Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007125.1 Hibiscus syriacus cultivar Beakdansim tig00018616_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: 86141
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:122 original size:15 final size:15
Alignment explanation
Indices: 78--122 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
68 AACCGGTTTC
*
78 GGTTTTAAAAAAACC
1 GGTTTTAAAAAAACG
*
93 GGTTTTTAAAAAACG
1 GGTTTTAAAAAAACG
*
108 GGTTATAAAAAAACG
1 GGTTTTAAAAAAACG
123 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.27
Consensus pattern (15 bp):
GGTTTTAAAAAAACG
Found at i:529 original size:13 final size:13
Alignment explanation
Indices: 508--559 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
498 AAGTTCGATA
*
508 AATTTAAATACTT
1 AATTGAAATACTT
521 AATTGAAATACTT
1 AATTGAAATACTT
* *
534 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
548 AATTGAAATACT
1 AATTGAAATACT
560 AAATACTTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 3 0.10
13 18 0.58
14 7 0.23
15 3 0.10
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.37
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:603 original size:33 final size:33
Alignment explanation
Indices: 548--644 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
538 AACTCAACAT
* *
548 AATTGAAATAC-TAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
580 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
*
613 AATTCAAATACTT-AAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
644 A
1 A
645 TTGAAAACAA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
31 11 0.18
32 17 0.28
33 33 0.54
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTTGATA
Found at i:2961 original size:23 final size:24
Alignment explanation
Indices: 2935--2982 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2925 AGACCGGTTT
* *
2935 TTTTTTTTCCGG-ATAAAAACCGG
1 TTTTTTATCCGGTAAAAAAACCGG
2958 TTTTTTATCCGGTAAAAAAACCGG
1 TTTTTTATCCGGTAAAAAAACCGG
2982 T
1 T
2983 CTAGGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TTTTTTATCCGGTAAAAAAACCGG
Found at i:6993 original size:31 final size:31
Alignment explanation
Indices: 6968--7108 Score: 255
Period size: 31 Copynumber: 4.5 Consensus size: 31
6958 TCCATAGATT
* * *
6968 CCGAAGAACCTAGGTAAACAGTCCATATGTT
1 CCGAAGAACATAGGTAAACAGTCCGTATGTC
6999 CCGAAGAACATAGGTAAACAGTCCGTATGTC
1 CCGAAGAACATAGGTAAACAGTCCGTATGTC
7030 CCGAAGAACATAGGTAAACAGTCCGTATGTC
1 CCGAAGAACATAGGTAAACAGTCCGTATGTC
7061 CCGAAGAACATAGGTAAACAGTCCGTATGTC
1 CCGAAGAACATAGGTAAACAGTCCGTATGTC
7092 CCGAAGAACATAGGTAA
1 CCGAAGAACATAGGTAA
7109 CCCTCGACCC
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 107 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCGTATGTC
Found at i:11333 original size:31 final size:31
Alignment explanation
Indices: 11295--11443 Score: 202
Period size: 31 Copynumber: 5.0 Consensus size: 31
11285 CCCGAAGGAC
* *
11295 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
11326 CAGTCCATATGTTCCGAAGAACATAGGT-AA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
11356 CAGTCCGTATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
11387 CAGTCCGTATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
11418 CAGTCC----GTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
11444 CCCTCGACCC
Statistics
Matches: 113, Mismatches: 3, Indels: 8
0.91 0.02 0.06
Matches are distributed among these distances:
27 20 0.18
30 28 0.25
31 64 0.57
32 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:11377 original size:61 final size:62
Alignment explanation
Indices: 11308--11443 Score: 210
Period size: 61 Copynumber: 2.3 Consensus size: 62
11298 TCCATAGATT
* *
11308 CCGAAGAACCTAGGTAAACAGTCCATATGTTCCGAAGAACATAGGT-AACAGTCCGTATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCGTATGTC
*
11369 CCGAAGAACATAGGTAAACAGTCCGTATGTCCCGAAGAACATAGGTAAACAGTCC----GTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCGTATGTC
11427 CCGAAGAACATAGGTAA
1 CCGAAGAACATAGGTAA
11444 CCCTCGACCC
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
58 20 0.28
61 43 0.61
62 8 0.11
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (62 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCGTATGTC
Found at i:29374 original size:21 final size:21
Alignment explanation
Indices: 29333--29391 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
29323 ACAAGCCCGT
* *
29333 CGATTTACATG-CGAACCTTC
1 CGATTTACATGTTGAGCCTTC
29353 CGATTTACATGTTGAGCCTTC
1 CGATTTACATGTTGAGCCTTC
*
29374 CAATTTACATGTTGAGCC
