Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009204.1 Hibiscus syriacus cultivar Beakdansim tig00112790_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: 147273
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4968 original size:40 final size:41
Alignment explanation
Indices: 4924--5017 Score: 156
Period size: 40 Copynumber: 2.3 Consensus size: 41
4914 CGATTTTCCC
*
4924 AATTCGCAATGCGAA-ATGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
4964 AATTCGC-ATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
5004 AAATCGCAATGCGA
1 AATTCGCAATGCGA
5018 TACTGACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 7 0.14
40 37 0.74
41 6 0.12
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:4976 original size:20 final size:20
Alignment explanation
Indices: 4927--5017 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
4917 TTTTCCCAAT
* *
4927 TCGCAATGCGAAAT-GTAAA
1 TCGCAATGCGAATTGGGAAA
*
4946 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATTGGGAAA
** *
4966 TTCGC-ATGCGAATAAGTAAA
1 -TCGCAATGCGAATTGGGAAA
*
4986 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGG-AAA
5007 TCGCAATGCGA
1 TCGCAATGCGA
5018 TACTGACTAT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 16 0.29
20 23 0.41
21 17 0.30
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATTGGGAAA
Found at i:5031 original size:20 final size:20
Alignment explanation
Indices: 5006--5098 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
4996 AATTGGGAAA
*
5006 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
5026 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
5047 ATCGCAACGAGATACTTA-T
1 ATCGCAACGCGATACTGACT
*
5066 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
5086 TTCGCAACGCGAT
1 ATCGCAACGCGAT
5099 TTACTTAGCG
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.25
20 30 0.51
21 14 0.24
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:5048 original size:41 final size:40
Alignment explanation
Indices: 5003--5079 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 40
4993 GCGAATTGGG
* * *
5003 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGA-TATCGCAACGCGATAATAA
* *
5044 AAAATCGCAACGAGATACTTATTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGATATCGCAACGCGATA
5080 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 13 0.42
41 18 0.58
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (40 bp):
AAAATCGCAACGAGATACTGATATCGCAACGCGATAATAA
Found at i:5072 original size:19 final size:20
Alignment explanation
Indices: 5048--5094 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
5038 TAATAAAAAA
*
5048 TCGCAACGAGATACTTA-TT
1 TCGCAACGAGATACTGACTT
*
5067 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
5087 TCGCAACG
1 TCGCAACG
5095 CGATTTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:5645 original size:19 final size:19
Alignment explanation
Indices: 5607--5673 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
5597 TTCGAGAATG
*
5607 AAAATCGCAAAGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
5627 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
5646 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
5665 AAAATCGCA
1 AAAATCGCA
5674 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:5749 original size:19 final size:19
Alignment explanation
Indices: 5669--5738 Score: 131
Period size: 19 Copynumber: 3.7 Consensus size: 19
5659 GAAACCAAAA
*
5669 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5688 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5707 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5726 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5739 CTCTCGTCGC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5749 original size:38 final size:37
Alignment explanation
Indices: 5669--5776 Score: 118
Period size: 38 Copynumber: 3.0 Consensus size: 37
5659 GAAACCAAAA
* *
5669 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCAT-T
1 TCGC-TTGCGATTTTCATTTCGCGTTGCGATTCTC-TCG
5707 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TCGC-TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
5745 T--C--GCGATAGTCATTTCGCGTTGCGATTCTCTC
1 TCGCTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
5777 ATTGCGATAG
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
33 28 0.44
36 1 0.02
37 1 0.02
38 34 0.53
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (37 bp):
TCGCTTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:5758 original size:33 final size:33
Alignment explanation
Indices: 5721--5810 Score: 126
Period size: 33 Copynumber: 2.6 Consensus size: 33
5711 GTTGCGATTT
*
5721 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
5754 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
5787 TCATTTTTCCGCGTTGCAATTCTC
1 TCA--TTT-CGCGTTGCGATTCTC
5811 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
33 34 0.67
35 3 0.06
36 14 0.27
ACGTcount: A:0.13, C:0.27, G:0.20, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:7875 original size:21 final size:21
Alignment explanation
Indices: 7851--7917 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
7841 TCATTCCTCG
7851 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
7872 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
7893 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
7914 AGAG
1 AGAG
7918 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:9281 original size:13 final size:14
Alignment explanation
Indices: 9256--9290 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
9246 ATTGTTTAAT
9256 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
9270 TGATTTGT-AAAGT
1 TGATTTGTAAAAGG
9283 TGATTTGT
1 TGATTTGT
9291 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:9299 original size:13 final size:14
Alignment explanation
Indices: 9243--9291 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
9233 TGCTTATTTT
*
9243 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
*
9255 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
9269 GTGATTTG-TAAAG
1 TTGATTTGTTAAAG
9282 TTGATTTGTT
1 TTGATTTGTT
9292 TAATTGATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 4 0.14
13 17 0.59
14 8 0.28
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:9451 original size:19 final size:18
Alignment explanation
Indices: 9396--9466 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
9386 CAAAAGTACT
*
9396 ATCGCAATGCGAAATGAA
1 ATCGCAACGCGAAATGAA
*
9414 ATCGCAA--CGAGA-G-A
1 ATCGCAACGCGAAATGAA
9428 ATCGCAACGCGAAAATGAA
1 ATCGCAACGCG-AAATGAA
*
9447 ATCGCAACGCGAAATTAA
1 ATCGCAACGCGAAATGAA
9465 AT
1 AT
9467 TCGCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 8 0.18
15 1 0.02
16 6 0.13
17 2 0.04
18 16 0.36
19 12 0.27
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (18 bp):
ATCGCAACGCGAAATGAA
Found at i:9470 original size:19 final size:19
Alignment explanation
Indices: 9396--9460 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
9386 CAAAAGTACT
*
9396 ATCGCAATGCG-AAATGAA
1 ATCGCAACGCGAAAATGAA
*
9414 ATCGCAA--CG-AGA-G-A
1 ATCGCAACGCGAAAATGAA
9428 ATCGCAACGCGAAAATGAA
1 ATCGCAACGCGAAAATGAA
9447 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
9461 TTAAATTCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 8 0.20
15 1 0.03
16 6 0.15
17 2 0.05
18 8 0.20
19 15 0.38
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAAATGAA
Found at i:9548 original size:33 final size:33
Alignment explanation
Indices: 9470--9564 Score: 172
Period size: 34 Copynumber: 2.8 Consensus size: 33
9460 ATTAAATTCG
9470 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
9503 CGTTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CG-TTGCGATTTTCATTTCGCATTGCGATTCCCT
9537 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
9565 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
33 28 0.47
34 32 0.53
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:11840 original size:12 final size:12
Alignment explanation
