Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009393.1 Hibiscus syriacus cultivar Beakdansim tig00113294_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: 93263
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4658 original size:6 final size:6
Alignment explanation
Indices: 4647--4694 Score: 78
Period size: 6 Copynumber: 7.7 Consensus size: 6
4637 AATTTTTATC
4647 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTCTTAAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TT-TT-AA TTTT
4695 TAAATATCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 32 0.80
7 4 0.10
8 4 0.10
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:6264 original size:14 final size:15
Alignment explanation
Indices: 6232--6267 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
6222 ATATTTAGCT
*
6232 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGTC
6247 GGGCGGGCGGATG-C
1 GGGCGGGCGGATGTC
6261 GGGCGGG
1 GGGCGGG
6268 TAATGTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.06, C:0.17, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGTC
Found at i:7643 original size:30 final size:31
Alignment explanation
Indices: 7599--7682 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 31
7589 GTACTGAAAT
* *
7599 AAAATAA-AAATTAAACATT-AAATATGATTTA
1 AAAATAATAATTTAAATATTAAAATA-GA-TTA
7630 AAAA-AAT-ATTTAAATATTAAAATAGATTA
1 AAAATAATAATTTAAATATTAAAATAGATTA
7659 AAAATTAATAATTTAAATATTAAA
1 AAAA-TAATAATTTAAATATTAAA
7683 GTTATATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
29 7 0.15
30 13 0.28
31 12 0.26
32 14 0.30
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (31 bp):
AAAATAATAATTTAAATATTAAAATAGATTA
Found at i:8774 original size:2 final size:2
Alignment explanation
Indices: 8767--8832 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
8757 ACAATGAATG
8767 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
8809 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
8833 CAATGTATGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9503 original size:27 final size:28
Alignment explanation
Indices: 9473--9528 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
9463 TTTTAGTATC
* *
9473 TAGTATTTAA-ATTTTAGTCTAAAATTT
1 TAGTATGTAATATTTTAATCTAAAATTT
*
9500 TAGTATGTAATATTTTAATCTAAATTTT
1 TAGTATGTAATATTTTAATCTAAAATTT
9528 T
1 T
9529 GGTTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (28 bp):
TAGTATGTAATATTTTAATCTAAAATTT
Found at i:10859 original size:24 final size:23
Alignment explanation
Indices: 10832--10878 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
10822 TGGAATGATT
10832 ATTTATTTATTTAT-TATATCTTAA
1 ATTTATTT-TTTATATATAT-TTAA
10856 ATTTATTTTTTATATATATTTAA
1 ATTTATTTTTTATATATATTTAA
10879 CGATCGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTATTTTTTATATATATTTAA
Found at i:27891 original size:24 final size:25
Alignment explanation
Indices: 27864--27971 Score: 116
Period size: 24 Copynumber: 4.5 Consensus size: 25
27854 AAATATTTTA
*
27864 TCTGATTTCCGACT-TGAATTCTGT
1 TCTGATTTCTGACTCTGAATTCTGT
* * *
27888 TCTGATATATGAC-CTGAATTTTGT
1 TCTGATTTCTGACTCTGAATTCTGT
*
27912 TCTGATTTCTGA-TCTGGATTCTGT
1 TCTGATTTCTGACTCTGAATTCTGT
* *
27936 TCTGATATCTG-TTCTGAATTCTGT
1 TCTGATTTCTGACTCTGAATTCTGT
*
27960 TTTGATTTCTGA
1 TCTGATTTCTGA
27972 TATCTCCGTT
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.49
Consensus pattern (25 bp):
TCTGATTTCTGACTCTGAATTCTGT
Found at i:27933 original size:48 final size:49
Alignment explanation
Indices: 27864--27972 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 49
27854 AAATATTTTA
* *
27864 TCTGATTTCCGA-CTTGAATTCTGTTCTGATATATGACCTGAATTTTGT
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATATATGACCTGAATTCTGT
* * **
27912 TCTGATTTCTGATC-TGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATATATGACCTGAATTCTGT
*
27960 TTTGATTTCTGAT
1 TCTGATTTCTGAT
27973 ATCTCCGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTGTTCTGATATATGACCTGAATTCTGT
Found at i:27969 original size:12 final size:12
Alignment explanation
Indices: 27882--27970 Score: 74
Period size: 12 Copynumber: 7.4 Consensus size: 12
27872 CCGACTTGAA
27882 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* * **
27894 ATATGACCTGAAT
1 TTCTGTTCTG-AT
27907 TT-TGTTCTGAT
1 TTCTGTTCTGAT
*
27918 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
27930 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* *
27942 ATCTGTTCTGAA
1 TTCTGTTCTGAT
*
27954 TTCTGTTTTGAT
1 TTCTGTTCTGAT
27966 TTCTG
1 TTCTG
27971 ATATCTCCGT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
11 6 0.10
12 48 0.81
13 5 0.08
ACGTcount: A:0.16, C:0.15, G:0.18, T:0.52
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:35404 original size:20 final size:20
Alignment explanation
Indices: 35379--35472 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