1 CGATTTACATGTTGAGCC
29392 CCCATGGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 11 0.31
21 24 0.69
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (21 bp):
CGATTTACATGTTGAGCCTTC
Found at i:30595 original size:56 final size:56
Alignment explanation
Indices: 30507--30659 Score: 191
Period size: 58 Copynumber: 2.7 Consensus size: 56
30497 TGGTAAATTT
* * *
30507 TTCTATGGTTCATCATCTAGTTTTCCTAGGAAAATTTTCCATTTCT-TATTCATATA
1 TTCTATGGTTCATCAACTAGTTTTCCTGGGAAAATTTTCCATTT-TATATTCAGATA
* * *
30563 TTCTATGGATCATCAACTAGTTTTCCTGGGAAAAAAATTTCCGTTTTATATTCAGATA
1 TTCTATGGTTCATCAACTAGTTTTCCTGGG--AAAATTTTCCATTTTATATTCAGATA
* * *
30621 TTCCACGGTTCATCAACCAGTTTTCCTGGGAAAATTTTC
1 TTCTATGGTTCATCAACTAGTTTTCCTGGGAAAATTTTC
30660 GTTTTTGAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
56 35 0.42
57 1 0.01
58 47 0.57
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (56 bp):
TTCTATGGTTCATCAACTAGTTTTCCTGGGAAAATTTTCCATTTTATATTCAGATA
Found at i:33125 original size:37 final size:38
Alignment explanation
Indices: 33046--33153 Score: 120
Period size: 37 Copynumber: 3.0 Consensus size: 38
33036 AAGTATTAAA
***
33046 ATGGTTTTC-AAGTTTGGT-AAT-CAACTTTGAAAAA-
1 ATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAAT
33080 ATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAAT
1 ATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAAT
* * *
33118 A-GTTTTTCAAAGTTTGGTAGATGTTT-GTTGAAAAAT
1 ATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAAT
33154 GATAATGAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
34 9 0.14
35 9 0.14
36 12 0.19
37 33 0.52
38 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (38 bp):
ATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAAT
Found at i:33584 original size:16 final size:16
Alignment explanation
Indices: 33563--33595 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33553 TACTATTCAT
*
33563 GTGAATAGTGAAGTTC
1 GTGAATAGTGAAATTC
33579 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
33595 G
1 G
33596 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:37710 original size:37 final size:38
Alignment explanation
Indices: 37655--37738 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
37645 TGGTAACCAA
37655 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
37692 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
37729 -GTTGAAAAAT
1 CTTTGAAAAAT
37739 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:42059 original size:14 final size:14
Alignment explanation
Indices: 42042--42072 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42032 TCATACTCTA
42042 TCGATCAAGTCTTT
1 TCGATCAAGTCTTT
*
42056 TCGATCTAGTCTTT
1 TCGATCAAGTCTTT
42070 TCG
1 TCG
42073 CAGGAGATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.45
Consensus pattern (14 bp):
TCGATCAAGTCTTT
Found at i:42613 original size:3 final size:3
Alignment explanation
Indices: 42607--42711 Score: 165
Period size: 3 Copynumber: 34.7 Consensus size: 3
42597 TTTTTATCCA
* * *
42607 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT CAT TAT TAAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
*
42653 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42701 TAT TAT TAT TA
1 TAT TAT TAT TA
42712 AATATATTAA
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
3 90 0.97
4 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:42751 original size:20 final size:19
Alignment explanation
Indices: 42710--42766 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
42700 CTATTATTAT
* *
42710 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
42729 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
42749 TAAATA-A-TAAAAA-AAA
1 TAAATATATTAAAAACAAA
42765 TA
1 TA
42767 TAATTACAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 1 0.03
19 6 0.18
20 16 0.47
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:44125 original size:19 final size:19
Alignment explanation
Indices: 44089--44124 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
44079 TAATTTAGTC
44089 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
44108 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
44125 TTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:44191 original size:20 final size:21
Alignment explanation
Indices: 44154--44194 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
44144 AGAAATTTTC
**
44154 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
44175 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