Indices: 11823--11847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11813 TCTTCGGGGA
11823 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11835 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11847 C
1 C
11848 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:13321 original size:14 final size:14
Alignment explanation
Indices: 13304--13340 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
13294 ACATCATTAA
13304 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
13318 ACAAATCATCTTTT
1 ACAAATCAACATTT
13332 ACAAATCAA
1 ACAAATCAA
13341 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:13907 original size:14 final size:13
Alignment explanation
Indices: 13888--13923 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
13878 CATCAATTAA
13888 ACAAATCAACATTT
1 ACAAATCAAC-TTT
*
13902 ACAAATCATCTTT
1 ACAAATCAACTTT
13915 ACAAATCAA
1 ACAAATCAA
13924 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (13 bp):
ACAAATCAACTTT
Found at i:14316 original size:582 final size:589
Alignment explanation
Indices: 12934--15341 Score: 4590
Period size: 581 Copynumber: 4.1 Consensus size: 589
12924 TTTAACAATT
12934 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
12999 CTTGCATTATGTGTATTTTA-GTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
13063 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
13128 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
13193 TCGTTGCGATAACCATTTCGCGTTGCGATAG--TGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
13256 TC-ACAAATCAACTATTACATTTCAACAC-AATTATGTACACATC-ATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
13318 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
13383 ATTATTGAATCAAGAATCAACAACTTTGTGA-CCCGTACATCCATTTCACGCAGCTCACTTAAGG
456 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
*
13447 ATTAACATGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
521 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
13512 GCAA
586 GCAA
13516 ATTATTGAATTCTAGGTACTTAA-CAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
13580 CTTGCATTATGTGTATTTTATGTGTGCAATTTTAACATTTTCAGTTAGGCATGTATTAGT-ACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
*
13644 GAGTTTGAACATTGCTATGATATGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
13709 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAA-CGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
13773 TCGTTGCGATAACCATTTCGCGTTGCG-TAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
13837 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
13902 ACAAATCATC-TTTACAAATCAATTAAACAATCAAAAAAT-ATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
13965 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACAT-CATTTCACGCAGCTCACTTAAGG
456 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
*
14029 ATT-ACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAATA
521 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
14093 GCAA
586 GCAA
14097 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
14162 CTTGCATTATGTG-ATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACAT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
14226 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
14291 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
14356 TCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
261 TCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
14421 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
326 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
14486 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
391 ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
14551 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
456 ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
*
14616 ATTAACCTGCAGAAATCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
521 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
14681 GCAA
586 GCAA
14685 ATTATTTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAA
1 ATTA-TTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAA
14750 ACTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACT
65 ACTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACT
14815 TGAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCG
130 TGAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCG
*
14880 CAATGCGAAAATGGTTATCGCAATGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTT
195 CAATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTT
14945 CTCGTTGCGATAACCA-TTCGCGTTGCGATAGTC-GTTTTGCCTTCAACATAAAGCAGATTGAAA
260 CTCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAA
15008 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
325 ATCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATT
15073 TACAAATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAAT-ATTCTTATTTCTTCATC
390 TACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATC
15136 -ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
455 AATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAG
15200 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
520 GATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAAC
15265 AGCAA
585 AGCAA
15270 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATAT-TTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
15334 CTTGCATT
66 CTTGCATT
15342 TGACTTACCA
Statistics
Matches: 1797, Mismatches: 12, Indels: 33
0.98 0.01 0.02
Matches are distributed among these distances:
579 3 0.00
580 42 0.02
581 343 0.19
582 338 0.19
583 112 0.06
584 192 0.11
585 166 0.09
586 82 0.05
587 38 0.02
588 196 0.11
589 91 0.05
590 194 0.11
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (589 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCATTGCGATTTTC
TCGTTGCGATAACCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAAATCAACATTT
ACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCA
ATTATTGAATCAAGAATCAACAACTTTGTGACCCCGTACATCCATTTCACGCAGCTCACTTAAGG
ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
GCAA
Found at i:14491 original size:14 final size:14
Alignment explanation
Indices: 14472--14508 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
14462 CATCAATTAA
14472 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
14486 ACAAATCATCTTTT
1 ACAAATCAACATTT
14500 ACAAATCAA
1 ACAAATCAA
14509 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:15079 original size:14 final size:14
Alignment explanation
Indices: 15060--15096 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
15050 CATCAATTAA
15060 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
15074 ACAAATCATCTTTT
1 ACAAATCAACATTT
15088 ACAAATCAA
1 ACAAATCAA
15097 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:16984 original size:20 final size:19
Alignment explanation
Indices: 16949--17024 Score: 98
Period size: 20 Copynumber: 3.9 Consensus size: 19
16939 GAAACTTAAA
16949 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
16968 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* *
16988 ATCGCAATGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
*
17008 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
17025 AAAATCGCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
19 16 0.30
20 37 0.70
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:17032 original size:40 final size:39
Alignment explanation
Indices: 16946--17036 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
16936 CACGAAACTT
16946 AAAATCGCAACGCGAAATGACTATCGCAACGCGGAAATG
1 AAAATCGCAACGCGAAATGACTATCGCAACGCGGAAATG
*** * * *
16985 GCTATCGCAATGCGGAAATGGCTATCGCAATGC-GAAATG
1 AAAATCGCAACGC-GAAATGACTATCGCAACGCGGAAATG
17024 AAAAATCGCAACG
1 -AAAATCGCAACG
17037 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
39 15 0.38
40 25 0.62
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.15
Consensus pattern (39 bp):
AAAATCGCAACGCGAAATGACTATCGCAACGCGGAAATG
Found at i:17044 original size:14 final size:14
