Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006391.1 Hibiscus syriacus cultivar Beakdansim tig00015396_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: 144483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4396 original size:12 final size:11
Alignment explanation
Indices: 4381--4436 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
4371 AACCATCTAA
4381 AACAATGACAAT
1 AACAAT-ACAAT
4393 AACAATACAAT
1 AACAATACAAT
*
4404 AAACCAT-CGAA-
1 -AACAATAC-AAT
4415 AACAATGACAAT
1 AACAAT-ACAAT
4427 AACAATACAA
1 AACAATACAA
4437 AAGTATCCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
10 5 0.14
11 12 0.32
12 20 0.54
ACGTcount: A:0.61, C:0.20, G:0.05, T:0.14
Consensus pattern (11 bp):
AACAATACAAT
Found at i:4407 original size:34 final size:34
Alignment explanation
Indices: 4367--4436 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
4357 ACCCATTTCT
*
4367 AATAAACCATCTAAAACAATGACAATAACAATAC
1 AATAAACCATCGAAAACAATGACAATAACAATAC
4401 AATAAACCATCGAAAACAATGACAATAACAATAC
1 AATAAACCATCGAAAACAATGACAATAACAATAC
4435 AA
1 AA
4437 AAGTATCCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.60, C:0.20, G:0.04, T:0.16
Consensus pattern (34 bp):
AATAAACCATCGAAAACAATGACAATAACAATAC
Found at i:4436 original size:17 final size:17
Alignment explanation
Indices: 4382--4436 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
4372 ACCATCTAAA
4382 ACAATGACAATAACAAT
1 ACAATGACAATAACAAT
* * *
4399 ACAAT-A-AACCATCGAAA
1 ACAATGACAA-TAAC-AAT
4416 ACAATGACAATAACAAT
1 ACAATGACAATAACAAT
4433 ACAA
1 ACAA
4437 AAGTATCCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
15 2 0.07
16 3 0.11
17 18 0.64
18 3 0.11
19 2 0.07
ACGTcount: A:0.60, C:0.20, G:0.05, T:0.15
Consensus pattern (17 bp):
ACAATGACAATAACAAT
Found at i:5237 original size:9 final size:9
Alignment explanation
Indices: 5223--5251 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5213 CGTTATAATT
5223 AAAAAAATC
1 AAAAAAATC
5232 AAAAAAATC
1 AAAAAAATC
5241 AAAAAAATC
1 AAAAAAATC
5250 AA
1 AA
5252 TGATATACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:11457 original size:2 final size:2
Alignment explanation
Indices: 11450--11479 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11440 ATAAGAGCAT
11450 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
11480 GAGGCAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12641 original size:20 final size:20
Alignment explanation
Indices: 12616--12667 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
12606 TAGTTGAAAA
12616 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
12636 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
12656 TTGCGTTGCGAT
1 TCGCGTTGCGAT
12668 AGTCTACAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:12713 original size:19 final size:21
Alignment explanation
Indices: 12659--12773 Score: 103
Period size: 22 Copynumber: 5.6 Consensus size: 21
12649 TTCCATTTTG
12659 CGTTGCGATAGTCTACAATGT
1 CGTTGCGATAGTCTACAATGT
**
12680 CGTTGCGATTTTCTA-AAT-T
1 CGTTGCGATAGTCTACAATGT
*
12699 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACA-ATGT
* * *
12721 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACA-ATGT
** *
12743 CGTTGCGATTTTCCA-AAT-T
1 CGTTGCGATAGTCTACAATGT
12762 CGTTGCGATAGT
1 CGTTGCGATAGT
12774 TTAAAAAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
19 25 0.33
20 5 0.07
21 15 0.20
22 31 0.41
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAATGT
Found at i:12728 original size:22 final size:22
Alignment explanation
Indices: 12659--12751 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 22
12649 TTCCATTTTG
*
12659 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
** *
12680 CGTTGCGATTTTCTA-A-AT-T
1 CGTTGCGATAGTCTACAGTTGT
12699 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
12721 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
12743 CGTTGCGAT
1 CGTTGCGAT
12752 TTTCCAAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
19 14 0.23
20 4 0.07
21 14 0.23
22 28 0.47
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:12728 original size:41 final size:41
Alignment explanation
Indices: 12639--12715 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
12629 TTCCATTTCG
**
12639 CGTTGCGATTTTCCATTTTGCGTTGCGATAGTCTACAATGT
1 CGTTGCGATTTTCCAAATTGCGTTGCGATAGTCTACAATGT
*
12680 CGTTGCGATTTTCTAAATT-CGTTGCGATAGTCTACA
1 CGTTGCGATTTTCCAAATTGCGTTGCGATAGTCTACA
12716 GTTGTTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 17 0.52
41 16 0.48
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTGCGTTGCGATAGTCTACAATGT
Found at i:12862 original size:6 final size:6
Alignment explanation
Indices: 12851--12941 Score: 182
Period size: 6 Copynumber: 15.2 Consensus size: 6
12841 GACACGTATT
12851 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
12899 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
12942 GACGGACGGC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:13476 original size:6 final size:5
Alignment explanation
Indices: 13430--13475 Score: 65
Period size: 5 Copynumber: 8.6 Consensus size: 5
13420 CCGTCTCGTC
13430 TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
13476 TACGTGTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 23 0.57
6 17 0.43
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:13632 original size:20 final size:20
Alignment explanation
Indices: 13607--13698 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
13597 ACTGTAGACT
13607 ATCGCAACGCGAATTGGAAA
1 ATCGCAACGCGAATTGGAAA
* ** *
13627 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTGGAA-A
*
13648 ATCGCAACGCGAACTGG-AA
1 ATCGCAACGCGAATTGGAAA
**
13667 ATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAATTGGAAA
13687 ATCGCAACGCGA
1 ATCGCAACGCGA
13699 TTTTCAACTA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
19 15 0.25
20 31 0.53
21 13 0.22
ACGTcount: A:0.37, C:0.26, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAATTGGAAA
Found at i:13649 original size:41 final size:41
Alignment explanation
Indices: 13573--13741 Score: 146
Period size: 41 Copynumber: 4.1 Consensus size: 41
13563 ATTTTCGCAA
* * *
13573 CGAATTTGGAAAATCGCAACGACAACTGT-AGACTATCGCAACG
1 CGAA-TTGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACG
13616 CGAATTGGAAAATCGCAACGCGATTTTCAACTATCGCAACG
1 CGAATTGGAAAATCGCAACGCGATTTTCAACTATCGCAACG
* ***** *
13657 CGAACTGG-AAATCGCAACGCGAAACGGAA-AATCGCAACG
1 CGAATTGGAAAATCGCAACGCGATTTTCAACTATCGCAACG
* ** * *
13696 CGATTTTCAACTATCGCAACGCGATTTTCAATTATCGCAACG
1 CGAATTGGAA-AATCGCAACGCGATTTTCAACTATCGCAACG
13738 CGAA
1 CGAA
13742 ATGCAACGCG
Statistics
Matches: 100, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
39 13 0.13
40 17 0.17
41 37 0.37
42 29 0.29
43 4 0.04
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (41 bp):
CGAATTGGAAAATCGCAACGCGATTTTCAACTATCGCAACG
Found at i:13653 original size:21 final size:20
Alignment explanation
Indices: 13606--13747 Score: 115
Period size: 21 Copynumber: 7.0 Consensus size: 20
13596 AACTGTAGAC
*
13606 TATCGCAACGCGAATTGGAA
1 TATCGCAACGCGAATTGCAA
* * *
13626 AATCGCAACGCGATTTTCAA
1 TATCGCAACGCGAATTGCAA
* *
13646 CTATCGCAACGCGAACTGGAA
1 -TATCGCAACGCGAATTGCAA
** *
13667 -ATCGCAACGCGAAACGGAA
1 TATCGCAACGCGAATTGCAA
* * *
13686 AATCGCAACGCGATTTTCAA
1 TATCGCAACGCGAATTGCAA
* *
13706 CTATCGCAACGCGATTTTCAA
1 -TATCGCAACGCGAATTGCAA
*
13727 TTATCGCAACGCGAAATGCAA
1 -TATCGCAACGCGAATTGCAA
13748 CGCGAATTTG
Statistics
Matches: 98, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
19 17 0.17
20 30 0.31
21 51 0.52
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
TATCGCAACGCGAATTGCAA
Found at i:13686 original size:60 final size:60
Alignment explanation
Indices: 13607--13719 Score: 208
Period size: 60 Copynumber: 1.9 Consensus size: 60
13597 ACTGTAGACT
**
13607 ATCGCAACGCGAATTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAA
1 ATCGCAACGCGAAACGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAA
13667 ATCGCAACGCGAAACGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGA
1 ATCGCAACGCGAAACGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGA
13720 TTTTCAATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (60 bp):
ATCGCAACGCGAAACGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAA
Found at i:15196 original size:24 final size:25
Alignment explanation
Indices: 15177--15226 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
15167 TTTTTAACGG
*
15177 GGTGAATTTTTAAAATTTTAGGAGGA
1 GGTGAATTTATAAAATTTTA-GAGGA
*
15203 GGTGAATTTATAAAATTCTAGAGG
1 GGTGAATTTATAAAATTTTAGAGG
15227 GATAAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (25 bp):
GGTGAATTTATAAAATTTTAGAGGA
Found at i:16439 original size:20 final size:20
Alignment explanation
Indices: 16397--16439 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
16387 AAACACAACT
** *
16397 ATTCGCAACGCGAATTTGGA
1 ATTCGCAACGCGAACATGCA
*
16417 ATTCGCAACTCGAACATGCA
1 ATTCGCAACGCGAACATGCA
16437 ATT
1 ATT
16440 AGAACATGGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTCGCAACGCGAACATGCA
Found at i:16507 original size:93 final size:93
Alignment explanation
Indices: 16347--16526 Score: 308
Period size: 93 Copynumber: 1.9 Consensus size: 93
16337 TTCGCAACTC
*
16347 GAACATAGAAATTTTCGCAACGCTAATGACTGATATAGGTAAACACAACTATTCGCAACGCGAAT
1 GAACATAGAAATTTTCGCAACGCTAATGACCGATATAGGTAAACACAACTATTCGCAACGCGAAT
16412 TTGGAATTCGCAACTCGAACATGCAATTA
66 TT-GAATTCGCAACTCGAACATGCAATTA
* *
16441 GAACATGGAAA-TTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAACGCGAAT
1 GAACATAGAAATTTTCGCAACGCTAATGACCGATATAGGTAAACACAACTATTCGCAACGCGAAT
*
16505 TTGAATTCGCAATTCGAACATG
66 TTGAATTCGCAACTCGAACATG
16527 AAAATTTTCG
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 19 0.23
93 53 0.65
94 10 0.12
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (93 bp):
GAACATAGAAATTTTCGCAACGCTAATGACCGATATAGGTAAACACAACTATTCGCAACGCGAAT
TTGAATTCGCAACTCGAACATGCAATTA
Found at i:17108 original size:20 final size:20
Alignment explanation
Indices: 17083--17120 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
17073 TTAGCGTTGT
17083 GAAATTCGAGTTGCGAATTC
1 GAAATTCGAGTTGCGAATTC
17103 GAAATTCGAGTTGCGAAT
1 GAAATTCGAGTTGCGAAT
17121 AGCTGTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (20 bp):
GAAATTCGAGTTGCGAATTC
Found at i:17128 original size:72 final size:72
Alignment explanation
Indices: 17007--17158 Score: 232
Period size: 72 Copynumber: 2.1 Consensus size: 72
16997 CGAATTCGAT
* * * *
17007 TTGCGAAATTCGCGTTGCGAAAACGAAATTCGTGTTGTGAATAGTTGTGTTTACATATATCGGTA
1 TTGCGAAATTCGAGTTGCGAAAACGAAATTCGAGTTGCGAATAGCTGTGTTTACATATATCGGTA
17072 ATTAGCG
66 ATTAGCG
* ** *
17079 TTGTGAAATTCGAGTTGCGAATTCGAAATTCGAGTTGCGAATAGCTGTGTTTACCTATATCGGTA
1 TTGCGAAATTCGAGTTGCGAAAACGAAATTCGAGTTGCGAATAGCTGTGTTTACATATATCGGTA
17144 ATTAGCG
66 ATTAGCG
17151 TTGCGAAA
1 TTGCGAAA
17159 ATTTCAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (72 bp):
TTGCGAAATTCGAGTTGCGAAAACGAAATTCGAGTTGCGAATAGCTGTGTTTACATATATCGGTA
ATTAGCG
Found at i:19234 original size:20 final size:19
Alignment explanation
Indices: 19193--19229 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19183 TATTTAGATT
*
19193 TTAAAAAATATTATTTTTA
1 TTAAAAAACATTATTTTTA
19212 TTAAAAAACATT-TTTTTA
1 TTAAAAAACATTATTTTTA
19230 AATTATCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAAAACATTATTTTTA
Found at i:26523 original size:23 final size:24
Alignment explanation
Indices: 26478--26523 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
26468 AAATTTATGT
*
26478 TTTTTTAATATATATATAATTTTA
1 TTTTTTAATATATACATAATTTTA
* *
26502 TTTTTTAAT-TTTACATATTTTT
1 TTTTTTAATATATACATAATTTT
26524 TAAATTATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTTTAATATATACATAATTTTA
Found at i:26535 original size:17 final size:17
Alignment explanation
Indices: 26500--26537 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