35369 AATTGGGAAA
35379 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
35399 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
35419 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
35440 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
35460 TTCGCAACGCGAT
1 ATCGCAATGCGAT
35473 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:36132 original size:20 final size:19
Alignment explanation
Indices: 36067--36156 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
36057 GAAACAAAAA
*
36067 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
36086 TCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
36105 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
36124 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
36144 TCGCGTTGTGATT
1 TCGCGTTGCGATT
36157 GTCTGGTCGC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 46 0.72
20 18 0.28
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:36149 original size:39 final size:38
Alignment explanation
Indices: 36067--36156 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 38
36057 GAAACAAAAA
* *
36067 TCGCATTGCGATTTTCATTTCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
36105 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
*
36144 TCGCGTTGTGATT
1 TCGCGTTGCGATT
36157 GTCTGGTCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 21 0.45
39 26 0.55
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:36167 original size:39 final size:39
Alignment explanation
Indices: 36086--36167 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
36076 GATTTTCATT
* * **
36086 TCGC-GTTGTGATTTTCATTTCGCGTTGCGATTTTTATT
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
*
36124 TCGCGGTTGCGATTTTCATTTCGCGTTGTGATTGTCT-GG
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATT-TCTAGG
36163 TCGCG
1 TCGCG
36168 ATAGTCATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 4 0.11
39 31 0.84
40 2 0.05
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (39 bp):
TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
Found at i:36197 original size:14 final size:14
Alignment explanation
Indices: 36180--36216 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
36170 AGTCATTTCG
*
36180 CGTTGCGATTCTCT
1 CGTTGCGATTCTAT
36194 CGTTGCGATTCTAT
1 CGTTGCGATTCTAT
*
36208 CGTTTCGAT
1 CGTTGCGAT
36217 AGTCATTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTAT
Found at i:36202 original size:33 final size:33
Alignment explanation
Indices: 36129--36202 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
36119 TTATTTCGCG
** * * *
36129 GTTGCGATTTTCATTTCGCGTTGTGATTGTCTG
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
*
36162 GTCGCGATAGTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
36195 GTTGCGAT
1 GTTGCGAT
36203 TCTATCGTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.20, G:0.27, T:0.42
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
Found at i:36242 original size:20 final size:20
Alignment explanation
Indices: 36219--36265 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
36209 GTTTCGATAG
*
36219 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCAATTC
* *
36239 TCATTAT-CTCGTTGCAATTT
1 TCATT-TCCGCGTTGCAATTC
36259 TCATTTC
1 TCATTTC
36266 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:38349 original size:21 final size:21
Alignment explanation
Indices: 38325--38391 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
38315 TCATTCCTCG
38325 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
38346 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
38367 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
38388 AGAG
1 AGAG
38392 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:38349 original size:42 final size:42
Alignment explanation
Indices: 38273--38391 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
38263 GACTCGCCTG
* * * *
38273 TCATCC-CTGAAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATCCTC-GAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
38315 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
38357 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
38392 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 50 0.79
43 8 0.13
44 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:39768 original size:14 final size:14
Alignment explanation
Indices: 39749--39784 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39739 ATTGTTTAAT
39749 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
39763 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
39777 TGATTTGT
1 TGATTTGT
39785 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:39985 original size:19 final size:19
Alignment explanation
Indices: 39963--40113 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