Alignment explanation
Indices: 17025--17082 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
17015 TGCGAAATGA
17025 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
17039 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
17055 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
17071 AAAATCGCAACG
1 AAAATCGCAACG
17083 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:17067 original size:32 final size:33
Alignment explanation
Indices: 17008--17087 Score: 135
Period size: 32 Copynumber: 2.4 Consensus size: 33
16998 GGAAATGGCT
*
17008 ATCGCAATGCGAAATGAAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAAATCGCAACGACAAA
17042 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
17074 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
17088 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 30 0.67
34 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:17116 original size:19 final size:18
Alignment explanation
Indices: 17094--17189 Score: 75
Period size: 19 Copynumber: 5.6 Consensus size: 18
17084 GAAACACAAA
17094 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
*
17113 TCGCGTTGCGATTTT--GT
1 TCGC-TTGCGATTTTCATT
17130 T-G-TTGCGA-TTTCATT
1 TCGCTTGCGATTTTCATT
*
17145 TCGCGTTGCGA-TTT--TG
1 TCGC-TTGCGATTTTCATT
17161 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
17178 TCGCATTGCGAT
1 TCGC-TTGCGAT
17190 AGCCATTTCC
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
13 3 0.05
14 12 0.19
15 5 0.08
16 6 0.10
17 6 0.10
18 9 0.15
19 21 0.34
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:17136 original size:14 final size:14
Alignment explanation
Indices: 17117--17173 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
17107 TTCATTTCGC
17117 GTTGCGATTTTGTT
1 GTTGCGATTTTGTT
17131 GTTGCGATTTCAT-TT
1 GTTGCGATTT--TGTT
*
17146 CGCGTTGCGATTTTGTC
1 ---GTTGCGATTTTGTT
17163 GTTGCGATTTT
1 GTTGCGATTTT
17174 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
14 21 0.58
15 2 0.06
16 2 0.06
17 1 0.03
18 10 0.28
ACGTcount: A:0.09, C:0.14, G:0.26, T:0.51
Consensus pattern (14 bp):
GTTGCGATTTTGTT
Found at i:17180 original size:33 final size:33
Alignment explanation
Indices: 17099--17189 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
17089 ACAAATCGCA
*
17099 TTGCGATTTTCATTTCGCGTTGCGATTTTGTTG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
17132 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
17164 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
17190 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:17208 original size:20 final size:19
Alignment explanation
Indices: 17174--17228 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
17164 TTGCGATTTT
*
17174 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
17193 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
17213 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
17229 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:17726 original size:18 final size:18
Alignment explanation
Indices: 17700--17744 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
17690 GTCGATCAGA
*
17700 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
17718 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
17736 TGATGGCTC
1 TGATGGCTC
17745 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:19077 original size:20 final size:20
Alignment explanation
Indices: 19052--19105 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
19042 AATAGTTTCT
19052 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
19072 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
19092 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
19106 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:19364 original size:22 final size:22
Alignment explanation
Indices: 19339--19382 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19329 GATTTAGATA
19339 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
19361 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
19383 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:19593 original size:20 final size:20
Alignment explanation
Indices: 19568--19661 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
19558 GATTATGTAT
19568 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
19588 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
19608 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
19629 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
19649 TATCGCATTGCGA
1 TATCGCGTTGCGA
19662 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:19633 original size:41 final size:42
Alignment explanation
Indices: 19588--19723 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
19578 CGAAAGTCAG
* * * *
19588 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
19629 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
19671 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
19712 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
19724 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:19662 original size:20 final size:20
Alignment explanation
Indices: 19548--19662 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
19538 CGCTTTGAAA
*
19548 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
19569 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
19589 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
19609 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
19630 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
19650 ATCGCATTGCGAT
1 ATCGCATTGCGAT
19663 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:19695 original size:20 final size:20
Alignment explanation
Indices: 19651--19743 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
19641 ATAGTCAGTA
*
19651 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
19672 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
19692 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
19713 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
19733 TCGCATTGCGA
1 TCGCATTGCGA
19744 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:19724 original size:41 final size:41
Alignment explanation
Indices: 19651--19746 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
19641 ATAGTCAGTA
* *
19651 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
19692 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
19733 TCGCATTGCGAATT
1 TCGCATTGCGAATT
19747 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:37822 original size:2 final size:2
Alignment explanation
Indices: 37817--37843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37807 TATACGTATG
37817 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 T
37844 TCTTCTGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41611 original size:2 final size:2
Alignment explanation
Indices: 41604--41636 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
41594 ATAATAAATA
*
41604 AT AT AT AT TT AT A- 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
41637 TGTTGGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:41617 original size:17 final size:19
Alignment explanation
Indices: 41594--41635 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41584 TAAATAGTTA
* *
41594 ATAATAAATAATATATATTT
1 ATAATATAT-ATATATATAT
41614 ATAATATATATATATATAT
1 ATAATATATATATATATAT
41633 ATA
1 ATA
41636 TTGTTGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATATATATATATATAT
Found at i:44005 original size:39 final size:36
Alignment explanation
Indices: 43957--44029 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 36
43947 TATTTTGGAG
*
43957 ACTTGAATATACAAGCATCAAAACGACGTTGTTTTGAAAA
1 ACTTGAATATAC-A-C--CAAAACGACGTCGTTTTGAAAA
43997 ACTT-AATATACACCAAAACGACGTCGTTTTGAA
1 ACTTGAATATACACCAAAACGACGTCGTTTTGAA
44030 TCCTATATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 19 0.59
37 1 0.03
38 1 0.03
39 7 0.22
40 4 0.12
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (36 bp):
