Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008262.1 Hibiscus syriacus cultivar Beakdansim tig00110916_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: 68419
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:94 original size:16 final size:16
Alignment explanation
Indices: 73--106 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
63 TTACTATTCA
*
73 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
89 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
105 CG
1 CG
107 GGTCGGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:4168 original size:35 final size:35
Alignment explanation
Indices: 4122--4208 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 35
4112 TTGTTAAAAG
*
4122 TTTCAAAGTTTGGTAA-CCAACTTTGGAAAATGTTT
1 TTTCAAAGTTTGGTAATCCAACTTTGAAAAATG-TT
****
4157 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGTT
1 TTTCAAAGTTTGGT-AATCCAACTTTGAAAAATGTT
4193 TTTCAAAGTTTGGTAA
1 TTTCAAAGTTTGGTAA
4209 AATTTTGGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 16 0.36
36 18 0.40
37 11 0.24
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (35 bp):
TTTCAAAGTTTGGTAATCCAACTTTGAAAAATGTT
Found at i:5579 original size:2 final size:2
Alignment explanation
Indices: 5574--5605 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5564 AACTGTGGGT
5574 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
5606 ACAGATTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5848 original size:10 final size:11
Alignment explanation
Indices: 5833--5878 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
5823 AAATTCAAAG
5833 AAAAATAAA-A
1 AAAAATAAATA
5843 AAAAATAAATA
1 AAAAATAAATA
**
5854 AACCATAAA-A
1 AAAAATAAATA
*
5864 ATAAATAAATA
1 AAAAATAAATA
5875 AAAA
1 AAAA
5879 GAAACTAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
10 16 0.57
11 12 0.43
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:5861 original size:21 final size:21
Alignment explanation
Indices: 5837--5876 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5827 TCAAAGAAAA
5837 ATAAAAAAAAATAAATAAACC
1 ATAAAAAAAAATAAATAAACC
*
5858 ATAAAAATAAATAAATAAA
1 ATAAAAAAAAATAAATAAA
5877 AAGAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (21 bp):
ATAAAAAAAAATAAATAAACC
Found at i:7515 original size:63 final size:63
Alignment explanation
Indices: 7436--7563 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
7426 GTAGGGGTGG
*
7436 CCTCAATTGATAAGCTTGATTTGGTTTAGGATTTGGTCCATGGCTCAAGTTCAGATGATCTCT
1 CCTCAATTAATAAGCTTGATTTGGTTTAGGATTTGGTCCATGGCTCAAGTTCAGATGATCTCT
7499 CCTCAATTAATAAGCTTGATTTGGTTTAGGATTTGGTCCATGGCTCAAGTTCAGATGATCTCT
1 CCTCAATTAATAAGCTTGATTTGGTTTAGGATTTGGTCCATGGCTCAAGTTCAGATGATCTCT
7562 CC
1 CC
7564 ATCATGGATT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (63 bp):
CCTCAATTAATAAGCTTGATTTGGTTTAGGATTTGGTCCATGGCTCAAGTTCAGATGATCTCT
Found at i:9737 original size:32 final size:32
Alignment explanation
Indices: 9701--9766 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
9691 AGTCATCAAA
* *
9701 AACCCTAAAAGATTGCATTTAAACTAAAAGAT
1 AACCCTAAAAGATTACATTCAAACTAAAAGAT
9733 AACCCTAAAAGATTACATTCAAACTAAAAGAT
1 AACCCTAAAAGATTACATTCAAACTAAAAGAT
9765 AA
1 AA
9767 TTATGAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.23
Consensus pattern (32 bp):
AACCCTAAAAGATTACATTCAAACTAAAAGAT
Found at i:10253 original size:24 final size:23
Alignment explanation
Indices: 10210--10310 Score: 105
Period size: 23 Copynumber: 4.3 Consensus size: 23
10200 TTTGTTTATC
* *
10210 TTCATTTATTGTGTTAGTTTATG
1 TTCATTTATTGTGTTCGTTTACG
10233 TTCA-TTAGTTTGTGTTCGTTTACG
1 TTCATTTA--TTGTGTTCGTTTACG
*
10257 TTCGTTTATTGTGTTCGTTTACG
1 TTCATTTATTGTGTTCGTTTACG
** * *
10280 TTTGTTTATTGTGTTCATTTATG
1 TTCATTTATTGTGTTCGTTTACG
*
10303 TTCGTTTA
1 TTCATTTA
10311 CATCCTTTCA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
22 3 0.04
23 46 0.68
24 16 0.24
25 3 0.04
ACGTcount: A:0.13, C:0.09, G:0.19, T:0.59
Consensus pattern (23 bp):
TTCATTTATTGTGTTCGTTTACG
Found at i:10274 original size:13 final size:13
Alignment explanation
Indices: 10256--10301 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
10246 GTTCGTTTAC
10256 GTTCGTTTATTGT
1 GTTCGTTTATTGT
*
10269 GTTCGTTTA-CGT
1 GTTCGTTTATTGT
10281 -TT-GTTTATTGT
1 GTTCGTTTATTGT
*
10292 GTTCATTTAT
1 GTTCGTTTAT
10302 GTTCGTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
10 5 0.19
11 4 0.15
12 4 0.15
13 14 0.52
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.61
Consensus pattern (13 bp):
GTTCGTTTATTGT
Found at i:13534 original size:31 final size:31
Alignment explanation
Indices: 13495--13580 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
13485 ACAAATGGTC
13495 CCTCGACTATATAGTGTTGCTTTATTAAGTA
1 CCTCGACTATATAGTGTTGCTTTATTAAGTA