44195 ATATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:55552 original size:10 final size:10
Alignment explanation
Indices: 55537--55611 Score: 62
Period size: 11 Copynumber: 7.1 Consensus size: 10
55527 ATGCTTGAAG
55537 AGAAAAAAGA
1 AGAAAAAAGA
55547 AGAAAAAAGA
1 AGAAAAAAGA
*
55557 GAAAAAAATAGA
1 -AGAAAAA-AGA
*
55569 AAATGAAAAAGA
1 AGA--AAAAAGA
*
55581 AAAAAAAGAGA
1 AGAAAAA-AGA
55592 AGAAAAAA-A
1 AGAAAAAAGA
*
55601 GGAAAAAAGA
1 AGAAAAAAGA
55611 A
1 A
55612 AAAGGGGGTC
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
9 8 0.15
10 16 0.29
11 18 0.33
12 9 0.16
13 4 0.07
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.03
Consensus pattern (10 bp):
AGAAAAAAGA
Found at i:55554 original size:12 final size:12
Alignment explanation
Indices: 55533--55615 Score: 59
Period size: 12 Copynumber: 7.1 Consensus size: 12
55523 TATTATGCTT
*
55533 GAAGAGAAAAAA
1 GAAGAAAAAAAA
55545 GAAG--AAAAAA
1 GAAGAAAAAAAA
55555 G-AGAAAAAAATA
1 GAAGAAAAAAA-A
*
55567 GAA-AATGAAAAA
1 GAAGAA-AAAAAA
*
55579 GAA-AAAAAAGA
1 GAAGAAAAAAAA
*
55590 GAAGAAAAAAAG
1 GAAGAAAAAAAA
*
55602 GAAAAAAGAAAAA
1 GAAGAAA-AAAAA
55615 G
1 G
55616 GGGGTCAAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
9 2 0.04
10 7 0.12
11 12 0.21
12 26 0.46
13 10 0.18
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
GAAGAAAAAAAA
Found at i:55583 original size:21 final size:20
Alignment explanation
Indices: 55534--55613 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 20
55524 ATTATGCTTG
*
55534 AAGAGAAAAAAGAAGAA-AAA
1 AAGAAAAAAAAGAA-AAGAAA
55554 AGAGAAAAAAATAGAAAATGAAA
1 A-AGAAAAAAA-AGAAAA-GAAA
*
55577 AAGAAAAAAAAGAGAAGAAA
1 AAGAAAAAAAAGAAAAGAAA
55597 AA-AAGGAAAAAAGAAAA
1 AAGAA--AAAAAAGAAAA
55614 AGGGGGTCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
19 2 0.04
20 7 0.14
21 25 0.49
22 13 0.25
23 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.03
Consensus pattern (20 bp):
AAGAAAAAAAAGAAAAGAAA
Found at i:55584 original size:23 final size:22
Alignment explanation
Indices: 55539--55608 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
55529 GCTTGAAGAG
55539 AAAAA-AGAAGAAAAAAGAGAAA
1 AAAAAGAGAAGAAAAAA-AGAAA
*
55561 AAAATAGA-AA-ATGAAAAAGAAA
1 AAAA-AGAGAAGA-AAAAAAGAAA
*
55583 AAAAAGAGAAGAAAAAAAGGAA
1 AAAAAGAGAAGAAAAAAAGAAA
55605 AAAA
1 AAAA
55609 GAAAAAGGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 3 0.08
22 28 0.70
23 8 0.20
24 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (22 bp):
AAAAAGAGAAGAAAAAAAGAAA
Found at i:55613 original size:36 final size:34
Alignment explanation
Indices: 55540--55615 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
55530 CTTGAAGAGA
* *
55540 AAAAAGAAGAAAAAAGAGAAAAAAATAGAAAATG
1 AAAAAGAAGAAAAAAGAGAAAAAAAAAGAAAAAG
55574 AAAAAGAA-AAAAAAGAGAAGAAAAAAAGGAAAAAAG
1 AAAAAGAAGAAAAAAGAGAA-AAAAAAA-G-AAAAAG
55610 AAAAAG
1 AAAAAG
55616 GGGGTCAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 11 0.30
34 14 0.38
35 1 0.03
36 11 0.30
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (34 bp):
AAAAAGAAGAAAAAAGAGAAAAAAAAAGAAAAAG
Found at i:56881 original size:83 final size:83
Alignment explanation
Indices: 56742--57251 Score: 801
Period size: 83 Copynumber: 6.2 Consensus size: 83
56732 AAACATTAAA
56742 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTAAC
56807 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
56825 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTAAC
56890 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
* * * *
56908 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTTAAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTAAC
56973 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
* * *
56991 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTCAGC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTAAC
57056 AGAA-CAATCATTGAATT
66 AGAACCAATCATTGAATT
* * * * *
57073 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCT-GATTATA
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTA-A
* * *
57137 TAGAATCAAGCATTGAATT
65 CAGAACCAATCATTGAATT
* * ** **
57156 TGGAAGATGAATTTTCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGGAC
1 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTAAC
57221 AGAA-CAATCATTGAATT
66 AGAACCAATCATTGAATT
57238 TGGAAGATGAATTT
1 TGGAAGATGAATTT
57252 GCTCATAGTA
Statistics
Matches: 396, Mismatches: 28, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
81 3 0.01
82 96 0.24
83 295 0.74
84 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (83 bp):
TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTAAC
AGAACCAATCATTGAATT
Found at i:57016 original size:166 final size:165
Alignment explanation
Indices: 56742--57253 Score: 855
Period size: 165 Copynumber: 3.1 Consensus size: 165
56732 AAACATTAAA
* * * *
56742 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGACCTGGTTTAAC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTTAAC
56807 AGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
* *
56872 TATATGACCTGGTTTAACAGAACCAATCATTGAATT
131 TATCTGACCTGGTTCAACAGAA-CAATCATTGAATT
56908 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTTAAC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTTAAC
56973 AGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
57038 TATCTGACCTGGTTCAGCAGAACAATCATTGAATT
131 TATCTGACCTGGTTCAACAGAACAATCATTGAATT
*
57073 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGA-TTATA
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTTA-A
* * * *
57137 TAGAATCAAGCATTGAATTTGGAAGATGAATTTTCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
65 CAGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAG
** **
57202 TTATCTGATTTGGTTGGACAGAACAATCATTGAATT
130 TTATCTGACCTGGTTCAACAGAACAATCATTGAATT
57238 TGGAAGATGAATTTGC
1 TGGAAGATGAATTTGC
57254 TCATAGTAAA
Statistics
Matches: 327, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
164 3 0.01
165 179 0.55
166 145 0.44
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (165 bp):
TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTTAAC
AGAACCAATCATTGAATTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGACCTGGTTCAACAGAACAATCATTGAATT
Found at i:58174 original size:113 final size:113
Alignment explanation
Indices: 57876--58643 Score: 1408
Period size: 113 Copynumber: 6.9 Consensus size: 113
57866 TCAAATCCAC
57876 TTGATGGATCATTCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-TCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
57941 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-TTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
57989 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
58054 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
58102 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
58167 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
58215 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
58280 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
58328 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
58393 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCA-
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
58440 -TGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
58504 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAC
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* * * *
58552 TTGAT---T-ATCTTTTCCGGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
58612 AGTTCATAATAAGAAGAACTTGTTCAACTTTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTT
58644 GGCATAATTC
Statistics
Matches: 646, Mismatches: 6, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
108 69 0.11
109 12 0.02
110 1 0.00
111 110 0.17
112 88 0.14
113 366 0.57
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (113 bp):
TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
Found at i:58968 original size:3 final size:3
Alignment explanation
Indices: 58962--59052 Score: 128
Period size: 3 Copynumber: 29.7 Consensus size: 3
58952 TTTTTATCCA
* * *
58962 TAT TAT TAT TAT TAT TAT TAC TAT TAT CAT TAT TAAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
*
59008 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA
59053 AATATATTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
3 72 0.92
4 6 0.08
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:59061 original size:37 final size:36
Alignment explanation
Indices: 58972--59052 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 36
58962 TATTATTATT
58972 ATTATTATTACTATTATCATTATTAATTATTACTATT
1 ATTATTATTACTATTATCATTA-TAATTATTACTATT
* * *
59009 ATTATTATTATTATTATTATTATTATTTATTACTATT
1 ATTATTATTACTATTATCATTA-TAATTATTACTATT
59046 ATTATTA
1 ATTATTA
59053 AATATATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (36 bp):
ATTATTATTACTATTATCATTATAATTATTACTATT
Found at i:59092 original size:20 final size:19
Alignment explanation
Indices: 59051--59095 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
59041 CTATTATTAT
* *
59051 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