26490 TATATAATTT
*
26500 TATTTTTTAATTTTACA
1 TATTTTTTAATTATACA
26517 TATTTTTTAAATTAT-CA
1 TATTTTTT-AATTATACA
26534 TATT
1 TATT
26538 ATGACACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTTTAATTATACA
Found at i:27807 original size:23 final size:22
Alignment explanation
Indices: 27768--27845 Score: 57
Period size: 23 Copynumber: 3.4 Consensus size: 22
27758 TAAACTGTTA
* * *
27768 AATTATAAAGTACTAAACATAT
1 AATTATAAATTATTAAAAATAT
*
27790 AATTATAAATTAGTTAAAAATTT
1 AATTATAAATTA-TTAAAAATAT
* * *
27813 AAATATAATTTAATTAAATATAGT
1 AATTATAAATT-ATTAAAAATA-T
*
27837 ATTTATAAA
1 AATTATAAA
27846 ACATTAGTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
22 11 0.26
23 23 0.55
24 8 0.19
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTATAAATTATTAAAAATAT
Found at i:28140 original size:16 final size:16
Alignment explanation
Indices: 28119--28156 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28109 ATAAAAACTA
28119 ATATTTT-ATAAATATT
1 ATATTTTAATAAA-ATT
*
28135 ATATTTTAATTAAATT
1 ATATTTTAATAAAATT
28151 ATATTT
1 ATATTT
28157 AAATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTAATAAAATT
Found at i:28161 original size:16 final size:18
Alignment explanation
Indices: 28132--28171 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
28122 TTTTATAAAT
*
28132 ATTATATTTTAA-TTA-A
1 ATTATATTTAAATTTATA
28148 ATTATATTTAAATTTATA
1 ATTATATTTAAATTTATA
28166 ATTATA
1 ATTATA
28172 CATTGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 3 0.14
18 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATATTTAAATTTATA
Found at i:28595 original size:15 final size:15
Alignment explanation
Indices: 28572--28612 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
28562 TTCGTAAAAT
*
28572 AAATTATATTTTTTA
1 AAATAATATTTTTTA
28587 AAATAATATTTTTTA
1 AAATAATATTTTTTA
28602 AAA-AATATTTT
1 AAATAATATTTT
28613 ACGATGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AAATAATATTTTTTA
Found at i:28767 original size:20 final size:17
Alignment explanation
Indices: 28742--28781 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
28732 TATTTTTAAA
28742 TATTAAAATAATTTATTTAT
1 TATTAAAAT--TTTATTT-T
28762 TATTAAAATTTTATTTT
1 TATTAAAATTTTATTTT
28779 TAT
1 TAT
28782 AATTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
20 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTAAAATTTTATTTT
Found at i:28776 original size:14 final size:14
Alignment explanation
Indices: 28757--28797 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28747 AAATAATTTA
28757 TTTATTATTAAAAT
1 TTTATTATTAAAAT
* *
28771 TTTATTTTTATAAT
1 TTTATTATTAAAAT
*
28785 TTTATTAATAAAA
1 TTTATTATTAAAA
28798 ATATTAATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATTATTAAAAT
Found at i:28788 original size:49 final size:49
Alignment explanation
Indices: 28687--28781 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 49
28677 ATTACAAATA
28687 TTAAATATAATAAATAATATTATTTATCATAAAATTTAATATTATTATTT
1 TTAAATATAATAAATAATATTATTTATCATAAAATTT-ATATTATTATTT
* * *
28737 TTAAATATTA-AAATAAT-TTATTTATTATTAAAATTT-TATTTTTAT
1 TTAAATATAATAAATAATATTATTTATCA-TAAAATTTATATTATTAT
28782 AATTTTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 8 0.20
48 9 0.22
49 15 0.37
50 9 0.22
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (49 bp):
TTAAATATAATAAATAATATTATTTATCATAAAATTTATATTATTATTT
Found at i:28799 original size:49 final size:47
Alignment explanation
Indices: 28693--28800 Score: 110
Period size: 49 Copynumber: 2.2 Consensus size: 47
28683 AATATTAAAT
*
28693 ATAATAAATAATATTATTTATCATAAAATTTAATATTATTATTTTTAA
1 ATAA-AAATAATATTATTTATCATAAAATTTAATATTATAATTTTTAA
* * * *
28741 ATATTAAAATAAT-TTATTTATTATTAAAATTTTATTTTTATAATTTTATTA
1 ATA--AAAATAATATTATTTATCA-TAAAA-TTTAATATTATAATTTT-TAA
28792 ATAAAAATA
1 ATAAAAATA
28801 TTAATATTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
48 12 0.24
49 18 0.36
50 15 0.30
51 5 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (47 bp):
ATAAAAATAATATTATTTATCATAAAATTTAATATTATAATTTTTAA
Found at i:28921 original size:23 final size:22
Alignment explanation
Indices: 28873--28940 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 22
28863 ATAGTGTTAT
**
28873 ATATTTTAAAATATTAATTAGT
1 ATATTTTAAAATATTAATTAAA
* *
28895 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAA-ATATTAATTAAA
* *
28918 ATATTATTAGATTATTATATTAA
1 ATATT-TTAAAATATTA-ATTAA
28941 TATTAAATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 10 0.29
23 16 0.46
24 9 0.26
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTTTAAAATATTAATTAAA
Found at i:28934 original size:19 final size:19
Alignment explanation
Indices: 28910--28984 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
28900 TTAAATATCT
*
28910 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
28929 TTATTATATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
28948 TATATAAAAAATATTATT-CA
1 T-TAT-TAAAATATTATTAAA
28968 TTATTAATAATATTATT
1 TTATTAA-AATATTATT
28985 TCTATGAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
18 2 0.05
19 28 0.65
20 5 0.12
21 8 0.19
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:29077 original size:23 final size:23
Alignment explanation
Indices: 29047--29097 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
29037 TTAAAATAAA
29047 AATATAATAT-CTTATATTATTAT
1 AATATAAT-TGCTTATATTATTAT
* *
29070 AATATAATTGGTTATTTTATTAT
1 AATATAATTGCTTATATTATTAT
29093 AATAT
1 AATAT
29098 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
AATATAATTGCTTATATTATTAT
Found at i:29115 original size:22 final size:23
Alignment explanation
Indices: 29087--29133 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
29077 TTGGTTATTT
29087 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
29109 TATTATACTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
29132 TA
1 TA
29134 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:29147 original size:21 final size:23