* * * * *
13526 TCTCGACTATATAATATTGTTTTATTAAGTC
1 CCTCGACTATATAGTGTTGCTTTATTAAGTA
13557 CCTCGACTATATAGTGTTGCTTTA
1 CCTCGACTATATAGTGTTGCTTTA
13581 ATAATTTCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (31 bp):
CCTCGACTATATAGTGTTGCTTTATTAAGTA
Found at i:13597 original size:31 final size:30
Alignment explanation
Indices: 13496--13597 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
13486 CAAATGGTCC
*
13496 CTCGACTATATAGTGTTGCTTTATTAAGTAT
1 CTCGACTATATAGTGTTGCTTTATTAA-TTT
* * * **
13527 CTCGACTATATAATATTGTTTTATTAAGTCC
1 CTCGACTATATAGTGTTGCTTTATTAA-TTT
*
13558 CTCGACTATATAGTGTTGCTTTAATAATTT
1 CTCGACTATATAGTGTTGCTTTATTAATTT
*
13588 CATCAACTAT
1 C-TCGACTAT
13598 TAAAAGTTAC
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
30 2 0.03
31 56 0.97
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (30 bp):
CTCGACTATATAGTGTTGCTTTATTAATTT
Found at i:15161 original size:2 final size:2
Alignment explanation
Indices: 15154--15206 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
15144 CGTCAATCCA
15154 AT 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 AT
15196 AT AT AT AT AT A
1 AT AT AT AT AT A
15207 GCTCATTTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17546 original size:29 final size:29
Alignment explanation
Indices: 17504--17584 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 29
17494 TAATGAATTA
*
17504 TAAAA-AATTGATAAATTTAATAATATTT
1 TAAAATAATTAATAAATTTAATAATATTT
* * *
17532 TAAAATAATTCATAAAATTAGTAAATATTT
1 TAAAATAATTAATAAATTTAAT-AATATTT
* * *
17562 TATAATTATTAAAAAATTTAATA
1 TAAAATAATTAATAAATTTAATA
17585 TTGATAATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
28 5 0.12
29 14 0.33
30 23 0.55
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (29 bp):
TAAAATAATTAATAAATTTAATAATATTT
Found at i:18476 original size:21 final size:21
Alignment explanation
Indices: 18359--18496 Score: 77
Period size: 21 Copynumber: 6.7 Consensus size: 21
18349 ACGCGAAATA
**
18359 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
18379 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
18399 AAAATCGCAACGCTATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
18420 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
18441 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * *
18462 AAAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
18482 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
18497 ACACATAAAT
Statistics
Matches: 88, Mismatches: 26, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
19 1 0.01
20 39 0.44
21 46 0.52
22 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:18525 original size:20 final size:20
Alignment explanation
Indices: 18463--18655 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
18453 CGATTTTCCA
* ** *
18463 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
18483 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
18503 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
18523 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
18543 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
18563 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
18583 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
18603 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
18623 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
18643 AAATCGCAACGCG
1 AAATCGCAACGCG
18656 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:19078 original size:33 final size:33
Alignment explanation
Indices: 19038--19108 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
19028 TTCACTTAGA
* *
19038 TTTCATTTCGCGTTACGATTTTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
19071 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
19104 TTTCA
1 TTTCA
19109 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:19261 original size:21 final size:21
Alignment explanation
Indices: 19186--19263 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
19176 TTTGCAGAAG
*
19186 AATCGCAACGAGATAAATGAA
1 AATCGCAACGAGAGAAATGAA
*
19207 AATCGCAACGAGAG-AATGAC
1 AATCGCAACGAGAGAAATGAA
**
19227 TGTCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAGAAATGAA
19248 AATCGCAACGAGAGAA
1 AATCGCAACGAGAGAA
19264 TCGCAACGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.35
21 32 0.65
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.12
Consensus pattern (21 bp):
AATCGCAACGAGAGAAATGAA
Found at i:19267 original size:14 final size:14
Alignment explanation
Indices: 19248--19304 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
19238 GAGAAATGAA
19248 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
19262 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
19281 AATCACAACGAGAG