39953 CGAAATTAAA
*
39963 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
39982 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
39998 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
40015 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
40029 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
40048 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
40064 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
** *
40081 TTCGCATTGCGATAGTAAT
1 TTCGCATTGCGATTTTCAT
40100 TTCCGCATTGCGAT
1 TT-CGCATTGCGAT
40114 AGACATTAAG
Statistics
Matches: 100, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
14 23 0.23
16 13 0.13
17 13 0.13
19 40 0.40
20 11 0.11
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:40009 original size:33 final size:32
Alignment explanation
Indices: 39967--40093 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
39957 ATTAAATTCG
39967 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
40000 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
40033 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
40066 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
40094 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:40056 original size:66 final size:66
Alignment explanation
Indices: 39960--40092 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
39950 ACGCGAAATT
*
39960 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
40025 G
66 G
*
40026 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
40091 G
66 G
40092 A
1 A
40093 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:42402 original size:12 final size:12
Alignment explanation
Indices: 42385--42409 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42375 TCTTCGGGGA
42385 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42397 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42409 C
1 C
42410 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:42618 original size:24 final size:24
Alignment explanation
Indices: 42584--42637 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
42574 CTGAAACATC
* *
42584 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
42608 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
42632 ATCAAA
1 ATCAAA
42638 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:43718 original size:20 final size:20
Alignment explanation
Indices: 43693--43750 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
43683 ATTCATTTGA
*
43693 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
43713 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
43733 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
43751 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:43793 original size:14 final size:14
Alignment explanation
Indices: 43774--43827 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
43764 GAAAATCGCA
43774 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
43788 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
43805 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
43821 TTGCGAT
1 TTGCGAT
43828 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:43793 original size:33 final size:33
Alignment explanation
Indices: 43756--43826 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
43746 AAAATCGCAA
43756 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
43789 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
43822 TGCGA
1 TGCGA
43827 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:43827 original size:33 final size:33
Alignment explanation
Indices: 43769--43846 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
43759 GAAATGAAAA
***
43769 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
43802 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
43835 TCGCGTTGCGAT
1 TCGCATTGCGAT
43847 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:45846 original size:19 final size:19
Alignment explanation
Indices: 45822--45895 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
45812 GAAACTTAAA
45822 ATCGCAACGCAAAATGACT
1 ATCGCAACGCAAAATGACT
* * *
45841 ATCGCAATGCGGAAATGGCT
1 ATCGCAACGC-AAAATGACT
* * **
45861 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCAAAATGACT
45880 ATCGCAACGACAAAAT
1 ATCGCAACG-CAAAAT
45896 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 23 0.51
20 22 0.49
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCAAAATGACT
Found at i:45862 original size:20 final size:19
Alignment explanation
Indices: 45822--45877 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
45812 GAAACTTAAA
* *
45822 ATCGCAACGCAAAATGACT
1 ATCGCAATGCGAAATGACT
*
45841 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGACT
45861 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