Alignment explanation
Indices: 29123--29166 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
29113 ATACTATTAG
29123 AAATA-TTAATAAAT-ATATTTT
1 AAATATTTAATAAATAATATTTT
*
29144 AAATATTTAATAATTAATATTTT
1 AAATATTTAATAAATAATATTTT
29167 GATTAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATATTTAATAAATAATATTTT
Found at i:29205 original size:23 final size:24
Alignment explanation
Indices: 29155--29205 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
29145 AATATTTAAT
29155 AATT-AATATTTTGATTAAAATGA
1 AATTAAATATTTTGATTAAAATGA
* * *
29178 TATTAAATATTTT-ATTAATATTA
1 AATTAAATATTTTGATTAAAATGA
29201 AATTA
1 AATTA
29206 TAAAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AATTAAATATTTTGATTAAAATGA
Found at i:36835 original size:2 final size:2
Alignment explanation
Indices: 36830--36890 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
36820 ACCTTTTTTT
36830 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
36872 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
36891 GAAAATATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44106 original size:15 final size:16
Alignment explanation
Indices: 44088--44120 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
44078 GTGGCAGATC
44088 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
44103 AAAATCCAGAACGGGA
1 AAAATCCAGAACGGGA
44119 AA
1 AA
44121 GAAAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.52, C:0.18, G:0.24, T:0.06
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:48352 original size:36 final size:36
Alignment explanation
Indices: 48305--48375 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
48295 GTAAACGAGA
48305 TGAGATAGATTTACGAGTTATTCGAGTTTAATTCAG
1 TGAGATAGATTTACGAGTTATTCGAGTTTAATTCAG
** *
48341 TGAGATAGATTTGTGAGTTATTTGAGTTTAATTCA
1 TGAGATAGATTTACGAGTTATTCGAGTTTAATTCA
48376 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.42
Consensus pattern (36 bp):
TGAGATAGATTTACGAGTTATTCGAGTTTAATTCAG
Found at i:55109 original size:16 final size:16
Alignment explanation
Indices: 55088--55144 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
55078 TCAGAGTCAC
*
55088 TAAATCATTCAACATT
1 TAAATCATTCAGCATT
55104 TAAATCATTCAGCATT
1 TAAATCATTCAGCATT
* *
55120 TGAATCATTCAGCACT
1 TAAATCATTCAGCATT
55136 T-AATCATTC
1 TAAATCATTC
55145 TGAAGTAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 8 0.21
16 30 0.79
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (16 bp):
TAAATCATTCAGCATT
Found at i:62068 original size:2 final size:2
Alignment explanation
Indices: 62061--62089 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62051 TTCATGTCAT
62061 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
62090 GACAGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:63805 original size:28 final size:28
Alignment explanation
Indices: 63774--63828 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
63764 CATAAAACTT
*
63774 AATAATATTA-TTATTATTTAAATATTAA
1 AATAAT-TTATTTATTATTAAAATATTAA
63802 AATAATTTATTTATTATTAAAATATTA
1 AATAATTTATTTATTATTAAAATATTA
63829 TTTTTGCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATAATTTATTTATTATTAAAATATTAA
Found at i:64177 original size:22 final size:22
Alignment explanation
Indices: 64149--64229 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
64139 TTGATTATTT
64149 TATTATAATATTAAAAATATAA
1 TATTATAATATTAAAAATATAA
* *
64171 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATA-TAA
* * *
64194 TA-AATATATTTTAATAAT-TAA
1 TATTATA-ATATTAAAAATATAA
*
64215 TATTTTAATAATTAA
1 TATTATAAT-ATTAA
64230 TATTTTGATT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
21 7 0.16
22 26 0.58
23 12 0.27
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
TATTATAATATTAAAAATATAA
Found at i:64219 original size:15 final size:15
Alignment explanation
Indices: 64190--64235 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
64180 ATTAGAAATA
*
64190 TTAATAAAT-ATATT
1 TTAATAATTAATATT
64204 TTAATAATTAATATT
1 TTAATAATTAATATT
64219 TTAATAATTAATATT
1 TTAATAATTAATATT
64234 TT
1 TT
64236 GATTAAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAATAATTAATATT
Found at i:64433 original size:15 final size:15
Alignment explanation
Indices: 64413--64441 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
64403 TTACGTTGAC
64413 CAACCAGTTTTCCTT
1 CAACCAGTTTTCCTT
64428 CAACCAGTTTTCCT
1 CAACCAGTTTTCCT
64442 CCAATCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.34, G:0.07, T:0.38
Consensus pattern (15 bp):
CAACCAGTTTTCCTT
Found at i:64865 original size:16 final size:15
Alignment explanation
Indices: 64835--64870 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
64825 TAATTAAAAA
64835 ATTACAATAAATTTTT
1 ATTA-AATAAATTTTT
64851 ATTAAATAAATTTTT
1 ATTAAATAAATTTTT
64866 ATTAA
1 ATTAA
64871 TTTGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAAATAAATTTTT
Found at i:71297 original size:2 final size:2
Alignment explanation
Indices: 71292--71317 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71282 TCTTTTTTAA
71292 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
71318 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74453 original size:27 final size:28
Alignment explanation
Indices: 74415--74469 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
74405 GAAATCCGAA
74415 AAGAATGGAACTTT-AATCACTATATAT
1 AAGAATGGAACTTTAAATCACTATATAT
74442 AAGAATGGAACTTTAAATCACTATATAT
1 AAGAATGGAACTTTAAATCACTATATAT
74470 CGATATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (28 bp):
AAGAATGGAACTTTAAATCACTATATAT
Found at i:86351 original size:39 final size:39
Alignment explanation
Indices: 86297--86413 Score: 234
Period size: 39 Copynumber: 3.0 Consensus size: 39
86287 TTCCCTTAAA
86297 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
1 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
86336 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
1 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