1 AATCGCAACGAGAG
19295 AATCGCAACG
1 AATCGCAACG
19305 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:19280 original size:33 final size:33
Alignment explanation
Indices: 19184--19320 Score: 139
Period size: 33 Copynumber: 3.8 Consensus size: 33
19174 AATTTGCAGA
19184 AGAATCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATCGCAACGAG--AAATGAAAATCGCAACGAG
19219 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AG-A--A---TCGCAAC--GAGAAATGAAAATCGCAACGAG
* *
19260 AGAATCGCAACGCGAAATGAAAATCACAACGAG
1 AGAATCGCAACGAGAAATGAAAATCGCAACGAG
* **
19293 AGAATCGCAACGCGAAACCAAAATCGCA
1 AGAATCGCAACGAGAAATGAAAATCGCA
19321 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 18
0.79 0.04 0.16
Matches are distributed among these distances:
33 45 0.51
35 9 0.10
36 1 0.01
38 2 0.02
40 1 0.01
41 28 0.31
43 3 0.03
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
AGAATCGCAACGAGAAATGAAAATCGCAACGAG
Found at i:19338 original size:19 final size:19
Alignment explanation
Indices: 19316--19413 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
19306 GAAACCAAAA
*
19316 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19335 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
19349 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19368 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
19382 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19401 TCGCGTTGCGATT
1 TCGCGTTGCGATT
19414 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
16 6 0.09
17 6 0.09
19 32 0.50
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19357 original size:14 final size:14
Alignment explanation
Indices: 19338--19427 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
19328 TTTCATTTCG
19338 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
19352 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
19371 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
19385 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
19404 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
19418 CGTTGCGATT
1 CGTTGCGATT
19428 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:19363 original size:33 final size:33
Alignment explanation
Indices: 19321--19435 Score: 230
Period size: 33 Copynumber: 3.5 Consensus size: 33
19311 CAAAATCGCA
19321 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
19354 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
19387 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
19420 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
19436 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:21292 original size:93 final size:93
Alignment explanation
Indices: 21133--21791 Score: 1257
Period size: 93 Copynumber: 7.1 Consensus size: 93
21123 TAGATTGCTT
21133 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
21198 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
21226 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
21291 TTCGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
21319 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
21384 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
21412 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
21477 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
21505 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
21570 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
21598 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
21663 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
21691 AGTAAATAAATTTGTTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAT
1 AG----TAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAT
21756 AGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
62 AGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
21787 AGTAA
1 AGTAA
21792 TGCAATCCAT
Statistics
Matches: 559, Mismatches: 3, Indels: 9
0.98 0.01 0.02
Matches are distributed among these distances:
92 3 0.01
93 465 0.83
96 3 0.01
97 88 0.16
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:21879 original size:19 final size:19
Alignment explanation
Indices: 21839--21967 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
21829 TAGTTTACTT
* *
21839 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
21859 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
21878 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
21897 TCGCAA--CG--A-CATAA
1 TCGCAACGCGAAACCAAAA
21911 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
21930 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
21944 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
21963 TCGCA
1 TCGCA
21968 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:21918 original size:33 final size:32