59070 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
59090 TAAATA
1 TAAATA
59096 ATAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:60467 original size:19 final size:19
Alignment explanation
Indices: 60431--60466 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
60421 TAATTTAGTC
60431 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
60450 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
60467 TTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:60533 original size:20 final size:21
Alignment explanation
Indices: 60496--60536 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
60486 AGAATTTTTC
**
60496 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
60517 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
60537 ATATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:61470 original size:2 final size:2
Alignment explanation
Indices: 61465--61504 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
61455 TTTAATGTTA
61465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61505 TTGGAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68244 original size:2 final size:2
Alignment explanation
Indices: 68233--68264 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
68223 TGATTGTGTT
68233 TA TA -A 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 T
68265 TAATGTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:68843 original size:25 final size:26
Alignment explanation
Indices: 68797--68852 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
68787 TGAATATCTT
68797 AATAATTGCTTATATTTT-AAAATTA
1 AATAATTGCTTATATTTTAAAAATTA
*
68822 AATAATTTCTTA-ATTTTAAAAAAATTA
1 AATAATTGCTTATATTTT--AAAAATTA
68849 AATA
1 AATA
68853 GGTCCTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 11 0.41
27 11 0.41
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (26 bp):
AATAATTGCTTATATTTTAAAAATTA
Found at i:69351 original size:20 final size:20
Alignment explanation
Indices: 69326--69500 Score: 129
Period size: 20 Copynumber: 8.6 Consensus size: 20
69316 GATTCGGAAC
*
69326 GCGATTCTGACTATCGCATT
1 GCGATTCTGACTATCGCAAT
** * **
69346 GCGATT-TTCCAAATTCGCGTT
1 GCGATTCTGAC-TA-TCGCAAT
69367 GCGATTTTCTGACTATCGCAAT
1 GCGA-TT-CTGACTATCGCAAT
* * * *
69389 CCGAATATGTA-AATCGCAAT
1 GCGATTCTG-ACTATCGCAAT
* *
69409 GCAATTATGACTATCGCAAT
1 GCGATTCTGACTATCGCAAT
* *
69429 GCGATTCTGACTGTCGCAAC
1 GCGATTCTGACTATCGCAAT
*
69449 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAT
* *
69469 GAGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAT
*
69489 GCGATTTTGACT
1 GCGATTCTGACT
69501 GTTGCAACAC
Statistics
Matches: 123, Mismatches: 25, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.02
20 95 0.77
21 12 0.10
22 10 0.08
23 1 0.01
24 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAT
Found at i:69508 original size:20 final size:20
Alignment explanation
Indices: 69401--69500 Score: 137
Period size: 20 Copynumber: 5.0 Consensus size: 20
69391 GAATATGTAA
* * *
69401 ATCGCAATGCAATTATGACT
1 ATCGCAACGCGATTCTGACT
*
69421 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
69441 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
69461 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
69481 ATCGCAACGCGATTTTGACT
1 ATCGCAACGCGATTCTGACT
69501 GTTGCAACAC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:70366 original size:24 final size:23
Alignment explanation
Indices: 70329--70380 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
70319 GGTATTCGAA
*
70329 ATTTGATCTTGGTCAATACCCGG
1 ATTTTATCTTGGTCAATACCCGG
*
70352 ACTTTTATCTTGGTCAATACTCGG
1 A-TTTTATCTTGGTCAATACCCGG
70376 ATTTT
1 ATTTT
70381 GATGATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (23 bp):
ATTTTATCTTGGTCAATACCCGG
Found at i:72912 original size:140 final size:140
Alignment explanation
Indices: 72660--72929 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
72650 AAACGTTGTA
*
72660 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
72725 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
72790 TATGTGTATT
131 TATGTGTATT
72800 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
72865 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
72930 CGCAACGCGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:72925 original size:20 final size:20
Alignment explanation
Indices: 72900--73119 Score: 196
Period size: 20 Copynumber: 11.7 Consensus size: 20
72890 TTACACATTC
*
72900 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