86375 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
1 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
86414 TCTAGGTTCC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.15
Consensus pattern (39 bp):
CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
Found at i:87699 original size:30 final size:30
Alignment explanation
Indices: 87665--87725 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
87655 CTCTCTGAAT
*
87665 GTTAAGTGAACGATTTGAAGCATTGAACAA
1 GTTAAGTGAACAATTTGAAGCATTGAACAA
87695 GTTAAGTGAACAATTTGAAGCATTGAACAA
1 GTTAAGTGAACAATTTGAAGCATTGAACAA
87725 G
1 G
87726 AATGAGTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (30 bp):
GTTAAGTGAACAATTTGAAGCATTGAACAA
Found at i:87723 original size:17 final size:17
Alignment explanation
Indices: 87671--87724 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
87661 GAATGTTAAG
*
87671 TGAACGATTTGAAGCAT
1 TGAACAATTTGAAGCAT
*
87688 TGAACAAGTT-AAG---
1 TGAACAATTTGAAGCAT
87701 TGAACAATTTGAAGCAT
1 TGAACAATTTGAAGCAT
87718 TGAACAA
1 TGAACAA
87725 GAATGAGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 9 0.30
14 3 0.10
16 3 0.10
17 15 0.50
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (17 bp):
TGAACAATTTGAAGCAT
Found at i:90938 original size:31 final size:31
Alignment explanation
Indices: 90895--90962 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
90885 CATATGTTCT
* *
90895 CAAAGTATGACTCTCATTTTAAATTAATCCA
1 CAAATTATGACTCTCATTCTAAATTAATCCA
* * *
90926 TAAATTATGACTCTGATTCTAAATTGATCCA
1 CAAATTATGACTCTCATTCTAAATTAATCCA
90957 CAAATT
1 CAAATT
90963 TTTGAACATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (31 bp):
CAAATTATGACTCTCATTCTAAATTAATCCA
Found at i:91008 original size:60 final size:60
Alignment explanation
Indices: 90941--91053 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
90931 TATGACTCTG
* *
90941 ATTCTAAATT-GATCCACAAA-TTTTTGAACATTTC-AGTTTCATCCCCAAACTATGACCTTC
1 ATTCTAAATTGGATCC-CAAACTTCTTGAACA-TTCAAATTTCAT-CCCAAACTATGACCTTC
91001 ATTCTAAATTGGATCCCAAACTTCTTGAACATTCAAATTTCATCCCAAACTAT
1 ATTCTAAATTGGATCCCAAACTTCTTGAACATTCAAATTTCATCCCAAACTAT
91054 ATATATACAC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
60 27 0.56
61 21 0.44
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (60 bp):
ATTCTAAATTGGATCCCAAACTTCTTGAACATTCAAATTTCATCCCAAACTATGACCTTC
Found at i:98002 original size:16 final size:16
Alignment explanation
Indices: 97969--98000 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
97959 TTTAATTAAA
97969 TATTAGTTATATTTTT
1 TATTAGTTATATTTTT
97985 TATTAG-TATATTTTT
1 TATTAGTTATATTTTT
98000 T
1 T
98001 TAAAAGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TATTAGTTATATTTTT
Found at i:99438 original size:22 final size:23
Alignment explanation
Indices: 99400--99447 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
99390 TTTTTATTGG
99400 ATTTTTCATTCTCAATA-CCTAA
1 ATTTTTCATTCTCAATATCCTAA
* *
99422 ATTTCTTCA-TCTTAATATTCTAA
1 ATTT-TTCATTCTCAATATCCTAA
99445 ATT
1 ATT
99448 CTTAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTTTCATTCTCAATATCCTAA
Found at i:107208 original size:2 final size:2
Alignment explanation
Indices: 107201--107227 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
107191 CTACCAAATG
107201 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
107228 GTTAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:108802 original size:23 final size:21
Alignment explanation
Indices: 108775--108816 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
108765 TTTTAGTTTA
*
108775 ATTTTTATTTTATATATATTTT
1 ATTTTTA-TTTAAATATATTTT
108797 ATTTTTATTTAAATATATTT
1 ATTTTTATTTAAATATATTT
108817 AAATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTTATTTAAATATATTTT
Found at i:108851 original size:16 final size:16
Alignment explanation
Indices: 108832--108870 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
108822 ATTAATTCCA
108832 ATAATTATTTAATAGC
1 ATAATTATTTAATAGC
108848 ATAATTATTTAATAGC
1 ATAATTATTTAATAGC
108864 AT-ATTAT
1 ATAATTAT
108871 ATATAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
ATAATTATTTAATAGC
Found at i:110114 original size:20 final size:20
Alignment explanation
Indices: 110091--110159 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
110081 CACGGAATGT
110091 AAGATTACTAGTGAGAATAA
1 AAGATTACTAGTGAGAATAA
* * *
110111 AAGATTACCAATGGGAATAA
1 AAGATTACTAGTGAGAATAA
110131 AAGATTACTAG-G-GAAT--
1 AAGATTACTAGTGAGAATAA
110147 AAGATTACT-GTGA
1 AAGATTACTAGTGA
110160 ATGTTGTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
15 1 0.02
16 10 0.24
18 4 0.10
19 1 0.02
20 26 0.62
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (20 bp):
AAGATTACTAGTGAGAATAA
Found at i:114412 original size:6 final size:6
Alignment explanation
Indices: 114401--116740 Score: 2547
Period size: 6 Copynumber: 395.2 Consensus size: 6
114391 GTATTTTACG
114401 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114449 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114497 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114545 CAC--A CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114591 CACATA CACATA CACATA CACATA CACATA CACATA CACAT- -ACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114637 CACATA CACATA CACATA CACATA CAC--A CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114683 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114731 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATACA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACAT--A
114781 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114829 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114877 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114925 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
114973 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
115021 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