Alignment explanation
Indices: 21875--21967 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
21865 CGCGAAACCA
**
21875 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
21907 ATAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
21940 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
21968 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:21965 original size:52 final size:52
Alignment explanation
Indices: 21839--21967 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
21829 TAGTTTACTT
**
21839 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
21891 T-G-AAAATCGCAACGACATAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
21944 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
21968 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:21989 original size:19 final size:18
Alignment explanation
Indices: 21967--22062 Score: 91
Period size: 19 Copynumber: 5.6 Consensus size: 18
21957 CCAAAATCGC
21967 ATTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCG
21985 TATTGCGA--TTC-TTTCG
1 -ATTGCGATTTTCATTTCG
22001 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCG
*
22018 CATTGCGA--TTC-TGTCG
1 -ATTGCGATTTTCATTTCG
22034 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCG
*
22051 CGTTGCGATTTT
1 -ATTGCGATTTT
22063 GGTTTCGTGT
Statistics
Matches: 65, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
14 12 0.18
16 15 0.23
17 15 0.23
19 23 0.35
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (18 bp):
ATTGCGATTTTCATTTCG
Found at i:22001 original size:16 final size:16
Alignment explanation
Indices: 21980--22034 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
21970 GCGATTTTCA
21980 TTTCGTATTGCGATTC
1 TTTCGTATTGCGATTC
21996 TTTCG--TTGCGATTTTC
1 TTTCGTATTGCGA--TTC
*
22012 ATTTCGCATTGCGATTC
1 -TTTCGTATTGCGATTC
*
22029 TGTCGT
1 TTTCGT
22035 TGCGATTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 6 0.19
16 12 0.38
17 8 0.25
19 6 0.19
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.49
Consensus pattern (16 bp):
TTTCGTATTGCGATTC
Found at i:22006 original size:14 final size:14
Alignment explanation
Indices: 21987--22041 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
21977 TCATTTCGTA
21987 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
22001 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
*
22018 CATTGCGATTCTGTCG
1 --TTGCGATTCTTTCG
22034 TTGCGATT
1 TTGCGATT
22042 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.40
16 7 0.20
17 8 0.23
19 6 0.17
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:22010 original size:33 final size:33
Alignment explanation
Indices: 21968--22060 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
21958 CAAAATCGCA
* *
21968 TTGCGATTTTCATTTCGTATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
22001 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
*
22034 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
22061 TTGGTTTCGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
Found at i:22068 original size:19 final size:19
Alignment explanation
Indices: 21963--22077 Score: 88
Period size: 19 Copynumber: 6.6 Consensus size: 19
21953 GAAACCAAAA
*
21963 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
21982 TCGTATTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
21998 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
22015 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
22031 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
22048 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
22067 TCGTGTTGCGA
1 TCGCGTTGCGA
22078 AAGTAAACTA
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
14 13 0.17
16 11 0.14
17 11 0.14
19 41 0.54
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:24020 original size:14 final size:14
Alignment explanation
Indices: 24001--24036 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
23991 ATTGTTTAAT
24001 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
24015 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
24029 TGATTTGT
1 TGATTTGT
24037 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:24159 original size:19 final size:19
Alignment explanation
Indices: 24143--24240 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
24133 AAAAATGACT
24143 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
24162 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
24181 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
24195 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
24214 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
24234 ATCGCAA
1 ATCGCAA
24241 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:24272 original size:53 final size:53
