACA
66 ACACACA
76511 GTTGCGCGTC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (85 bp):
TTCATTTATGAAGGGGGCTTCAATGACACGCAATGTAAGTCATAAATGCACGTCATAAATTTATG
ACACACAAATGTGTGTCATC
Found at i:77410 original size:20 final size:20
Alignment explanation
Indices: 77385--77422 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
77375 ATAATCAAAT
77385 TTAATCCTTAG-ATTAATTAA
1 TTAATCC-TAGCATTAATTAA
77405 TTAATCCTAGCATTAATT
1 TTAATCCTAGCATTAATT
77423 TAATCCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAATCCTAGCATTAATTAA
Found at i:78760 original size:11 final size:11
Alignment explanation
Indices: 78744--78783 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
78734 GAATAAACCA
78744 TAATTTATTTT
1 TAATTTATTTT
*
78755 TAATTTATTGT
1 TAATTTATTTT
*
78766 TAGATTTTTTTT
1 TA-ATTTATTTT
78778 TAATTT
1 TAATTT
78784 TGTGTGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (11 bp):
TAATTTATTTT
Found at i:82467 original size:132 final size:132
Alignment explanation
Indices: 82301--82561 Score: 432
Period size: 132 Copynumber: 2.0 Consensus size: 132
82291 TATTCATCTC
82301 TGAATTGTCCTTTTATCTTTTTTATTATCGTATTTGTACTAACTAATTACTTGTTCTAATGTCAT
1 TGAATTGTCCTTTTATCTTTTTTATTATCGTATTTGTACTAACTAATTACTTGTTCTAATGTCAT
* *
82366 TTTTGCCTTTTTGCATAATATCATCATCACATGATACAAATGTGTTGGTTCATATATGAATATCA
66 TTTTGCCTTTTTGCATAATATCATCATCACATGATACAAATATGTTGATTCATATATGAATATCA
82431 CA
131 CA
* * * * *
82433 TGAATTGTCCTTTTATTTTTTTTATTATCTTATTTGTACTAACTTATTTCTTGTTCTTATGTCAT
1 TGAATTGTCCTTTTATCTTTTTTATTATCGTATTTGTACTAACTAATTACTTGTTCTAATGTCAT
* * *
82498 TTTTTCCTTTTTGCATCATATTATCATCACATGATACAAATATGTTGATTCATATATGAATATC
66 TTTTGCCTTTTTGCATAATATCATCATCACATGATACAAATATGTTGATTCATATATGAATATC
82562 TAAGTGAAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 119 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (132 bp):
TGAATTGTCCTTTTATCTTTTTTATTATCGTATTTGTACTAACTAATTACTTGTTCTAATGTCAT
TTTTGCCTTTTTGCATAATATCATCATCACATGATACAAATATGTTGATTCATATATGAATATCA
CA
Found at i:93299 original size:18 final size:18
Alignment explanation
Indices: 93276--93322 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
93266 ATGCTAAAAT
*
93276 GGTATCGATACTGAAGTC
1 GGTATCGATACTAAAGTC
*
93294 GGTATCGATACTAAAGTG
1 GGTATCGATACTAAAGTC
93312 GGTATCGATAC
1 GGTATCGATAC
93323 CATAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (18 bp):
GGTATCGATACTAAAGTC
Found at i:93953 original size:23 final size:24
Alignment explanation
Indices: 93922--94018 Score: 101
Period size: 24 Copynumber: 4.1 Consensus size: 24
93912 GAGTCGAGGG
* *
93922 TTCTATGTGGTCGTTCGGGACAAA
1 TTCTACGTGGTCATTCGGGACAAA
*
93946 -TCTATGTGGTCATTCGGGACAAA
1 TTCTACGTGGTCATTCGGGACAAA
* * *
93969 TTCTACGCGGTCCTTCGGTACAAA
1 TTCTACGTGGTCATTCGGGACAAA
93993 TTCTACGTGG-CACTTCGGTG-CAAA
1 TTCTACGTGGTCA-TTCGG-GACAAA
94017 TT
1 TT
94019 ATATGAGCAG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
23 23 0.37
24 39 0.63
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (24 bp):
TTCTACGTGGTCATTCGGGACAAA
Found at i:95178 original size:17 final size:17
Alignment explanation
Indices: 95158--95201 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
95148 ACAATTTGTC
*
95158 AAGATAAAGATTCAGCA
1 AAGATAAAGACTCAGCA
95175 AAGATAAAGACTCAGCA
1 AAGATAAAGACTCAGCA
95192 AAGATAAAGA
1 AAGATAAAGA
95202 AGTAAAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.57, C:0.11, G:0.18, T:0.14