45878 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:45896 original size:14 final size:14
Alignment explanation
Indices: 45877--45934 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
45867 ATGCGAAATG
45877 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
45891 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
45907 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
45923 AAAATCGCAACG
1 AAAATCGCAACG
45935 CGAAACATAA
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:45919 original size:32 final size:33
Alignment explanation
Indices: 45861--45939 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
45851 GGAAATGGCT
*
45861 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
45894 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
45926 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
45940 CATAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:45968 original size:19 final size:19
Alignment explanation
Indices: 45946--45995 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
45936 GAAACATAAA
45946 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
45965 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
45984 TCGCATTGCGAT
1 TCGCATTGCGAT
45996 AGCCATTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:46014 original size:20 final size:19
Alignment explanation
Indices: 45946--46023 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
45936 GAAACATAAA
* **
45946 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
**
45965 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
* *
45984 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATAGTCATT
46003 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATAGTCATT
46023 T
1 T
46024 TTGTATTGCG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 34 0.67
20 17 0.33
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:46542 original size:18 final size:18
Alignment explanation
Indices: 46516--46560 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
46506 GTCGATCAGA
46516 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
*
46534 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
46552 TGATGGCTC
1 TGATGGCTC
46561 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGG
Found at i:47928 original size:20 final size:20
Alignment explanation
Indices: 47880--47938 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
47870 AATAGTTTCT
** *
47880 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
47900 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
47920 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
47939 AGATAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:48229 original size:22 final size:22
Alignment explanation
Indices: 48201--48244 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
48191 GATGGATATA
48201 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
48223 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
48245 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:48458 original size:20 final size:20
Alignment explanation
Indices: 48432--48545 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
48422 GATTATGTAT
48432 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
48452 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
48472 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
48492 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
48513 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
48533 TATCGCATTGCGA
1 TATCGCGTTGCGA
48546 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:48549 original size:41 final size:41
Alignment explanation
Indices: 48412--48547 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
48402 CGCTTTGAAA
*
48412 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
48453 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
48493 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
48534 ATCGCATTGCGATT
1 ATCGCATTGCGATT
48548 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 42 0.54
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:48564 original size:21 final size:21
Alignment explanation
Indices: 48535--48627 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
48525 ATAGTCAGTA
48535 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
48556 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
48576 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
48597 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
48617 TCGCATTGCGA
1 TCGCATTGCGA
48628 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:48565 original size:41 final size:41
Alignment explanation
Indices: 48474--48608 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
48464 AAAGTCAGTA
* * * ** *
48474 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
48514 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