Alignment explanation
Indices: 24143--24258 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
24133 AAAAATGACT
24143 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
24195 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
24248 ATCGCAATGCG
1 ATCGCAATGCG
24259 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:24292 original size:14 final size:14
Alignment explanation
Indices: 24273--24327 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
24263 TAATTTCGCA
24273 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
24287 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
24304 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
24320 TTGCGATT
1 TTGCGATT
24328 TTTATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:24311 original size:19 final size:19
Alignment explanation
Indices: 24287--24485 Score: 186
Period size: 19 Copynumber: 11.4 Consensus size: 19
24277 GATTCTCTCG
24287 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
24306 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
24320 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
24339 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
24358 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
24372 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
24392 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
24411 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
*
24425 TTGCGATTTTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
24445 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
24459 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
24478 TTGCGATT
1 TTGCGATT
24486 CTCTCGTTGC
Statistics
Matches: 148, Mismatches: 10, Indels: 44
0.73 0.05 0.22
Matches are distributed among these distances:
14 29 0.20
16 22 0.15
17 18 0.12
18 5 0.03
19 47 0.32
20 27 0.18
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:24473 original size:67 final size:67
Alignment explanation
Indices: 24265--24518 Score: 275
Period size: 67 Copynumber: 3.7 Consensus size: 67
24255 TGCGTTTATA
* *
24265 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC-TCGTTGCGATTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATCGTTGCGATTT
*
24329 TT
66 TC
* * * *
24331 ATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTATCTCGTTGCGATTTTCATTTCCGCAT
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCGTTGCGATTTTCA--T-CG--T
24393 TGCGATTTTC
58 TGCGATTTTC
* *
24403 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCGTTGCGATTTTCAT-GTTGGGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCGTTGCGATTTTCATCGTTGCGATT
24467 TTC
65 TTC
* * *
24470 ATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGTGTTGCGAT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCGTTGCGAT
24519 AGTCAAATGC
Statistics
Matches: 159, Mismatches: 16, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
64 9 0.06
65 5 0.03
66 29 0.18
67 55 0.35
69 2 0.01
70 2 0.01
71 1 0.01
72 27 0.17
73 20 0.13
74 9 0.06
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (67 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATCGTTGCGATTT
TC
Found at i:24485 original size:53 final size:53
Alignment explanation
Indices: 24287--24457 Score: 308
Period size: 53 Copynumber: 3.2 Consensus size: 53
24277 GATTCTCTCG
* *
24287 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTTATTT-CGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCA
24339 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCA
*
24392 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCA
24445 TTGCGATTTTCAT
1 TTGCGATTTTCAT
24458 GTTGGGATTT
Statistics
Matches: 115, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
52 46 0.40
53 69 0.60
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCA
Found at i:24507 original size:33 final size:33
Alignment explanation
Indices: 24265--24499 Score: 246
Period size: 33 Copynumber: 6.9 Consensus size: 33
24255 TGCGTTTATA
24265 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
24298 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
24331 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * *
24371 GTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTC
*
24403 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* * *
24436 ATTTCCGCGTTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
24470 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
24500 GTAATTTCCG
Statistics
Matches: 171, Mismatches: 16, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
32 10 0.06
33 87 0.51
34 42 0.25
35 7 0.04
36 4 0.02
37 2 0.01
38 8 0.05
39 3 0.02
40 8 0.05
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:26799 original size:12 final size:12