115069 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
115117 CACAT- -ACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
115163 CACAT- -ACATA CACATA CACATA CACAT- -ACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
*
115207 CACATA CACATA CACATA CACAT- -ACATA CACATA CACATA CACAGA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
*
115253 CACATA CACAT- -ACAGA CACATA CACATA CAC--A CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
*
115297 CAC--A CACATA CAC--A CACATA CACAGA CAC--A CACATA CAC--A
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
115337 CACACA CACACA CACACA CACACA CACACA CACACA CACACA CACACA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * *
115385 CACACA CACATA CACACA CACACA CACACA CACACA CACACA CACATACA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACAT--A
* * * * * * *
115435 CACACA CACATA CACACA CACACA CACACA CATACA CACACA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * *
115483 CACACA CACACA CACATA CACATA CACACA CACACA CACACA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * *
115531 CAC--A CACACA CATACA CACACA CACATA CACATA CAC--A CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
115575 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * *
115623 CACATA CACATA CACATA CACATACA CACACA CACATA CACACA CACACA
1 CACATA CACATA CACATA CACAT--A CACATA CACATA CACATA CACATA
* * * * * * *
115673 CACACA TACACA CACACA CACATA CAC--A CACACA CACACA CACACA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * *
115719 CATACA CACATA CACATA CAC--A CACATA CAC--A CACATA CACACA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * * *
115763 CACACA CACACA CACACA CACACA CACACA -ACACA CACACA CATACA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
*
115810 CACACA CACATA CACATACA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACAT--A CACATA CACATA CACATA CACATA CACATA
*
115860 CACATA CACATA CACATA CACATA CACATA CACATATA CACATA CACACA
1 CACATA CACATA CACATA CACATA CACATA CAC--ATA CACATA CACATA
* * * * * * *
115910 CACACA CACACA CACACA CACACA CACACA CACACA CACACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACA--TA CACATA
* * * * * * * *
115960 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116008 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116056 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGT-
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116103 -ACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116150 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116198 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116246 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116294 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116342 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116390 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116438 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116486 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * *
116534 CACGTA CACGTA CACGTA CACGTA CACGTA CACACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACA--TA CACATA CACATA
* * * * * * * *
116584 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * * * * *
116632 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* * * * *
116680 CACGTA CACAT- -ACGTA CACGTA CACGTA CACAT- -ACGTA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
116724 CACAT- -ACATA CACATA C
1 CACATA CACATA CACATA C
116741 GTATACGTAT
Statistics
Matches: 2231, Mismatches: 44, Indels: 118
0.93 0.02 0.05
Matches are distributed among these distances:
4 85 0.04
5 5 0.00
6 2104 0.94
8 37 0.02
ACGTcount: A:0.45, C:0.36, G:0.06, T:0.14
Consensus pattern (6 bp):
CACATA
Found at i:116721 original size:10 final size:10
Alignment explanation
Indices: 116681--116743 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
116671 GTACACGTAC
116681 ACGTACACAT
1 ACGTACACAT
*
116691 ACGTACACGTAC
1 ACGTACAC--AT
116703 ACGTACACAT
1 ACGTACACAT
116713 ACGTACAC--
1 ACGTACACAT
116721 A--TACACAT
1 ACGTACACAT
*
116729 ACATACACAT
1 ACGTACACAT
116739 ACGTA
1 ACGTA
116744 TACGTATATG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
6 5 0.11
8 2 0.05
10 28 0.64
12 9 0.20
ACGTcount: A:0.41, C:0.30, G:0.10, T:0.19
Consensus pattern (10 bp):
ACGTACACAT
Found at i:116746 original size:6 final size:6
Alignment explanation
Indices: 116737--116788 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
116727 ATACATACAC
* **
116737 ATACGT ATACGT ATATGT ATACGT ATACAC ATACGT ATACGT ATACGT
1 ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT
116785 ATAC
1 ATAC
116789 ACCTTATCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (6 bp):
ATACGT
Found at i:116789 original size:24 final size:24
Alignment explanation
Indices: 116743--116790 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
116733 ACACATACGT
*
116743 ATACGTATATGTATACGTATACAC
1 ATACGTATACGTATACGTATACAC
116767 ATACGTATACGTATACGTATACAC
1 ATACGTATACGTATACGTATACAC
116791 CTTATCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (24 bp):
ATACGTATACGTATACGTATACAC
Found at i:118401 original size:29 final size:31
Alignment explanation
Indices: 118369--118454 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
118359 TATTCAATTA
*
118369 TTTTGAAAGGTTAGGCCCTTA-TTGAAC-CC
1 TTTTGAAAGGTTAGGCCCTTACTTGAACAAC
* ** *
118398 TTTTGAAAGCTTAATCCCTTATTTGAACAAC
1 TTTTGAAAGGTTAGGCCCTTACTTGAACAAC
* * *
118429 TTCTAAAAGGTTAGGCTCTTACTTGA
1 TTTTGAAAGGTTAGGCCCTTACTTGA
118455 GTATTTAACC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 18 0.41
30 6 0.14
31 20 0.45
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTTGAAAGGTTAGGCCCTTACTTGAACAAC
Found at i:119441 original size:31 final size:31
Alignment explanation
Indices: 119406--119469 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
119396 AGAATTGGTT
119406 TTAACTTCTTAATAGAAATTTTAACAATCTG
1 TTAACTTCTTAATAGAAATTTTAACAATCTG