72920 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
72940 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
72959 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
72974 ATTTAACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
72994 ATATGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
73014 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
73034 ATTTGATTATTGCAACGGGT
1 ATTTGACTATCGCAACGCGA
*
73054 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
73074 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
73088 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
73108 A-TTGACTTTCGC
1 ATTTGACTATCGC
73120 GTTGCGATTT
Statistics
Matches: 160, Mismatches: 28, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
14 19 0.12
15 3 0.02
16 1 0.01
18 1 0.01
19 12 0.08
20 124 0.77
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:73138 original size:20 final size:21
Alignment explanation
Indices: 73109--73164 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
73099 GCAACGCGAA
73109 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
73129 TTG-GCTTTCGCATTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
73149 TTGAG-TTTAGCGTTGC
1 TTGAGCTTTCGCGTTGC
73165 AAAAGTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.11, C:0.18, G:0.27, T:0.45
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:73325 original size:14 final size:14
Alignment explanation
Indices: 73288--73326 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
73278 TTAATATTAA
*
73288 ACAAATCAACTTTT
1 ACAAATCAATTTTT
73302 ACAAATCAATTTTT
1 ACAAATCAATTTTT
*
73316 ATAAATCAATT
1 ACAAATCAATT
73327 AAACAAGCAA
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:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:74766 original size:21 final size:21
Alignment explanation
Indices: 74736--74837 Score: 89
Period size: 21 Copynumber: 4.9 Consensus size: 21
74726 TGGGAGGGAA
* *
74736 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGATGACAGGGGC
* ** *
74757 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGATGACAGGGGC
** *
74778 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGACAGGGGC
**
74799 CTCTTGAACGAT-AGGGGAGGC
1 CTCTTGAACGATGACAGG-GGC
74820 CTCTTGAACGATGACAGG
1 CTCTTGAACGATGACAGG
74838 TGAGTCGGCC
Statistics
Matches: 61, Mismatches: 18, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 55 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGACAGGGGC
Found at i:74791 original size:42 final size:42
Alignment explanation
Indices: 74726--74808 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
74716 TCTAGAATGT
*
74726 TGGGAGGGAACTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGGAACTCTTCAACGATGACAGGGGCCTCTTGAACGG
* * ** *
74768 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACG
1 TGGGAGGGAACTCTTCAACGATGACAGGGGCCTCTTGAACG
74809 ATAGGGGAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.22
Consensus pattern (42 bp):
TGGGAGGGAACTCTTCAACGATGACAGGGGCCTCTTGAACGG
Found at i:74824 original size:42 final size:42
Alignment explanation
Indices: 74745--74837 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
74735 ACTCTTCAAC
* * *
74745 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
74787 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
74829 GATGACAGG
1 GATGACAGG
74838 TGAGTCGGCC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:75610 original size:18 final size:18
Alignment explanation
Indices: 75587--75636 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
75577 TTTACTAAGC
75587 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
75605 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
75623 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
75637 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:77480 original size:20 final size:20
Alignment explanation
Indices: 77372--77483 Score: 125
Period size: 20 Copynumber: 5.6 Consensus size: 20
77362 GAAACTTAAA
** **
77372 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAATTTGACT
**
77392 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAATTTGACT
* *
77412 ATCGCAACGCGAATTTAACT
1 ATCGCAACACGAATTTGACT
* *
77432 ATCGCAACGCAAATTTGACT
1 ATCGCAACACGAATTTGACT
77452 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAATTTGACT
*
77472 ATTGCAACACGA
1 ATCGCAACACGA
77484 GAATCGCAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (20 bp):
ATCGCAACACGAATTTGACT
Found at i:78139 original size:20 final size:20
Alignment explanation