Alignment explanation
Indices: 26782--26806 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26772 TCTTCGGGGA
26782 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26794 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26806 C
1 C
26807 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:27015 original size:24 final size:24
Alignment explanation
Indices: 26981--27027 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26971 CTGAAACATC
26981 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
27005 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
27028 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:27738 original size:20 final size:20
Alignment explanation
Indices: 27710--27939 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
27700 AAATTTCAGT
* * *
27710 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27730 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
27750 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27770 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
27790 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27810 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
27830 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
27850 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
27870 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
27890 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
27910 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
27930 GTTGCGATTT
1 GTTGCGATTT
27940 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:27956 original size:21 final size:21
Alignment explanation
Indices: 27926--28008 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
27916 ATTTTCATAT
*
27926 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
27947 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
27968 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
* *
27989 TAGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
28009 CTGATTTGCG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:28366 original size:2 final size:2
Alignment explanation
Indices: 28324--28354 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28314 TATTTTATTT
28324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28355 TAGGAGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32579 original size:21 final size:21
Alignment explanation
Indices: 32553--32626 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
32543 ATTGCCTCGA
*
32553 TGGTTTTGAAATCATGATGTG
1 TGGTTTTGAAATCATGATGCG
32574 TGGTTTTGAAATCATGATGCG
1 TGGTTTTGAAATCATGATGCG
32595 TGGTTTTGAAATCATGATGCG
1 TGGTTTTGAAATCATGATGCG
32616 TGGTTTTGAAA
1 TGGTTTTGAAA
32627 AGGATGTCCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (21 bp):
TGGTTTTGAAATCATGATGCG
Found at i:33052 original size:140 final size:139
Alignment explanation
Indices: 32846--33246 Score: 531
Period size: 140 Copynumber: 2.9 Consensus size: 139
32836 GAGGACTAAA
* * * * *
32846 CCTAGAAATGTAGGCTCTAATATTAACCCTATTTTATTTTAACCAATTATTGATTCGAATAATCG
1 CCTA-AAATGGAGGCTCTAATATTAATCCTAATTCATTTTAACCAATTATTGATTCAAATAATCG
* * *
32911 AAATGGACCCTTGGGCATTAAGGCGAGGGCGAAGTCAAATTATTCCCTAAATTAAAGGACTAAAG
65 AAATGGACCCTTGGGCATTAAGGCGAGGGCCAAATCAAA-TATTCCCTAGATTAAAGGACTAAAG
32976 TG-AAATTAAG
129 TGAAAATTAAG
** * *
32986 CCTAAGGTGGAGGCTCTAATATTAATCCTAATTGATTTTTAACCAATTATTAATTCAAATAATCG
1 CCTAAAATGGAGGCTCTAATATTAATCCTAATTCA-TTTTAACCAATTATTGATTCAAATAATCG
* * * *
33051 AAATGGACCCTCGGGCATTAAGGCGAAGGCCAAATCAAAGTATTTCCTAGATTTAAGGACTAAAG
65 AAATGGACCCTTGGGCATTAAGGCGAGGGCCAAATCAAA-TATTCCCTAGATTAAAGGACTAAAG
33116 TGAAAATTAAG
129 TGAAAATTAAG
* *
33127 CCTAAAATGGAGGCTCT-ATGATTAATCCTAATTCACTTTAACTAATTATTGATTCAAATAATCG
1 CCTAAAATGGAGGCTCTAAT-ATTAATCCTAATTCATTTTAACCAATTATTGATTCAAATAATCG
* *
33191 AAAT-GATCCCTTGAGCATTAAAGCGAGGGCCAAAT-AGAATATTCCCTAGATTAAAG
65 AAATGGA-CCCTTGGGCATTAAGGCGAGGGCCAAATCA-AATATTCCCTAGATTAAAG
33247 AAAGTTCGAG
Statistics
Matches: 228, Mismatches: 28, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
139 43 0.19
140 148 0.65
141 37 0.16
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (139 bp):
CCTAAAATGGAGGCTCTAATATTAATCCTAATTCATTTTAACCAATTATTGATTCAAATAATCGA
AATGGACCCTTGGGCATTAAGGCGAGGGCCAAATCAAATATTCCCTAGATTAAAGGACTAAAGTG
AAAATTAAG
Found at i:33716 original size:62 final size:59
Alignment explanation
Indices: 33596--33712 Score: 177
Period size: 62 Copynumber: 2.0 Consensus size: 59
33586 CAACTAATGA
*
33596 CAAAAATATAAGGAAAAATAACATGTTTAATACCCTAACCTAACTGGAAGTAATAACAAAC
1 CAAAAATAAAAGGAAAAATAACATGTTTAATA-CC-AACCTAACTGGAAGTAATAACAAAC
33657 CAAAACATAAAAGGAAAAATAACATGTTTAATA-C-A-CTAACTGGAAGTAATAACAAA
1 CAAAA-ATAAAAGGAAAAATAACATGTTTAATACCAACCTAACTGGAAGTAATAACAAA