ACTTGAATATACACCAAAACGACGTCGTTTTGAAAA
Found at i:44130 original size:51 final size:51
Alignment explanation
Indices: 44036--44134 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
44026 TGAATCCTAT
** * * *
44036 ATTGAAAGTTGGGTGAGGAAAATAGGAGAGAGAGTAAAATTCAGTGAGCAA
1 ATTGAAAGTTGACTGAGGAAAATAAGAGAGAAAATAAAATTCAGTGAGCAA
* * *
44087 ATTGAAAGTTGACTGAGGGAAATAAGAGATAAAATAAAGTTCAGTGAG
1 ATTGAAAGTTGACTGAGGAAAATAAGAGAGAAAATAAAATTCAGTGAG
44135 GAACGATGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.44, C:0.04, G:0.30, T:0.21
Consensus pattern (51 bp):
ATTGAAAGTTGACTGAGGAAAATAAGAGAGAAAATAAAATTCAGTGAGCAA
Found at i:55931 original size:17 final size:16
Alignment explanation
Indices: 55909--55942 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
55899 TAAAAACAGT
55909 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
55926 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
55942 A
1 A
55943 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:57706 original size:21 final size:21
Alignment explanation
Indices: 57662--57703 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57652 AATTGATATT
*
57662 TTTTTCTACCGAAAATATTAA
1 TTTTTCTACCGAAAATAATAA
*
57683 TTTTTCTACCTAAAATTAATA
1 TTTTTCTACCGAAAA-TAATA
57704 TTTCCGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTTCTACCGAAAATAATAA
Found at i:57707 original size:19 final size:21
Alignment explanation
Indices: 57664--57707 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
57654 TTGATATTTT
*
57664 TTTCTACCGAAAATATTAATT
1 TTTCTACCGAAAATATTAATA
*
57685 TTTCTACC-TAAA-ATTAATA
1 TTTCTACCGAAAATATTAATA
57704 TTTC
1 TTTC
57708 CGATATTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTCTACCGAAAATATTAATA
Found at i:59755 original size:24 final size:23
Alignment explanation
Indices: 59718--59787 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
59708 TAGAAAATTT
*
59718 AATAAA-ATTATTATAATAATAA
1 AATAAATAATATTATAATAATAA
* *
59740 TAATAATTAATATTATATATATTAA
1 -AATAAATAATATTATA-ATAATAA
*
59765 AATAAATAAAATTTATAATAATA
1 AATAAATAATA-TTATAATAATA
59788 TTTTAACCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 5 0.13
24 22 0.58
25 11 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATAAATAATATTATAATAATAA
Found at i:60028 original size:36 final size:35
Alignment explanation
Indices: 59972--60057 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 35
59962 CTATATATAT
* * *
59972 ATATATATAACATATGATATTATATATT-TATTTTA
1 ATATATATAATAAATGATATTATATATTGTA-TTCA
* *
60007 ATAATATATAATAAATTATATTATTTATTGTATTCA
1 AT-ATATATAATAAATGATATTATATATTGTATTCA
*
60043 ATATTTATAATAAAT
1 ATATATATAATAAAT
60058 AGTTTTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
35 14 0.33
36 27 0.63
37 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (35 bp):
ATATATATAATAAATGATATTATATATTGTATTCA
Found at i:62598 original size:15 final size:15
Alignment explanation
Indices: 62578--62613 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
62568 GCAGACACAG
62578 GCCGCCATTAGCTCC
1 GCCGCCATTAGCTCC
62593 GCCGCCATTAGCTCC
1 GCCGCCATTAGCTCC
62608 GCCGCC
1 GCCGCC
62614 GACCACCGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.50, G:0.22, T:0.17
Consensus pattern (15 bp):
GCCGCCATTAGCTCC
Found at i:63351 original size:3 final size:3
Alignment explanation
Indices: 63345--63424 Score: 135
Period size: 3 Copynumber: 26.3 Consensus size: 3
63335 AATATTTTAT
63345 TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
63391 TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA T
63425 CAAATGAAGA
Statistics
Matches: 74, Mismatches: 0, Indels: 6
0.93 0.00 0.08
Matches are distributed among these distances:
2 2 0.03
3 67 0.91
4 5 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:67548 original size:3 final size:3
Alignment explanation
Indices: 67540--67576 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
67530 TAAATATTCG
67540 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
67577 ATTGTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:68502 original size:2 final size:2
Alignment explanation
Indices: 68495--68519 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68485 AATCTTAGTA
68495 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 A
68520 ATTATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84737 original size:2 final size:2
Alignment explanation
Indices: 84732--84794 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
84722 TCAATTTATC
84732 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
84774 AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
84795 GGCTATTCCA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85641 original size:21 final size:21
Alignment explanation
Indices: 85617--85687 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
85607 TGCATTTCGT
*
85617 GTTGCGATAGTTGAAAACCGC
1 GTTGCGATAGTTGAAAATCGC
85638 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGTTGAAAATCGC
85659 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGTTGAAAATCGC
85680 GTTGCGAT
1 GTTGCGAT
85688 TTTTCATTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (21 bp):
GTTGCGATAGTTGAAAATCGC
Found at i:85846 original size:12 final size:11
Alignment explanation
Indices: 85829--85864 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
85819 GACACGTATT
85829 ACCACGACCACG
1 ACCACGACC-CG
85841 ACCACGACCCG
1 ACCACGACCCG
85852 ACC-CGACCCG
1 ACCACGACCCG
85862 ACC
1 ACC
85865 CGAGACGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.28, C:0.56, G:0.17, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:85855 original size:5 final size:5
Alignment explanation
Indices: 85833--85867 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
85823 CGTATTACCA
85833 CGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
85868 GACGGATGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:91610 original size:31 final size:31
Alignment explanation
Indices: 91572--91696 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
91562 CCCGAAGGAC
* *
91572 CAGTCCATA-GATTCCTAAGAACCTAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* * *
91603 CAGTCCATATGTCCCAAAAAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
91634 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
91665 CAGTCCATATATTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
91696 C
1 C
91697 CCTCGACCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:92480 original size:20 final size:20
Alignment explanation
Indices: 92431--92483 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
92421 CGAAATTACC
*
92431 ATGCATCGACGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
*
92451 AAGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
92471 ATGCATCGATGCA
1 ATGCATCGATGCA
92484 TCTTCAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:93913 original size:64 final size:61
Alignment explanation
Indices: 93842--93998 Score: 161
Period size: 64 Copynumber: 2.4 Consensus size: 61
93832 TTCAGTTTGT
* *
93842 ATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCA-AGG-AGTGCATCGATGCACCCATT-AAAATGAAAACATCGAAGGCAATTAGTGC
* * ** * *
93906 ATCGATGCATAAGGAGTGCATCAATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGC--AAGGAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
*
93970 ATCGATGCATGAGTAGTGCATCGATGCAC
1 ATCGATGCA--AGGAGTGCATCGATGCAC
93999 TTGTTAAAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 67 0.86
65 8 0.10
66 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (61 bp):
ATCGATGCAAGGAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:94018 original size:24 final size:22
Alignment explanation
Indices: 93986--94049 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 22
93976 GCATGAGTAG
93986 TGCATCGATGCACTTGTTAAAGAA
1 TGCATCGATGCAC-T-TTAAAGAA
*
94010 TGCATCGATGCAC--TATAGAA
1 TGCATCGATGCACTTTAAAGAA
*
94030 TGCATCGATGCACTTCAAAG
1 TGCATCGATGCACTTTAAAG
94050 GGGAAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 19 0.54