Consensus pattern (17 bp):
AAGATAAAGACTCAGCA
Found at i:95637 original size:79 final size:79
Alignment explanation
Indices: 95537--95684 Score: 224
Period size: 79 Copynumber: 1.9 Consensus size: 79
95527 TCGATGAAGG
* * * *
95537 AGAAGAAGTTCCTAATTAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCATAGAAGGAGTTGG
1 AGAAGAAGTTCATAATGAGAAGAACATGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGTTGG
95602 ATCAACATTTCTAA
66 ATCAACATTTCTAA
** * *
95616 AGAAGAAGTTCATAATGAGAAGAACATGTTCGGCCTTTGCTTGATTCCATCACATAAGGAGTTGG
1 AGAAGAAGTTCATAATGAGAAGAACATGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGTTGG
95681 ATCA
66 ATCA
95685 GCATCACCAC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (79 bp):
AGAAGAAGTTCATAATGAGAAGAACATGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGTTGG
ATCAACATTTCTAA
Found at i:95905 original size:76 final size:77
Alignment explanation
Indices: 95770--95918 Score: 201
Period size: 76 Copynumber: 1.9 Consensus size: 77
95760 ATCCCAGAAG
** * * ** *
95770 GAGTTGGATTGGCATCTCCAAGAGAAGTTCATAATGAGAAGAACTTGTTTAAATTTTGCTTGATT
1 GAGTTGGATCAGCATCTCCAAGAGAAGTTCATAATGAGAAGAACTTGCTCAAACCTTGCTCGATT
95835 CTATCACAAAAT
66 CTATCACAAAAT
* * *
95847 GAGTTGGATCAGCATTTCCAA-AGAAGTTCATAATGATAAGAACTTGCTCAACCCTTGCTCGATT
1 GAGTTGGATCAGCATCTCCAAGAGAAGTTCATAATGAGAAGAACTTGCTCAAACCTTGCTCGATT
95911 CTATCACA
66 CTATCACA
95919 GAAGTAGTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
76 44 0.71
77 18 0.29
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (77 bp):
GAGTTGGATCAGCATCTCCAAGAGAAGTTCATAATGAGAAGAACTTGCTCAAACCTTGCTCGATT
CTATCACAAAAT
Found at i:96029 original size:79 final size:80
Alignment explanation
Indices: 95866--96017 Score: 198
Period size: 79 Copynumber: 1.9 Consensus size: 80
95856 CAGCATTTCC
* * * * * *
95866 AAAGAAGTTCATAATGATAAGAACTTGCTCAACCCTTGCTCGATTCTATCACAGAAGTAGTTAGC
1 AAAGAAGTTCATAATGATAAGAAATCGCTCAACCCTTGATCGATTCCATCACAGAAGAAGTTAGA
95931 TCAACATTCCCAAGA
66 TCAACATTCCCAAGA
* * * * *
95946 AAAGAAGTTCATAATGAT-AGAAATCGTTTAACCTTTGATCGATTCCATCATAGAAGAAGTTGGA
1 AAAGAAGTTCATAATGATAAGAAATCGCTCAACCCTTGATCGATTCCATCACAGAAGAAGTTAGA
96010 TCAACATT
66 TCAACATT
96018 TCCAGTGAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
79 43 0.70
80 18 0.30
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (80 bp):
AAAGAAGTTCATAATGATAAGAAATCGCTCAACCCTTGATCGATTCCATCACAGAAGAAGTTAGA
TCAACATTCCCAAGA
Found at i:99928 original size:22 final size:22
Alignment explanation
Indices: 99903--99947 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
99893 TCGATTTTCG
*
99903 TTTGGGTGTCGTTCTTCTTGAT
1 TTTGGGTATCGTTCTTCTTGAT
*
99925 TTTGGGTATTGTTCTTCTTGAT
1 TTTGGGTATCGTTCTTCTTGAT
99947 T
1 T
99948 GGGTTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.07, C:0.11, G:0.24, T:0.58
Consensus pattern (22 bp):
TTTGGGTATCGTTCTTCTTGAT
Found at i:100149 original size:24 final size:24
Alignment explanation
Indices: 100122--100169 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
100112 TCTGCTAGTA
100122 AGTTTGTT-ATTTTTTGGTTCTTTC
1 AGTTT-TTGATTTTTTGGTTCTTTC
* *
100146 AGTTTTTGTTTTTTTGTTTCTTTC
1 AGTTTTTGATTTTTTGGTTCTTTC
100170 CAAATTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.06, C:0.08, G:0.15, T:0.71
Consensus pattern (24 bp):
AGTTTTTGATTTTTTGGTTCTTTC
Done.