33713 ACAAGCTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
57 21 0.39
58 1 0.02
60 1 0.02
61 5 0.09
62 26 0.48
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.21
Consensus pattern (59 bp):
CAAAAATAAAAGGAAAAATAACATGTTTAATACCAACCTAACTGGAAGTAATAACAAAC
Found at i:42759 original size:11 final size:11
Alignment explanation
Indices: 42743--42767 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42733 ATTAAAATAA
42743 TTAAAACAAAT
1 TTAAAACAAAT
42754 TTAAAACAAAT
1 TTAAAACAAAT
42765 TTA
1 TTA
42768 TTATTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (11 bp):
TTAAAACAAAT
Found at i:45649 original size:2 final size:2
Alignment explanation
Indices: 45644--45696 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
45634 AAAAGAAAAC
45644 AT 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 AT
45686 AT AT AT AT AT A
1 AT AT AT AT AT A
45697 CATGCCGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47133 original size:18 final size:20
Alignment explanation
Indices: 47096--47137 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
47086 AAAGGAAAAC
47096 AATAATAGTAATAATAATAT
1 AATAATAGTAATAATAATAT
*
47116 AATAAT-GT-ATAATGATAT
1 AATAATAGTAATAATAATAT
47134 AATA
1 AATA
47138 TATGCACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
19 2 0.10
20 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (20 bp):
AATAATAGTAATAATAATAT
Found at i:47223 original size:2 final size:2
Alignment explanation
Indices: 47218--47255 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47208 GTACTTTACA
47218 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
47256 GTGTACGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48294 original size:3 final size:3
Alignment explanation
Indices: 48286--48346 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
48276 CCAGACCTGA
48286 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
48334 AAT -AT AAT TAT AA
1 AAT AAT AAT AAT AA
48347 ACTATTGTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:49549 original size:12 final size:11
Alignment explanation
Indices: 49532--49600 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
49522 GCAAAGGAAA
49532 AATAATAATAGT
1 AATAATAATA-T
49544 AATAATAATAT
1 AATAATAATAT
**
49555 AATAAT-GCAT
1 AATAATAATAT
49565 AATGATATAATAT
1 AAT-A-ATAATAT
*
49578 ATATACT-ATAT
1 A-ATAATAATAT
*
49589 AATAAAAATAT
1 AATAATAATAT
49600 A
1 A
49601 CTATGTAACT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
10 8 0.18
11 18 0.40
12 13 0.29
13 4 0.09
14 2 0.04
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (11 bp):
AATAATAATAT
Found at i:49593 original size:27 final size:26
Alignment explanation
Indices: 49569--49626 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
49559 ATGCATAATG
49569 ATATAATATATATACTATATAATAAAA
1 ATATAATATATA-ACTATATAATAAAA
* * * *
49596 ATATACTATGTAACTATATAGTATAA
1 ATATAATATATAACTATATAATAAAA
49622 ATATA
1 ATATA
49627 CAACTATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (26 bp):
ATATAATATATAACTATATAATAAAA
Found at i:49683 original size:28 final size:26
Alignment explanation
Indices: 49631--49694 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
49621 AATATACAAC
*
49631 TATATAATAATATATGTACTTTATAA
1 TATATAATAATATATGTACTCTATAA
*
49657 TATATATATATATATATGTA-TGCTATAC
1 TATATA-ATA-ATATATGTACT-CTATAA
*
49685 CATATAATAA
1 TATATAATAA
49695 ATGCATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 7 0.22
27 7 0.22
28 18 0.56
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (26 bp):
TATATAATAATATATGTACTCTATAA
Found at i:59972 original size:2 final size:2
Alignment explanation
Indices: 59967--60008 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
59957 AAAAGAAATA
59967 AT 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 AT
60009 CATGCCGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61469 original size:2 final size:2
Alignment explanation
Indices: 61462--61532 Score: 67
Period size: 2 Copynumber: 35.5 Consensus size: 2
61452 AACTATGTAG
* * *
61462 TA TA TA TA TA CA -A CTA TA TA -A TA -A TA TA TG TA CTT TA TA GTA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
61504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61533 GCTATACCAT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
1 3 0.05
2 51 0.88
3 4 0.07
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:62564 original size:3 final size:3
Alignment explanation
Indices: 62556--62601 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
62546 CCAGACCTGA
*
62556 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT TAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
62602 ACTATTGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Done.