22 3 0.09
24 13 0.37
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACTTTAAAGAA
Found at i:97988 original size:64 final size:64
Alignment explanation
Indices: 97885--98037 Score: 184
Period size: 64 Copynumber: 2.4 Consensus size: 64
97875 TTCAGTGTGT
* * *
97885 ATCGATGCA-CAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGG-AGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTAGTGC
* ** * *
97949 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCATAAGGAGTGCATCGATGCA-CCCATTAAAAATGAAAACATCGAAGGCAATTAGTGC
* *
98013 ATCGATGCATGAGTAGTGCATCGAT
1 ATCGATGCATAAGGAGTGCATCGAT
98038 ACACATGTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 69 0.90
65 8 0.10
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (64 bp):
ATCGATGCATAAGGAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:101374 original size:3 final size:3
Alignment explanation
Indices: 101366--101438 Score: 123
Period size: 3 Copynumber: 25.0 Consensus size: 3
101356 TCAGGTTTTA
101366 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT -TT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
101412 ATT ATT ATT ATT ATG ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
101439 CTATTAATAA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:102053 original size:24 final size:25
Alignment explanation
Indices: 102026--102078 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
102016 CACTTTTCAA
* *
102026 AAAAAAC-CCAACATAAAGAAAAAG
1 AAAAAACACAAACAAAAAGAAAAAG
102050 -AAAAACACAAACAAAAAGAAAAAG
1 AAAAAACACAAACAAAAAGAAAAAG
102074 AAAAA
1 AAAAA
102079 GGGGAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 15 0.60
25 4 0.16
ACGTcount: A:0.77, C:0.13, G:0.08, T:0.02
Consensus pattern (25 bp):
AAAAAACACAAACAAAAAGAAAAAG
Found at i:102071 original size:5 final size:6
Alignment explanation
Indices: 102040--102106 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
102030 AACCCAACAT
* * * ** *
102040 AAAGAA AAAGAA AAACAC AAACAA AAAGAA AAAGAA AAAGGG GAAG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
102087 AAAGAA AAAAAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AA
102107 GAGGGAGAGT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
5 3 0.06
6 46 0.94
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:103232 original size:15 final size:15
Alignment explanation
Indices: 103212--103279 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
103202 TACAAATATT
103212 TAATTTATTAAGTAC
1 TAATTTATTAAGTAC
*
103227 TAATTTATTAAGTAT
1 TAATTTATTAAGTAC
* ** * *
103242 TATTTTAAAAAATAT
1 TAATTTATTAAGTAC
103257 TAATTTATTAAGTAC
1 TAATTTATTAAGTAC
103272 TAATTTAT
1 TAATTTAT
103280 AGAGGTAACT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (15 bp):
TAATTTATTAAGTAC
Found at i:109768 original size:92 final size:92
Alignment explanation
Indices: 109611--109793 Score: 339
Period size: 92 Copynumber: 2.0 Consensus size: 92
109601 AGATTAGTTA
* *
109611 TTCTTTTGGTAGTTGCTTCCTACTCAAGGAATGTGGAACCAAATGAAATGTAGCTTATTATTAAT
1 TTCTTTCGGTAGTTGCTTCCTACTCAAGGAATGTGGAACCAAATGAAATGTAGCTTACTATTAAT
109676 GAAATTTAATTGGCTTCTTTTATCTTT
66 GAAATTTAATTGGCTTCTTTTATCTTT
109703 TTCTTTCGGTAGTTGCTTCCTACTCAAGGAATGTGGAACCAAATGAAATGTAGCTTACTATTAAT
1 TTCTTTCGGTAGTTGCTTCCTACTCAAGGAATGTGGAACCAAATGAAATGTAGCTTACTATTAAT
*
109768 GAAATTTAATTGGCTTCTTTTTTCTT
66 GAAATTTAATTGGCTTCTTTTATCTT
109794 GATCACAAGG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (92 bp):
TTCTTTCGGTAGTTGCTTCCTACTCAAGGAATGTGGAACCAAATGAAATGTAGCTTACTATTAAT
GAAATTTAATTGGCTTCTTTTATCTTT
Found at i:114225 original size:15 final size:16
Alignment explanation
Indices: 114205--114309 Score: 53
Period size: 15 Copynumber: 6.8 Consensus size: 16
114195 GAAAAAAGTT
114205 TAAAAT-ATAAATAAA
1 TAAAATAATAAATAAA
* *
114220 TAAAATCAT-ATTAACA
1 TAAAATAATAAATAA-A
114236 T-AAATAATAAA-AAA
1 TAAAATAATAAATAAA
*
114250 TAAAA-AAAAAATTAAA
1 TAAAATAATAAA-TAAA
* ** *
114266 TTAAATTTTAAAGGAAA
1 TAAAATAATAAA-TAAA
*
114283 T-AAATAAACAAATAAA
1 TAAAAT-AATAAATAAA
114299 T-AAATAATAAA
1 TAAAATAATAAA
114310 AAGAGTGAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
14 7 0.10
15 26 0.39
16 24 0.36
17 10 0.15
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.26
Consensus pattern (16 bp):
TAAAATAATAAATAAA
Found at i:115578 original size:38 final size:39
Alignment explanation
Indices: 115536--115623 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 39
115526 AAAATAAACA
115536 ATATTAATATA-ATATATAAAAAACATTTTC-AAAATTAT
1 ATATTAATATACAT-TATAAAAAACATTTTCAAAAATTAT
* * *
115574 ATATT-ATATACATTCTCAAAAATATTTTCAAAAATTAT
1 ATATTAATATACATTATAAAAAACATTTTCAAAAATTAT
115612 ATATTATATATA
1 ATATTA-ATATA
115624 TTTTTTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
37 18 0.42
38 20 0.47
40 5 0.12
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (39 bp):
ATATTAATATACATTATAAAAAACATTTTCAAAAATTAT
Found at i:115633 original size:28 final size:28
Alignment explanation
Indices: 115598--115662 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
115588 CTCAAAAATA
*
115598 TTTTCAAAAATTATATATTATATATATT
1 TTTTCAAAAACTATATATTATATATATT
115626 TTTTCAAAAACTATATATTATATATATT
1 TTTTCAAAAACTATATATTATATATATT
115654 TTTTCAAAA
1 TTTTCAAAA
115663 TGTTTTCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTCAAAAACTATATATTATATATATT
Found at i:115669 original size:39 final size:38
Alignment explanation
Indices: 115626--115913 Score: 365
Period size: 39 Copynumber: 7.6 Consensus size: 38
115616 TATATATATT
115626 TTTTCAAAAACTATATATTATATATATTTTTTCAAAATG
1 TTTTCAAAAACTATATATTATATATA-TTTTTCAAAATG
*
115665 TTTTCAAAAACTATATATTATATATACTTTTTCAAAATA
1 TTTTCAAAAACTATATATTATATATA-TTTTTCAAAATG
*
115704 TTTTCAAAAACTATATATTATATATATACTTTCAAAATG
1 TTTTCAAAAACTATATATTATATATAT-TTTTCAAAATG
*
115743 TTTTCAAAAACTATATATTATATATA-TATTCAAAATG
1 TTTTCAAAAACTATATATTATATATATTTTTCAAAATG
*
115780 TTTTCAAAAACTATATATTATATATA-TTTTCAAAAACG
1 TTTTCAAAAACTATATATTATATATATTTTTC-AAAATG
* * *
115818 TTTTCAAAAACTACATATTATATAT-GTTTTCAAAA-A
1 TTTTCAAAAACTATATATTATATATATTTTTCAAAATG
* * *
115854 TTTTC-AAAACTATATAATATATATA-TATTCGAAAACCG
1 TTTTCAAAAACTATATATTATATATATTTTTC-AAAA-TG
* *
115892 CTTTC-AAAACTATATAATATAT
1 TTTTCAAAAACTATATATTATAT
115914 TTTCAAAAAT
Statistics
Matches: 227, Mismatches: 15, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
35 21 0.09
36 9 0.04
37 43 0.19
38 56 0.25
39 98 0.43
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (38 bp):
TTTTCAAAAACTATATATTATATATATTTTTCAAAATG
Found at i:115794 original size:26 final size:26
Alignment explanation
Indices: 115765--115816 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
115755 ATATATTATA
*
115765 TATATATTCA-AAATGTTTTCAAAAAC
1 TATATATT-ATAAATATTTTCAAAAAC
*
115791 TATATATTATATATATTTTCAAAAAC
1 TATATATTATAAATATTTTCAAAAAC
115817 GTTTTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (26 bp):
TATATATTATAAATATTTTCAAAAAC
Found at i:116031 original size:2 final size:2
Alignment explanation
Indices: 116024--116051 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
116014 AGTGTCTACA
116024 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
116052 CAAGTAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120727 original size:13 final size:13
Alignment explanation
Indices: 120709--120745 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
120699 AGTAGTTCTC
*
120709 TTTTTTTCTTGTT
1 TTTTTTTCTGGTT
120722 TTTTTTTCTGGTT
1 TTTTTTTCTGGTT
120735 TTTTTTTCTGG
1 TTTTTTTCTGG
120746 GCTTCCCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (13 bp):
TTTTTTTCTGGTT
Found at i:121266 original size:3 final size:3
Alignment explanation
Indices: 121253--121328 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
121243 ATAAATGAGC
121253 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
121300 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
121329 TACAATTAGA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 70 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:121797 original size:134 final size:134