48556 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
48597 TCGCGTTGCGAT
1 TCGCGTTGCGAT
48609 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:48609 original size:41 final size:41
Alignment explanation
Indices: 48535--48627 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
48525 ATAGTCAGTA
48535 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
48576 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
48617 TCGCATTGCGA
1 TCGCATTGCGA
48628 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:51576 original size:2 final size:2
Alignment explanation
Indices: 51569--51598 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
51559 TAAAAAGTTA
*
51569 AT AT AT AT AT AC 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
51599 TTAATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55510 original size:322 final size:321
Alignment explanation
Indices: 54914--55518 Score: 905
Period size: 322 Copynumber: 1.9 Consensus size: 321
54904 GTAAATTGTT
*
54914 CATTCATTACTCAACTATCTTCTCACTCCTATTTTGGTACTTAAGTTTAAAAAATTTCAATTTAA
1 CATTCATTACTCAACTATATTCTCACTCCTATTTTGGTACTTAAGTTTAAAAAATTTCAATTTAA
* * * * * *
54979 CTATTCAACTTTCAAATTTATCCTATTTTCATCACTCTAATTTATTTTATTATTAATTTTTTTGA
66 CTACTCAACTTTCAAATTGATCCTATTTTAATCACTCTAATTTATTTTATTAATAAATTTTGTGA
** * *
55044 ATGATGTTTATTATTATCATTTTATTAATATATAGTTAAAAATAAAAAAATAAATTTGAAAGTTA
131 ATGACATTTATTATTATCATTTTATTAATATATAATTAAAAATAAAAAAATAAATTTAAAAGTTA
* * *
55109 GAGTGATTAAATTAGGAGGTATTTGAAAGTTAAGTAATTGAATTAAAAAAAACTAAACTTTAGTG
196 GAGTGATTAAATTAGGAGGTATTTGAAAATTAAGTAATTAAAGT-AAAAAAACTAAACTTTAGTG
55174 ACCAAAATAGGAGTGAGAAGATAAAAACGTAACGAAACTACATTTTTATGGGTAAATTACAA
260 ACCAAAATAGGAGTGAGAAGATAAAAACGTAACGAAACTACATTTTTATGGGTAAATTACAA
*
55236 CATTC-TTCACTCAACTATATTCTTACTCCTATTTTGGTACTTAAGTTTAAAAATATTTCAATTT
1 CATTCATT-ACTCAACTATATTCTCACTCCTATTTTGGTACTTAAGTTTAAAAA-ATTTCAATTT
* *
55300 AACTACTCAGCTTTCAAATTGCTCCTATTTTAATCACTCTAATTTATTTTATTAATAAATTTTGT
64 AACTACTCAACTTTCAAATTGATCCTATTTTAATCACTCTAATTTATTTTATTAATAAATTTTGT
* *
55365 GACATGACATTTATTATTATTATTTTTATTAATATATAATTAAAAAT-AAAAAATTAATTTAAAA
129 GA-ATGACATTTATTATTATCA-TTTTATTAATATATAATTAAAAATAAAAAAATAAATTT-AAA
** *
55429 AG-TAGAGTGATTAAATTAGGA-GTAATTTGAAAATTAAGTAATTAAAGT-AAAAAGTTAAATTT
191 AGTTAGAGTGATTAAATTAGGAGGT-ATTTGAAAATTAAGTAATTAAAGTAAAAAAACTAAACTT
*
55491 TATTGACCAAAATAGGAGTGAGAAGATA
255 TAGTGACCAAAATAGGAGTGAGAAGATA
55519 GTTGAATGAT
Statistics
Matches: 254, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
321 2 0.01
322 86 0.34
323 71 0.28
324 68 0.27
325 27 0.11
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (321 bp):
CATTCATTACTCAACTATATTCTCACTCCTATTTTGGTACTTAAGTTTAAAAAATTTCAATTTAA
CTACTCAACTTTCAAATTGATCCTATTTTAATCACTCTAATTTATTTTATTAATAAATTTTGTGA
ATGACATTTATTATTATCATTTTATTAATATATAATTAAAAATAAAAAAATAAATTTAAAAGTTA
GAGTGATTAAATTAGGAGGTATTTGAAAATTAAGTAATTAAAGTAAAAAAACTAAACTTTAGTGA
CCAAAATAGGAGTGAGAAGATAAAAACGTAACGAAACTACATTTTTATGGGTAAATTACAA
Found at i:56154 original size:2 final size:2
Alignment explanation
Indices: 56147--56201 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
56137 AAAATACCTC
56147 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
56189 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
56202 ATTTTATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59338 original size:21 final size:20
Alignment explanation
Indices: 59312--59370 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
59302 ACATATGTAA
59312 TCCTTTGGAACATATATGCGG
1 TCCTTTGGAACATATAT-CGG
* *
59333 TTCTTTGAGACACATAT-TTGG
1 TCCTTTG-GA-ACATATATCGG
*
59354 TCCTTTGGAATATATAT
1 TCCTTTGGAACATATAT
59371 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 5 0.16
20 3 0.10
21 14 0.45
22 3 0.10
23 6 0.19
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (20 bp):
TCCTTTGGAACATATATCGG
Found at i:59370 original size:2 final size:2
Alignment explanation
Indices: 59363--59402 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
59353 GTCCTTTGGA
59363 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
59403 GATCCTTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59480 original size:23 final size:23
Alignment explanation
Indices: 59453--59533 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
59443 TATATGACAT
59453 TTCAGTGCATTTCTATGCGGCAC
1 TTCAGTGCATTTCTATGCGGCAC
*
59476 TTCAGTGCATTTCTACGCGGCAC
1 TTCAGTGCATTTCTATGCGGCAC
* * *
59499 TTTAGTGCATTTCTATGTGGTAC
1 TTCAGTGCATTTCTATGCGGCAC
*
59522 TTTAGTGCATTT
1 TTCAGTGCATTT
59534 TATACGAGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (23 bp):
TTCAGTGCATTTCTATGCGGCAC
Found at i:60397 original size:24 final size:25
Alignment explanation
Indices: 60360--60407 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
60350 TGCATGATTC