Indices: 78114--78171 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
78104 GCGCTTTGAA
78114 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAT
*
78134 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAT
*
78154 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
78172 GGAAAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAT
Found at i:80969 original size:18 final size:18
Alignment explanation
Indices: 80946--80982 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
80936 TGAGTAAACC
80946 TAGACACAGAAAATAAAT
1 TAGACACAGAAAATAAAT
* *
80964 TAGACATATAAAATAAAT
1 TAGACACAGAAAATAAAT
80982 T
1 T
80983 TTGAGTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (18 bp):
TAGACACAGAAAATAAAT
Found at i:84416 original size:48 final size:48
Alignment explanation
Indices: 84339--85060 Score: 1058
Period size: 48 Copynumber: 15.3 Consensus size: 48
84329 CCTCCTGTCT
*
84339 ATGAACCTCC-AAGAAACCTCCGGTGTATGAACCTAAGCCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
* *
84386 ATGAACCTCCGAAGAAACCTCCGGTCTATGAACCTAAGCCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
* *
84434 ATGAACCTCCGAAGAGACCTCCAATGTATGAACCTAAGCCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
*
84482 ATGAACCTCCAAAGAAACCTCCA--GTATGAACCTAAGCCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
* *
84528 ATGAACCTCCGAAGAAACCTCCA-TCTATGAACCTAAGCCGCCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
*
84575 ATGAACCTCCAAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
* * *
84623 ATGAA-CTCCGAAAAAACCTCCAGTCTATGAACCTAAGCCGCCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
** *
84670 ATGAATATCCGAAGAGACCTCCAGTGTATGAACCTAAGCCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
* * * *
84718 ATGAACCTCCAAAGAGATCTCCAATGTATGAACCTAAGCCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
*
84766 ATGAACCTCC-AAGAAACCTCCGGTGTATGAACCTAAGCCACC-GTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
84812 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAG-C-CCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
* * * *
84858 ATG-ACATCCGAAGAGACCTCTAGTATATGAACCTAAGCCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
** *
84905 ATGAACCTCTAAAG-AACCTCCAGTGTATGAACCTAAACCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
* *
84952 ATGAA-CTCCAAAG-AACCTCCAGTCTATGAACCTAAGCCACCAGTTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
* *
84998 ATGAACCTCCAAAGAAACCTCCAGTGTATGAACCTAAACCACCA-TTC
1 ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
*
85045 ATGAACCTCCTAAGAA
1 ATGAACCTCCGAAGAA
85061 CTAAGCCCTA
Statistics
Matches: 615, Mismatches: 49, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
45 32 0.05
46 111 0.18
47 220 0.36
48 252 0.41
ACGTcount: A:0.34, C:0.31, G:0.15, T:0.20
Consensus pattern (48 bp):
ATGAACCTCCGAAGAAACCTCCAGTGTATGAACCTAAGCCACCAGTTC
Found at i:85473 original size:93 final size:94
Alignment explanation
Indices: 85328--85498 Score: 265
Period size: 93 Copynumber: 1.8 Consensus size: 94
85318 GACTGTTACA
* *
85328 ATGTCCAATCTTTGTACAACCCAACTTGTTCATGCAATCATGAATATAAAATAAATCTATAAAGT
1 ATGTCCAATCTTTGCACAACCCAACTTGTTCATGCAATAATGAATATAAAATAAATCTATAAAGT
85393 GG-TTCATGATAACAATTAGATCGTTTAT
66 GGTTTCATGATAACAATTAGATCGTTTAT
* * * *
85421 ATGTCCAATCTTTGCGCAACCCAACTTATTTCATGCAATAATGAATAT-AAATAAATCTTTCAAG
1 ATGTCCAATCTTTGCACAACCCAACTT-GTTCATGCAATAATGAATATAAAATAAATCTATAAAG
85485 TGGTTTCATGATAA
65 TGGTTTCATGATAA
85499 TAGAGAATAT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
93 42 0.60
94 28 0.40
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (94 bp):
ATGTCCAATCTTTGCACAACCCAACTTGTTCATGCAATAATGAATATAAAATAAATCTATAAAGT
GGTTTCATGATAACAATTAGATCGTTTAT
Found at i:85741 original size:76 final size:78
Alignment explanation
Indices: 85649--85801 Score: 265
Period size: 76 Copynumber: 2.0 Consensus size: 78
85639 ATGGGAATTT
* *
85649 TTGTAAAATTACAGAATTATACAAGCACCTATT-AACGTATTCT-AAAAGAAAATAGTCCATGAT
1 TTGTAAAATTACAGAATTATACAAGCACCAATTAAACGTATTCTAAAAAGAAAATAGTCCACGAT
85712 TTCTAGAACATGC
66 TTCTAGAACATGC
*
85725 TTGTAAAATTACAGAATTATACAAGCACCAATTAAAGGTATTCTAAAAAGAAAATAGTCCACGAT
1 TTGTAAAATTACAGAATTATACAAGCACCAATTAAACGTATTCTAAAAAGAAAATAGTCCACGAT
85790 TTCTAGAACATG
66 TTCTAGAACATG
85802 AAAACGTTAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
76 32 0.44
77 9 0.12
78 31 0.43
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (78 bp):
TTGTAAAATTACAGAATTATACAAGCACCAATTAAACGTATTCTAAAAAGAAAATAGTCCACGAT
TTCTAGAACATGC
Done.