Alignment explanation
Indices: 121528--121887 Score: 497
Period size: 134 Copynumber: 2.7 Consensus size: 134
121518 GTTCGGGTCG
* * * * * * *
121528 TCTAAGGGTGACATGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGTTGACACTGCTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGTTCCTACGT
* * * *
121593 GATGAAGA-GTTCTTGGCCATCTTTAGGAATGGTGATAACTCGGTTCCTACGCAATGAGGACGGC
66 GATGAGGACG-AC-TGGCCATCTTTAGGAATGGTGATAACTCGGCTCCTACGCAATGAGGACGAC
121657 TAGTTA
129 TAGTTA
* * *
121663 TCTAGGGGTGACACGGCTCCTACATGATGAAGAGATCTGGTCGAGGGATGACACGGTTCCTACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGTTCCTACGT
* * * * ** *
121728 GTTGAGGACGGCTGGCCATCTTTAGGAGTGGTGATAGCTCGGCTCCTACGTGATGAGGACGACTG
66 GATGAGGACGACTGGCCATCTTTAGGAATGGTGATAACTCGGCTCCTACGCAATGAGGACGACTA
121793 GTTA
131 GTTA
*
121797 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGGTTCCTACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGTTCCTACGT
121862 GATGAGGACGACTGGCCATCTTTAGG
66 GATGAGGACGACTGGCCATCTTTAGG
121888 GATCATGGTT
Statistics
Matches: 198, Mismatches: 26, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
134 135 0.68
135 62 0.31
136 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (134 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACGGTTCCTACGT
GATGAGGACGACTGGCCATCTTTAGGAATGGTGATAACTCGGCTCCTACGCAATGAGGACGACTA
GTTA
Found at i:121821 original size:43 final size:40
Alignment explanation
Indices: 121767--121876 Score: 141
Period size: 40 Copynumber: 2.7 Consensus size: 40
121757 GGTGATAGCT
121767 CGGCTCCTACGTGATGAGGACGACTGGTTATCTAAGGG-TGACA
1 CGGCTCCTACGTGATGAGGACGACTGG---TC-AAGGGATGACA
* * *
121810 CGGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACA
1 CGGCTCCTACGTGATGAGGACGACTGGTCAAGGGATGACA
*
121850 CGGTTCCTACGTGATGAGGACGACTGG
1 CGGCTCCTACGTGATGAGGACGACTGG
121877 CCATCTTTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
39 4 0.07
40 31 0.52
43 25 0.42
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.22
Consensus pattern (40 bp):
CGGCTCCTACGTGATGAGGACGACTGGTCAAGGGATGACA
Found at i:121988 original size:31 final size:28
Alignment explanation
Indices: 121895--121991 Score: 101
Period size: 28 Copynumber: 3.4 Consensus size: 28
121885 AGGGATCATG
* *
121895 GTTTCAAGAGAAATC-GATTCAAAGATTT
1 GTTTCAAAAGAAA-CAGACTCAAAGATTT
121923 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
121951 GTTTCAAGAA-AAACA-AGCTCAAAGATAATGT
1 GTTTCAA-AAGAAACAGA-CTCAAAGAT--T-T
121982 GTTTCAAAAG
1 GTTTCAAAAG
121992 CAACTGTCTC
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
27 2 0.03
28 45 0.75
29 2 0.03
30 3 0.05
31 8 0.13
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:122181 original size:66 final size:62
Alignment explanation
Indices: 121993--122181 Score: 164
Period size: 66 Copynumber: 2.9 Consensus size: 62
121983 TTTCAAAAGC
* * * * *
121993 AACTGTCTCGAAAGAGACAAAATTCGTTTCAAAGGAAACAACTCAAATATAG-CGTTTAAAGGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACATCTCAAAGAT-GTTGTTTAAAGGG
* * ** * * * *
122056 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACATTCTCAAAGATTGGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACA-TCTCAAAGA-TGTTGTTTAAAGG
122121 G
62 G
122122 AAACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGTTTGTTT
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAAC-ATCTCAAAGATG-TTGTTT
122182 GTTTCAAGGG
Statistics
Matches: 100, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
62 2 0.02
63 17 0.17
64 14 0.14
65 10 0.10
66 37 0.37
67 20 0.20
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (62 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACATCTCAAAGATGTTGTTTAAAGGG
Found at i:123010 original size:27 final size:27
Alignment explanation
Indices: 122987--123062 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 27
122977 ATGTTTTAAG
122987 AGAAACATACTCAAAGATTTTTTTCAAA
1 AGAAACA-ACTCAAAGATTTTTTTCAAA
*
123015 AGAAATAACTCAAAGATTTTTATTCAAA
1 AGAAACAACTCAAAGATTTTT-TTCAAA
123043 ATG-AACAAACTCAAAGATTT
1 A-GAAAC-AACTCAAAGATTT
123063 GTATTTCTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 14 0.33
28 15 0.35
29 14 0.33
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (27 bp):
AGAAACAACTCAAAGATTTTTTTCAAA
Found at i:123035 original size:28 final size:29
Alignment explanation
Indices: 122990--123067 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
122980 TTTTAAGAGA
*
122990 AACATACTCAAAGATTTTT-TTCAAAA-G
1 AACAAACTCAAAGATTTTTATTCAAAATG
123017 AA-ATAACTCAAAGATTTTTATTCAAAATG
1 AACA-AACTCAAAGATTTTTATTCAAAATG
*
123046 AACAAACTCAAAGATTTGTATT
1 AACAAACTCAAAGATTTTTATT
123068 TCTAGAAACT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.02
27 16 0.36
28 7 0.16
29 20 0.44
30 1 0.02
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (29 bp):
AACAAACTCAAAGATTTTTATTCAAAATG
Found at i:123094 original size:120 final size:116
Alignment explanation
Indices: 122792--123106 Score: 321
Period size: 118 Copynumber: 2.6 Consensus size: 116
122782 TGAGACGAAT
* * * *
122792 TTTTTTCCAAAGGAAACAATCTCAAAGGTTGGTTTTTCATTAGAAACTGTCTCAAGAGAGACAAA
1 TTTTTTCAAAAGG-AACAAACTCAAAGATT--TTTTT-AATAGAAACTGTCTCAAGAGAGACAAA
* * ** * *
122857 ATTTGTTTTTAAAGAAATAAACTAAAAGATGATTTTGTTAGTAGAAACACTCGAAGA
62 ATATG-TTTTAAAGAAACAAACTAAAAGAT-ATTTTGTTAAAAGAAAAACTCAAAGA
* * * *
122914 TTTTTTCAAAAGGAATAGACTCCAAGATTTTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATAT
1 TTTTTTCAAAAGGAACAAACTCAAAGATTTTTTTAATAGAAACTGTCTCAAGAGAGACAAAATAT
* *
122979 GTTTTAAGAGAAACATACTCAAAGAT-TTTT-TTCAAAAGAAATAACTCAAAGA
66 GTTTTAA-AGAAACAAACTAAAAGATATTTTGTT-AAAAGAAA-AACTCAAAGA
* *
123031 TTTTTATTCAAAATGAACAAACTCAAAGATTTGTATTT-CTAGAAACTGTCTCAAGAGAGACAAA
1 -TTTT-TTCAAAAGGAACAAACTCAAAGATTT-T-TTTAATAGAAACTGTCTCAAGAGAGACAAA
*
123095 AAATGTTTTAAA
62 ATATGTTTTAAA
123107 ATATTCAAAG
Statistics
Matches: 163, Mismatches: 23, Indels: 17
0.80 0.11 0.08
Matches are distributed among these distances:
115 2 0.01
116 10 0.06
117 14 0.09
118 48 0.29
119 28 0.17
120 35 0.21
121 14 0.09
122 12 0.07
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (116 bp):
TTTTTTCAAAAGGAACAAACTCAAAGATTTTTTTAATAGAAACTGTCTCAAGAGAGACAAAATAT
GTTTTAAAGAAACAAACTAAAAGATATTTTGTTAAAAGAAAAACTCAAAGA
Found at i:123343 original size:36 final size:36
Alignment explanation
Indices: 123298--123384 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
123288 ATCTCAAAGG
* * *
123298 GAAAATGTCTCAAGCGAGACGAAGTTTG-TTTTAAGA
1 GAAATTGTCTCAAGCGAGACAAACTTTGTTTTTAA-A
* * * *
123334 GAATTTGTCTTAAGTGATACAAACTTTGTTTTTAAA
1 GAAATTGTCTCAAGCGAGACAAACTTTGTTTTTAAA
123370 GAAATTGTCTCAAGC
1 GAAATTGTCTCAAGC
123385 AAAACAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
36 34 0.85
37 6 0.15
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (36 bp):
GAAATTGTCTCAAGCGAGACAAACTTTGTTTTTAAA
Found at i:123392 original size:36 final size:36
Alignment explanation
Indices: 123298--123397 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 36
123288 ATCTCAAAGG
* * * *
123298 GAAAATGTCTCAAGCGAGACGAAGTTTGTTTTAAGA
1 GAAATTGTCTCAAGCGAAACAAAATTTGTTTTAAGA
* * * * *
123334 GAATTTGTCTTAAGTGATACAAACTTTGTTTTTAA-A
1 GAAATTGTCTCAAGCGAAACAAAATTTG-TTTTAAGA
*
123370 GAAATTGTCTCAAGCAAAACAAAATTTG
1 GAAATTGTCTCAAGCGAAACAAAATTTG
123398 AGAAAACGAT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
36 44 0.88
37 6 0.12
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (36 bp):
GAAATTGTCTCAAGCGAAACAAAATTTGTTTTAAGA
Found at i:123430 original size:168 final size:166
Alignment explanation
Indices: 123238--123562 Score: 408
Period size: 167 Copynumber: 1.9 Consensus size: 166
123228 ATCTTTGAAA
* * * * *
123238 ATCTCAAGTGATATTAATTTTGTTTTAA-ACGAAGCAAATTCAAAATTTGTATCTCAAAGGGAAA
1 ATCTCAAGTGAGATCAACTTTG-TTTAATACGAAACAAATTCAAAATTTGTATCTC-AAGGAAAA
* ** * *
123302 ATGTCTCAAGCGAGAC-GAAGTTTG-TTTT-AAGAGAATTTGTCTTAAGTGATACAAACTTTGTT
64 ATGTCTCAAGCGAGACGGAA-TTTGTTTTTCAAGA-AA-TTGTCTCAAACGAGACAAAATTTGTT