119437 TTAACTTCTTAATAGAAATTTTAACAATCTG
1 TTAACTTCTTAATAGAAATTTTAACAATCTG
119468 TT
1 TT
119470 TCTTTTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (31 bp):
TTAACTTCTTAATAGAAATTTTAACAATCTG
Found at i:121069 original size:50 final size:50
Alignment explanation
Indices: 120993--121107 Score: 160
Period size: 50 Copynumber: 2.3 Consensus size: 50
120983 TTACCGGATT
* * * ** *
120993 AAAAAT-CGATTTTTTTTAAACTGGATAAAAATTCGGTTTTTTATCCGAA
1 AAAAATCCGGTTTTTTTCAAACCGGATAAAAAACCGGTTTTTTATACGAA
121042 AAAAATCCGGTTTTTTTCAAACCGGATAAAAAACCGGTTTTTTATACGAA
1 AAAAATCCGGTTTTTTTCAAACCGGATAAAAAACCGGTTTTTTATACGAA
*
121092 AAAAATCTGGTTTTTT
1 AAAAATCCGGTTTTTT
121108 AAAAAAACTG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 6 0.10
50 52 0.90
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (50 bp):
AAAAATCCGGTTTTTTTCAAACCGGATAAAAAACCGGTTTTTTATACGAA
Found at i:121078 original size:27 final size:25
Alignment explanation
Indices: 120973--121084 Score: 88
Period size: 27 Copynumber: 4.4 Consensus size: 25
120963 AAATTGAACG
*
120973 ACCGGTTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
* * *
120997 ATCGATTTTTTTTAAACTGGATAAAAA
1 ACCG-GTTTTTTT-AACCGGATAAAAA
** *
121024 TTCGG-TTTTTTATCC-GA-AAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
121046 ATCCGGTTTTTTTCAAACCGGATAAAAA
1 A-CCGGTTTTTTT--AACCGGATAAAAA
121074 ACCGGTTTTTT
1 ACCGGTTTTTT
121085 ATACGAAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
22 5 0.07
23 5 0.07
24 11 0.16
25 13 0.19
26 3 0.04
27 25 0.37
28 6 0.09
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATAAAAA
Found at i:121222 original size:40 final size:40
Alignment explanation
Indices: 121069--121204 Score: 202
Period size: 40 Copynumber: 3.4 Consensus size: 40
121059 CAAACCGGAT
* * * *
121069 AAAAAACCGGTTTTTTATACGAAAAAAATCTGG-TTTTTTA
1 AAAAAACTGGATTTTTATCCG-AAAAAATCCGGTTTTTTTA
121109 AAAAAACTGGATTTTTATCCGAAAAAATCCGGTTTTTTTA
1 AAAAAACTGGATTTTTATCCGAAAAAATCCGGTTTTTTTA
*
121149 AAAAAATTGGATTTTTATCCGAAAAAATCCGGTTTTTTTA
1 AAAAAACTGGATTTTTATCCGAAAAAATCCGGTTTTTTTA
*
121189 AAAAAACTGGTTTTTT
1 AAAAAACTGGATTTTT
121205 TGCAAACCGA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 10 0.11
40 78 0.89
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.39
Consensus pattern (40 bp):
AAAAAACTGGATTTTTATCCGAAAAAATCCGGTTTTTTTA
Found at i:121914 original size:38 final size:38
Alignment explanation
Indices: 121854--121930 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
121844 TGAGCTTCAC
* *
121854 AAATTTTATTATTTGAAAATAATTTTTTAGGTATTTTA
1 AAATTTTATTATTTGAAAATAATTTTTTAAGTAATTTA
* * *
121892 AAATTTTATTGTTTTAATATAATTTTTTAAGTAATTTA
1 AAATTTTATTATTTGAAAATAATTTTTTAAGTAATTTA
121930 A
1 A
121931 TATAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (38 bp):
AAATTTTATTATTTGAAAATAATTTTTTAAGTAATTTA
Found at i:121957 original size:18 final size:17
Alignment explanation
Indices: 121930--121963 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
121920 AAGTAATTTA
121930 ATATAATTATTTAAATAT
1 ATATAATTA-TTAAATAT
*
121948 ATATATTTATTAAATA
1 ATATAATTATTAAATA
121964 ATTGAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATAATTATTAAATAT
Found at i:122339 original size:63 final size:62
Alignment explanation
Indices: 122162--122350 Score: 344
Period size: 61 Copynumber: 3.0 Consensus size: 62
122152 TCTACGGGCT
122162 AAGATATAATAAGTTCATTTTTTCTCATTTTTCATTAAAAAATTGATGACAAATTAAGTTG-
1 AAGATATAATAAGTTCATTTTTTCTCATTTTTCATTAAAAAATTGATGACAAATTAAGTTGA
122223 AAGATATAATAAGTTCATTTTTTCTCATTTTTCATTAAAAAATTGATGACAAATTAAGTTGA
1 AAGATATAATAAGTTCATTTTTTCTCATTTTTCATTAAAAAATTGATGACAAATTAAGTTGA
**
122285 AAGATATAATAAGTTCATTTTTTCTCATTTTTTGTTAAAAAAATTGATGACAAATTAAGTTGA
1 AAGATATAATAAGTTCATTTTTTCTCATTTTTCATT-AAAAAATTGATGACAAATTAAGTTGA
122348 AAG
1 AAG
122351 TTAACCTATT
Statistics
Matches: 124, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
61 61 0.49
62 34 0.27
63 29 0.23
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (62 bp):
AAGATATAATAAGTTCATTTTTTCTCATTTTTCATTAAAAAATTGATGACAAATTAAGTTGA
Found at i:123577 original size:34 final size:34
Alignment explanation
Indices: 123531--123602 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
123521 ACAAGGACAA
* *
123531 GGACAGAACTAAGATGAATGATATGTGTGAGCAG
1 GGACAGAACTAAGATCAATGATATGAGTGAGCAG
*
123565 GGACA-AAGCTAAGATCAATGATATGAGTGAGCAT
1 GGACAGAA-CTAAGATCAATGATATGAGTGAGCAG
123599 GGAC
1 GGAC
123603 GGAGGGATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 2 0.06
34 32 0.94
ACGTcount: A:0.39, C:0.11, G:0.31, T:0.19
Consensus pattern (34 bp):
GGACAGAACTAAGATCAATGATATGAGTGAGCAG
Found at i:123817 original size:34 final size:34
Alignment explanation
Indices: 123779--123920 Score: 126
Period size: 34 Copynumber: 4.1 Consensus size: 34
123769 AACTAAGACG
*
123779 AATGATACGTGTGAG-ATGGGACGAAGTTAGGATC
1 AATGATACGTGTGAGCAT-GGACGAAGCTAGGATC
* *
123813 AATGATATGTGTGAGCATGGACGGAGCTAGGATCAATC
1 AATGATACGTGTGAGCATGGACGAAGCTAGG----ATC
* * * *
123851 AATGATATGTGCGAGCATCGACGGAGCTAGGATC
1 AATGATACGTGTGAGCATGGACGAAGCTAGGATC
* * *
123885 AATGATATGCGTGAGCATCGAC-AGAGCTAGGATC
1 AATGATACGTGTGAGCATGGACGA-AGCTAGGATC
123919 AA
1 AA
123921 ATATTAGGAG
Statistics
Matches: 94, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
34 60 0.64
35 2 0.02
38 32 0.34
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.22
Consensus pattern (34 bp):
AATGATACGTGTGAGCATGGACGAAGCTAGGATC
Found at i:123861 original size:38 final size:38
Alignment explanation
Indices: 123810--123920 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 38
123800 CGAAGTTAGG
*
123810 ATCAATGATATGTGTGAGCATGGACGGAGCTAGGATCA
1 ATCAATGATATGTGTGAGCATCGACGGAGCTAGGATCA
*
123848 ATCAATGATATGTGCGAGCATCGACGGAGCTAGG----
1 ATCAATGATATGTGTGAGCATCGACGGAGCTAGGATCA
* *
123882 ATCAATGATATGCGTGAGCATCGACAGAGCTAGGATCA
1 ATCAATGATATGTGTGAGCATCGACGGAGCTAGGATCA
123920 A
1 A
123921 ATATTAGGAG
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