*
123364 TTTAAAGAAA-TTGTCTCAAGCAAAACAAAATTTGAGAAAACG
126 TTT--AGAAAGCTGTCTCAAGCAAAACAAAATTTGAGAAAACG
**
123406 ATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAGGAAAAAT
1 ATCTCAAGTGAGATCAACTTTGTTTAATACGAAACAAATTCAAAATTTGTATCTCAAGGAAAAAT
*
123471 GTCTCAAGTGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAG
66 GTCTCAAGCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAG
* *
123536 AAAGCTGTCTCAAGCGAGACAAAATTT
131 AAAGCTGTCTCAAGCAAAACAAAATTT
123563 TCTTTGAAAG
Statistics
Matches: 136, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
165 5 0.04
166 20 0.15
167 55 0.40
168 52 0.38
169 4 0.03
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (166 bp):
ATCTCAAGTGAGATCAACTTTGTTTAATACGAAACAAATTCAAAATTTGTATCTCAAGGAAAAAT
GTCTCAAGCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAG
AAAGCTGTCTCAAGCAAAACAAAATTTGAGAAAACG
Found at i:123501 original size:38 final size:36
Alignment explanation
Indices: 123446--123604 Score: 135
Period size: 36 Copynumber: 4.4 Consensus size: 36
123436 GAAACAAATT
* * **
123446 CAAAATTTGTATCTCAAGGAAAAATGTCTCAAGTGAGA
1 CAAAATTTGTTTTTCAA-G-AAAATGTCTCAAACGAGA
** *
123484 CGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGA
1 CAAAATTTGTTTTTCAAGAAAATGTCTCAAACGAGA
* *
123520 CAAAATTTGTTTTT--AGAAAGCTGTCTCAAGCGAGA
1 CAAAATTTGTTTTTCAAGAAA-ATGTCTCAAACGAGA
** * *
123555 CAAAATTT-TCTTTGAAAGAAATTGTCTCAAGCGAGA
1 CAAAATTTGT-TTTTCAAGAAAATGTCTCAAACGAGA
123591 CAAAAATTTGTTTT
1 C-AAAATTTGTTTT
123605 AGAATTCTCA
Statistics
Matches: 102, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
34 6 0.06
35 24 0.24
36 42 0.41
37 16 0.16
38 14 0.14
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (36 bp):
CAAAATTTGTTTTTCAAGAAAATGTCTCAAACGAGA
Found at i:123520 original size:36 final size:35
Alignment explanation
Indices: 123470--123604 Score: 157
Period size: 36 Copynumber: 3.8 Consensus size: 35
123460 CAAGGAAAAA
* **
123470 TGTCTCAAGTGAGACGGAATTTGTTTTTCAAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-AAGAAAT
* *
123506 TGTCTCAAACGAGACAAAATTTGTTTTT-AGAAAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAA-T
*
123541 TGTCTCAAGCGAGACAAAATTT-TCTTTGAAAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGT-TTT-TAAGAAAT
123577 TGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGAC-AAAATTTGTTTT
123605 AGAATTCTCA
Statistics
Matches: 85, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
34 6 0.07
35 24 0.28
36 39 0.46
37 15 0.18
38 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:130498 original size:14 final size:13
Alignment explanation
Indices: 130460--130494 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
130450 AGTAGTTCTC
*
130460 TTTTTTTTCTTGT
1 TTTTTTTTCTGGT
130473 TTTTTTTTCTGGT
1 TTTTTTTTCTGGT
130486 TTTTTTTTC
1 TTTTTTTTC
130495 CTGGGCTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.83
Consensus pattern (13 bp):
TTTTTTTTCTGGT
Found at i:131018 original size:3 final size:3
Alignment explanation
Indices: 131005--131056 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
130995 ATAAATGAGC
131005 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
131052 ATA AT
1 ATA AT
131057 TACAATTAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:137660 original size:20 final size:20
Alignment explanation
Indices: 137635--137672 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
137625 TTTGGTTCAC
137635 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
137655 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
137673 GGAATAGGAT
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:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:137848 original size:22 final size:22
Alignment explanation
Indices: 137822--137891 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
137812 TAACAAGTTG
137822 AAAAATATTTATATATTTTCTTT
1 AAAAA-ATTTATATATTTTCTTT
*
137845 AAAAAAATTA-A-A--TTC-TT
1 AAAAAATTTATATATTTTCTTT
*
137862 --AAAATTTATGTATTTTCTTT
1 AAAAAATTTATATATTTTCTTT
137882 AAAAAATTTA
1 AAAAAATTTA
137892 AATTCATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 15
0.67 0.05 0.27
Matches are distributed among these distances:
15 7 0.19
17 3 0.08
18 3 0.08
19 3 0.08
20 3 0.08
21 1 0.03
22 12 0.32
23 5 0.14
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (22 bp):
AAAAAATTTATATATTTTCTTT
Found at i:137869 original size:37 final size:37
Alignment explanation
Indices: 137828--137915 Score: 140
Period size: 37 Copynumber: 2.4 Consensus size: 37
137818 GTTGAAAAAT
*
137828 ATTTATATATTTTCTTTAAAAAAATTAAATTCTTAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
* *
137865 ATTTATGTATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
137902 ATTTATATAATTTT
1 ATTTATAT-ATTTT
137916 TTTTTTACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 41 0.89
38 5 0.11
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
Found at i:138392 original size:14 final size:16
Alignment explanation
Indices: 138369--138400 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
138359 TAAATAAAGT
138369 AAAAGTTACTTT-ATA
1 AAAAGTTACTTTAATA
138384 AAAAG-TACTTTAATA
1 AAAAGTTACTTTAATA
138399 AA
1 AA
138401 TTACTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (16 bp):
AAAAGTTACTTTAATA
Found at i:139501 original size:15 final size:15
Alignment explanation
Indices: 139481--139510 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
139471 TAGTGAAATT
139481 AAATTAAAATAATAA
1 AAATTAAAATAATAA
*
139496 AAATTAATATAATAA
1 AAATTAAAATAATAA
139511 CTTGGTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTAAAATAATAA
Found at i:141351 original size:3 final size:3
Alignment explanation
Indices: 141324--141408 Score: 50
Period size: 3 Copynumber: 27.7 Consensus size: 3
141314 ATTAATGATA
* * * *
141324 AAT AAG AAT AAT ACT ATAT ATT AAT AAT ATAT ACT ATAT AAT AA- ATAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT A-AT AAT AAT A-AT
* *
141372 AAT -AT AAT AAAT AAT AAT TAT AAT TAT AAT -AT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
141409 CACTATAATG
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
2 5 0.08
3 46 0.74
4 11 0.18
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:141375 original size:5 final size:5
Alignment explanation
Indices: 141347--141636 Score: 171
Period size: 5 Copynumber: 56.0 Consensus size: 5
141337 CTATATATTA
141347 ATAAT AT-AT ACT-AT ATAAT A-AAT ATAAT ATAAT A-AAT AATAATT
1 ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAA-T
*
141391 ATAATT ATAAT ATAAT A-ACACT ATAAT GTAAT ACTAAT AT-AT A-ACAT
1 ATAA-T ATAAT ATAAT ATA-A-T ATAAT ATAAT A-TAAT ATAAT ATA-AT
* * *
141438 ATAACT ATAAG ACAAAT GATACT ATAAT ATAA- AT-AT ATACTAT ATAAT
1 ATAA-T ATAAT A-TAAT -ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT
*
141486 ATAAT AT-AT ATATAT ATAAT ATAA- AT-AT GATAAT ATATAT ATACCGT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT -ATAAT ATA-AT ATA--AT
*
141533 A-AAT ATAAAT ATAAT ATAAT ATAAT ATAAT ATACTAA ATAAT ATAAT
1 ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT
*
141580 AT-AT ATACT AT-AT AATAAT ATAAT ATATAT ATATAT ATACAT ACT-AT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATA-AT ATA-AT ATA-AT A-TAAT
141627 ATAAT ATAAT
1 ATAAT ATAAT
141637 CTATAACATG
Statistics
Matches: 232, Mismatches: 16, Indels: 74
0.72 0.05 0.23
Matches are distributed among these distances:
3 2 0.01
4 33 0.14
5 118 0.51
6 64 0.28
7 15 0.06
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:141416 original size:38 final size:38
Alignment explanation
Indices: 141346--141632 Score: 149
Period size: 38 Copynumber: 7.6 Consensus size: 38
141336 ACTATATATT
*
141346 AATAATATATACTATATAATAAATATAATATAATAAAT
1 AATAATATATAATATATAATAAATATAATATAATAAAT
*
141384 AATAAT-TATAAT-TATAATATAATA-ACACTATAATGTAAT
1 AATAATATATAATATATAATA-AATATA-A-TATAAT-AAAT
* * * * * *
141423 ACTAATATATAACATATAACTATAAGACAA-ATGAT-ACT
1 AATAATATATAATATATAA-TA-AATATAATATAATAAAT
*
141461 -ATAATATA-AATATATACTATATAATATAATAT-ATATAT