34 31 0.48
38 33 0.52
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (38 bp):
ATCAATGATATGTGTGAGCATCGACGGAGCTAGGATCA
Found at i:125990 original size:60 final size:60
Alignment explanation
Indices: 125916--126090 Score: 171
Period size: 60 Copynumber: 3.0 Consensus size: 60
125906 ATATGTTTTC
* * * *
125916 AAACTATAATTCTCATTTTAAATTGGTCTTTAAACTTTTGAATATTCTAATTCCATCCTC-
1 AAACTATGACTCTCATTTT-AATTAGTCTTTAAACTTTTGAATATTCTAATTTCATCCTCT
* * * *
125976 AAATTATGACTCTCATTCTAATTAGTCTTTAAAC--TTAAACATTCTAATTTCAT-CTCT
1 AAACTATGACTCTCATTTTAATTAGTCTTTAAACTTTTGAATATTCTAATTTCATCCTCT
* * ** *
126033 AAACTATGACACT-ATTTCTTAATTTGTCTCCAAACTTTTGAATATTTTAATTTCATCC
1 AAACTATGACTCTCA-TT-TTAATTAGTCTTTAAACTTTTGAATATTCTAATTTCATCC
126091 CAATTTAGGT
Statistics
Matches: 92, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
56 4 0.04
57 29 0.32
58 13 0.14
59 14 0.15
60 31 0.34
61 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.45
Consensus pattern (60 bp):
AAACTATGACTCTCATTTTAATTAGTCTTTAAACTTTTGAATATTCTAATTTCATCCTCT
Found at i:126041 original size:57 final size:59
Alignment explanation
Indices: 125914--126042 Score: 147
Period size: 57 Copynumber: 2.2 Consensus size: 59
125904 TCATATGTTT
* * * * * *
125914 TCAAACTATAATTCTCATTTTAAATTGGTCTTTAAACTTTTGAATATTCTAATTCCATCC
1 TCAAACTATGACTCTCATTCTAAATTAGTCTTTAAAC-TTTAAACATTCTAATTCCATCC
* *
125974 TCAAATTATGACTCTCATTCT-AATTAGTCTTTAAAC-TTAAACATTCTAATTTCAT-C
1 TCAAACTATGACTCTCATTCTAAATTAGTCTTTAAACTTTAAACATTCTAATTCCATCC
126030 TCTAAACTATGAC
1 TC-AAACTATGAC
126043 ACTATTTCTT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
56 3 0.05
57 25 0.42
59 14 0.24
60 17 0.29
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (59 bp):
TCAAACTATGACTCTCATTCTAAATTAGTCTTTAAACTTTAAACATTCTAATTCCATCC
Found at i:131389 original size:62 final size:61
Alignment explanation
Indices: 131315--131477 Score: 158
Period size: 60 Copynumber: 2.7 Consensus size: 61
131305 TATCATGTCC
* * *
131315 CCAAACTATGACTTTCATTTTAAATTGA-TCTTTAAATTTTTTTTG-ATATTCCAA-TTCCATCA
1 CCAAACTATGAC--TCATTTTAAATTGAGTCCTTAAA-CTTTTTTGAACATTCCAACTT-CATC-
131377 T
61 T
*
131378 -CAAACTATGACTCATTCTAAATT-AGTCCTTAAACTTTTTTGAACATTCCAACTTCATCT
1 CCAAACTATGACTCATTTTAAATTGAGTCCTTAAACTTTTTTGAACATTCCAACTTCATCT
* **
131437 CCAAACTATAACCCTCATTTTAAATTG-GTCCCCAAACTTTT
1 CCAAACTATGA--CTCATTTTAAATTGAGTCCTTAAACTTTT
131478 GAATCTTTCA
Statistics
Matches: 85, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
59 9 0.11
60 39 0.46
61 2 0.02
62 35 0.41
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (61 bp):
CCAAACTATGACTCATTTTAAATTGAGTCCTTAAACTTTTTTGAACATTCCAACTTCATCT
Found at i:131713 original size:60 final size:60
Alignment explanation
Indices: 131620--131735 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
131610 AGTATATACA
* **
131620 CATAGTTTGAGATTAAATTGAAATGTTTAAAAAGTTTGGGGACTAATTTAGAATGAAGGT
1 CATAGTTTGAGATGAAATTGAAATGTTTAAAAAGTTTAAGGACTAATTTAGAATGAAGGT
* * *
131680 CATAGTTTGGTGATGAAATTGAAATG-TTCAAAAGTTTAAGGACTAATTTATAATGA
1 CATAGTTT-GAGATGAAATTGAAATGTTTAAAAAGTTTAAGGACTAATTTAGAATGA
131736 GGTACAATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 34 0.69
61 15 0.31
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (60 bp):
CATAGTTTGAGATGAAATTGAAATGTTTAAAAAGTTTAAGGACTAATTTAGAATGAAGGT
Found at i:133522 original size:2 final size:2
Alignment explanation
Indices: 133517--133559 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
133507 TCTCTCTCTT
*
133517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
133559 T
1 T
133560 CATCTTCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:135496 original size:33 final size:33
Alignment explanation
Indices: 135447--135524 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
135437 TCATATTAAT
* *
135447 ATTTCCGAATG-AACATATCAATATTATCAAGA
1 ATTTCCAAATGCAACATATCAATATAATCAAGA
* *
135479 ATTTCCAAATGCAACATATCAATATAATTAAGT
1 ATTTCCAAATGCAACATATCAATATAATCAAGA
135512 ATTTCCAAATGCA
1 ATTTCCAAATGCA
135525 CATCATACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 10 0.24
33 31 0.76
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.32
Consensus pattern (33 bp):
ATTTCCAAATGCAACATATCAATATAATCAAGA
Found at i:137801 original size:36 final size:36
Alignment explanation
Indices: 137754--137997 Score: 382
Period size: 36 Copynumber: 6.8 Consensus size: 36
137744 ATCAAAAGTT
* * *
137754 CACTTCTGATTCAAGTAGAACGGAAGAAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
137790 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
*
137826 CACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
*
137862 CACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
* * *
137898 CACTTCTGATTCAAGTCGAACGGAAAGAAGCATCGA
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
**
137934 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCAA
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
137970 CACTTCCGATTCATA-TCGAACGGAAGGA
1 CACTTCCGATTCA-AGTCGAACGGAAGGA
137998 TGTGTCTTAC
Statistics
Matches: 196, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
36 195 0.99
37 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (36 bp):
CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
Found at i:140210 original size:20 final size:20
Alignment explanation
Indices: 140172--140211 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
140162 TGTATACAAT
*
140172 AGTAATAAACATTGATTAAG
1 AGTAATAAACATAGATTAAG
*
140192 AGTAATAAACATAGTTTAAG
1 AGTAATAAACATAGATTAAG
140212 TAGATCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (20 bp):
AGTAATAAACATAGATTAAG
Found at i:141722 original size:13 final size:13
Alignment explanation
Indices: 141706--141730 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
141696 TTAACAACAT
141706 ATATAAAAATATA
1 ATATAAAAATATA
141719 ATATAAAAATAT
1 ATATAAAAATAT
141731 TAAACACTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAAAAATATA
Done.