1 AATAATATATAATATATA--ATA-AATATAATATAATAAAT
* ***
141499 ATATAATATA-AATATGATAATATATAT-ATACCGTAAAT
1 A-ATAATATATAATAT-ATAATAAATATAATATAATAAAT
*
141537 -ATAA-ATAT-A-ATATAATATAATATAATATACTAAAT
1 AATAATATATAATATATAATA-AATATAATATAATAAAT
*
141572 AATATAATATATATACTATATAAT-AATATAATAT-ATATAT
1 -A-ATAATATATA-A-TATATAATAAATATAATATAATAAAT
* *
141612 -ATATATACATACTATATAATA
1 AATA-ATATATAATATATAATA
141633 TAATCTATAA
Statistics
Matches: 195, Mismatches: 25, Indels: 59
0.70 0.09 0.21
Matches are distributed among these distances:
33 6 0.03
34 6 0.03
35 12 0.06
36 27 0.14
37 33 0.17
38 36 0.18
39 15 0.08
40 26 0.13
41 19 0.10
42 7 0.04
43 8 0.04
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (38 bp):
AATAATATATAATATATAATAAATATAATATAATAAAT
Found at i:141422 original size:27 final size:26
Alignment explanation
Indices: 141347--141645 Score: 124
Period size: 27 Copynumber: 11.6 Consensus size: 26
141337 CTATATATTA
141347 ATAATAT-AT-ACTATATAA-TA-AAT
1 ATAATATAATAAC-ATATAATTATAAT
141370 ATAATATAATAA-ATAATAATTATAATT
1 ATAATATAATAACAT-ATAATTATAA-T
*
141397 ATAATATAATAACACTATAA-TGTAAT
1 ATAATATAATAACA-TATAATTATAAT
* *
141423 ACTAATAT-ATAACATATAACTATAAG
1 A-TAATATAATAACATATAATTATAAT
* *
141449 ACAA-ATGAT-AC-TATAA-TATAA-
1 ATAATATAATAACATATAATTATAAT
*
141470 AT-ATATACT---ATATAA-TATAAT
1 ATAATATAATAACATATAATTATAAT
*
141491 ATATATATATATAATATA-AATATGATAAT
1 ATA-ATATA-ATAACATATAAT-T-ATAAT
* *
141520 ATATATATACCGTAA-ATATAAATATAAT
1 ATA-ATATA--ATAACATATAATTATAAT
* *
141548 ATAATATAATATA-ATATACTAAATAAT
1 ATAATATAATA-ACATATAAT-TATAAT
141575 ATAATAT-ATATACTATATAATAATATAAT
1 ATAATATAATA-AC-ATATAAT--TATAAT
141604 ATATATATATATATACATACT-A-TATAAT
1 ATA-ATATA-ATA-ACATA-TAATTATAAT
*
141632 ATAATCT-ATAACAT
1 ATAATATAATAACAT
141646 GTATATAGTA
Statistics
Matches: 224, Mismatches: 18, Indels: 67
0.72 0.06 0.22
Matches are distributed among these distances:
20 11 0.05
21 6 0.03
22 5 0.02
23 19 0.08
24 15 0.07
25 17 0.08
26 28 0.12
27 46 0.21
28 29 0.13
29 28 0.12
30 9 0.04
31 4 0.02
32 7 0.03
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (26 bp):
ATAATATAATAACATATAATTATAAT
Found at i:141483 original size:2 final size:2
Alignment explanation
Indices: 141460--141690 Score: 147
Period size: 2 Copynumber: 120.0 Consensus size: 2
141450 CAAATGATAC
*
141460 TA TA -A TA TA AA TA TA TA CTA TA TA -A TA TA -A 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
* ** * *
141500 TA TA -A TA TA AA TA TGA TA -A TA TA TA TA TA CCG TA AA TA TA AA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
141542 TA TA -A TA TA -A TA TA -A TA TA -A TA TA CTA AA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
141579 TA TA TA TA CTA TA TA -A TA -A TA TA -A 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
* * * *
141619 CA TA CTA TA TA -A TA TA -A TC TA TA -A CA TG TA TA TA GTA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
*
141660 CTA TA TA TA TA CTA TA TA -A TA TA TA CA TA TA
1 -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
141691 AAAACAAAAA
Statistics
Matches: 179, Mismatches: 23, Indels: 54
0.70 0.09 0.21
Matches are distributed among these distances:
1 18 0.10
2 145 0.81
3 16 0.09
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (2 bp):
TA
Found at i:141524 original size:84 final size:86
Alignment explanation
Indices: 141339--141619 Score: 253
Period size: 89 Copynumber: 3.2 Consensus size: 86
141329 GAATAATACT
* *
141339 ATATATTAATA-ATATATACTATATA-ATAAATATAATATAATA-AATAATAATTATAAT-TATA
1 ATATA-TAATATATATATACTA-A-AGACAAATATAATATAATATAAT-ATAA-TATACTATATA
* *
141400 ATATAATA-ACACTATAATGTAATACT-A
61 ATATAATATATA-TAT-ATATAATA-TAA
* *
141427 ATATAT-A-ACATATA-ACTATAAGACAAATGATACTATAATATAA-AT-ATATACTATATAATA
1 ATATATAATATATATATACTA-AAGACAAAT-ATAATATAATATAATATAATATACTATATAATA
141487 TAATATATATATATATAATATAA
64 TAATATATATATATATAATATAA
* * *
141510 ATATGATAATATATATATACCGTAAATATAAATATAATATAATATAATATAATATACTAAATAAT
1 ATAT-ATAATATATATATA-C-TAAAGACAAATATAATATAATATAATATAATATACTATATAAT
141575 ATAATATATATACTATATAATAATATA
63 ATAATATATATA-TATATAAT-ATA-A
141602 ATATAT-ATATATATATAC
1 ATATATAATATATATATAC
141620 ATACTATATA
Statistics
Matches: 165, Mismatches: 10, Indels: 35
0.79 0.05 0.17
Matches are distributed among these distances:
82 1 0.01
83 17 0.10
84 19 0.12
85 17 0.10
86 22 0.13
87 17 0.10
88 15 0.09
89 28 0.17
90 19 0.12
91 5 0.03
92 5 0.03
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (86 bp):
ATATATAATATATATATACTAAAGACAAATATAATATAATATAATATAATATACTATATAATATA
ATATATATATATATAATATAA
Found at i:141629 original size:84 final size:86
Alignment explanation
Indices: 141334--141690 Score: 239
Period size: 84 Copynumber: 4.3 Consensus size: 86
141324 AATAAGAATA
* *
141334 ATACTATATATTA-ATAATATATACTATATA-ATA--AATATAATATAATA-AATAATAATTATA
1 ATACTATATAATATATAATATATAATATATATATACCAATATAATATAATATAAT-ATAA-TATA
141394 AT-TA-TAATATAATA-ACACTATA-
64 ATATACTAA-ATAATATA-A-TATAT
* * * * * *
141416 AT-GTAATACTAATATATAACATATAA-CTATA-AGA-CAA-AT--GATACTATAATATAA-AT-
1 ATACT-ATA-TAATATATAATATATAATATATATATACCAATATAATATAATATAATATAATATA
*
141472 ATATACTATATAATATAATATAT
64 ATATACTAAATAATATAATATAT
141495 ATA-TATATAATATA-AATATGATAATATATATATACCGTAAATATAAATATAATATAATATAAT
1 ATACTATATAATATATAATAT-ATAATATATATATACC---AATAT-AATATAATATAATATAAT
141558 ATAATATACTAAATAATATAATATAT
61 ATAATATACTAAATAATATAATATAT
*
141584 ATACTATATAATAATATAATATAT-ATATATATATA-C-ATACT-ATATAATATAATCT-ATA-A
1 ATACTATATAAT-ATATAATATATAATATATATATACCAATA-TAATATAATATAATATAATATA
* *
141643 CATGTA-TATAGT-ATATACTATATAT
64 -ATATACTA-AATAATATA--ATATAT
141668 ATACTATATAATATATACATATA
1 ATACTATATAATATATA-ATATA
141691 AAAACAAAAA
Statistics
Matches: 225, Mismatches: 18, Indels: 62
0.74 0.06 0.20
Matches are distributed among these distances:
76 4 0.02
77 11 0.05
78 13 0.06
79 16 0.07
80 4 0.02
81 10 0.04
82 16 0.07
83 28 0.12
84 49 0.22
85 3 0.01
86 1 0.00
87 13 0.06
88 2 0.01
89 26 0.12
90 19 0.08
91 5 0.02
92 5 0.02
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (86 bp):
ATACTATATAATATATAATATATAATATATATATACCAATATAATATAATATAATATAATATAAT
ATACTAAATAATATAATATAT
Found at i:141651 original size:36 final size:33
Alignment explanation
Indices: 141480--141688 Score: 77
Period size: 31 Copynumber: 6.8 Consensus size: 33
141470 ATATATACTA
* *
141480 TATAATATA-ATATATATATATATAATATA-AA
1 TATAATATACATATATATATACATACTATATAA
* * *
141511 TATGATA-ATATATATATACCGTAAATA-TAAATATAA
1 TATAATATACATATATATA---TACATACT--ATATAA
141547 TATAATATA-ATATA-ATATAC-TA--A-ATAA
1 TATAATATACATATATATATACATACTATATAA
141574 TATAATATA--TATACTATATA-ATA--ATATAA
1 TATAATATACATATA-TATATACATACTATATAA
* *
141603 TAT-ATATATATATATACATACTATA-TAATATAA
1 TATAATATACATATATATATAC-ATACT-ATATAA
* * *
141636 TCT-ATA-ACATGTATATAGTATATACTATAT-A
1 TATAATATACATATATATA-TACATACTATATAA
*
141667 TATACTAT--ATA-ATATATACATA
1 TATAATATACATATATATATACATA
141689 TAAAAACAAA
Statistics
Matches: 142, Mismatches: 14, Indels: 46
0.70 0.07 0.23
Matches are distributed among these distances:
26 4 0.03
27 13 0.09
28 14 0.10
29 17 0.12
30 10 0.07
31 25 0.18
32 19 0.13
33 15 0.11
34 5 0.04
35 6 0.04
36 13 0.09
37 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (33 bp):
TATAATATACATATATATATACATACTATATAA
Found at i:145346 original size:51 final size:51
Alignment explanation
Indices: 145283--145405 Score: 151
Period size: 51 Copynumber: 2.4 Consensus size: 51
145273 CAGTAAAGCG
* * * *
145283 CCCCTGAACCGCGCTATATGCTGATTTG-GCGCCACGTGGAGTATAGCGCGC
1 CCCCTGTACCGCGCTATACGCTGA-CTGAGCGACACGTGGAGTATAGCGCGC
** *
145334 CCCCTGTACCGCGCTATACGCTGACTGAGTTACACGTGGGGTATAGCGCGC
1 CCCCTGTACCGCGCTATACGCTGACTGAGCGACACGTGGAGTATAGCGCGC
145385 CCCCTGCT-CCGCGCTATACGC
1 CCCCTG-TACCGCGCTATACGC
145406 CACGTAAGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
50 2 0.03
51 60 0.95
52 1 0.02
ACGTcount: A:0.16, C:0.35, G:0.28, T:0.21
Consensus pattern (51 bp):
CCCCTGTACCGCGCTATACGCTGACTGAGCGACACGTGGAGTATAGCGCGC
Done.