60360 AAAAATG-ATCTTTTAAATTTTGAA
1 AAAAATGTATCTTTTAAATTTTGAA
* *
60384 AAAAATGTTTTTTTTTAAATTTTG
1 AAAAATG-TATCTTTTAAATTTTG
60408 GTTATGGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
26 13 0.65
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (25 bp):
AAAAATGTATCTTTTAAATTTTGAA
Found at i:66523 original size:18 final size:18
Alignment explanation
Indices: 66500--66536 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
66490 AAATAATTAA
66500 AATAATATGTTTTATAAT
1 AATAATATGTTTTATAAT
66518 AATAATATGTTTTATAAT
1 AATAATATGTTTTATAAT
66536 A
1 A
66537 TTTTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
AATAATATGTTTTATAAT
Found at i:66628 original size:14 final size:14
Alignment explanation
Indices: 66599--66627 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
66589 TTTTTTATAA
66599 TTAATTAATATATT
1 TTAATTAATATATT
66613 TTAA-TAATATATT
1 TTAATTAATATATT
66626 TT
1 TT
66628 TTAAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATTAATATATT
Found at i:66642 original size:2 final size:2
Alignment explanation
Indices: 66633--66669 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
66623 ATTTTTTAAA
66633 AT AT -T 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
66670 TCTATAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:66658 original size:35 final size:35
Alignment explanation
Indices: 66585--66661 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 35
66575 TATAAACTTT
* *
66585 TATATTTTTTATAATTAATTAATATATTTTAATAA
1 TATATTTTTTATAAATAATTAATATATTATAATAA
66620 TATATTTTTTA-AAAT-ATTATATATATATATATATATA
1 TATATTTTTTATAAATAATTA-ATATAT-TATA-ATA-A
66657 TATAT
1 TATAT
66662 ATATATATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
33 4 0.11
34 9 0.25
35 14 0.39
36 3 0.08
37 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
TATATTTTTTATAAATAATTAATATATTATAATAA
Found at i:69977 original size:3 final size:3
Alignment explanation
Indices: 69963--70000 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
69953 AAATATGTAA
*
69963 AAT AAT ATT AAT AAT AAT AAT AAT ACAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
70001 GAACGAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:70586 original size:29 final size:29
Alignment explanation
Indices: 70544--70611 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
70534 CCCTCTCTGG
*
70544 AATTTTATAAGTTC-AGATTCACCCCCTAA
1 AATTTTAAAAGTTCAAGATTC-CCCCCTAA
* *
70573 AATTTTAAAAGTTCAAGTTTCCCCCTTAA
1 AATTTTAAAAGTTCAAGATTCCCCCCTAA
70602 AATTTTAAAA
1 AATTTTAAAA
70612 ATTTAAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 30 0.86
30 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (29 bp):
AATTTTAAAAGTTCAAGATTCCCCCCTAA
Found at i:70619 original size:29 final size:28
Alignment explanation
Indices: 70565--70621 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
70555 TTCAGATTCA
*
70565 CCCCCTAAAATTTTAAAAGTTCAAGTTT
1 CCCCCTAAAATTTTAAAAATTCAAGTTT
*
70593 CCCCCTTAAAATTTTAAAAATTTAAGTTT
1 CCCCC-TAAAATTTTAAAAATTCAAGTTT
70622 GTTCTCCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (28 bp):
CCCCCTAAAATTTTAAAAATTCAAGTTT
Found at i:72514 original size:28 final size:26
Alignment explanation
Indices: 72490--72545 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
72480 CTCCTTTTAT
72490 TTTTCTCATTTTTTTCTCTTTCTTTCA
1 TTTT-TCATTTTTTTCTCTTTCTTTCA
*
72517 TTTTTCATTTTTTTGTC-TT-TTTCA
1 TTTTTCATTTTTTTCTCTTTCTTTCA
72541 TTTTT
1 TTTTT
72546 TAGTCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 10 0.36
25 2 0.07
26 12 0.43
27 4 0.14
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTTCATTTTTTTCTCTTTCTTTCA
Found at i:72537 original size:17 final size:17
Alignment explanation
Indices: 72517--72564 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
72507 CTTTCTTTCA
72517 TTTTTCATTTTTTTGTC
1 TTTTTCATTTTTTTGTC
*
72534 TTTTTCATTTTTTAGTC
1 TTTTTCATTTTTTTGTC
72551 TTTTTCATTTTTTT
1 TTTTTCATTTTTTT
72565 TCAGGCGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTCATTTTTTTGTC
Found at i:72546 original size:26 final size:27
Alignment explanation
Indices: 72484--72546 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
72474 TGAACCCTCC
*
72484 TTTT-ATTTTTCTCATTTTTTTCTCTT
1 TTTTCATTTTTTTCATTTTTTTCTCTT
*
72510 TCTTTCA--TTTTTCATTTTTTTGTC-T
1 T-TTTCATTTTTTTCATTTTTTTCTCTT
72535 TTTTCATTTTTT
1 TTTTCATTTTTT
72547 AGTCTTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
24 5 0.16
25 2 0.06
26 20 0.65
27 3 0.10
28 1 0.03
ACGTcount: A:0.08, C:0.14, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTCATTTTTTTCATTTTTTTCTCTT
Found at i:72554 original size:24 final size:24
Alignment explanation
Indices: 72512--72562 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
72502 TTTCTCTTTC
* *
72512 TTTCATTTTTCATTTTTTTGTC-TT
1 TTTCATTTTTCAGTCTTTT-TCATT
*
72536 TTTCATTTTTTAGTCTTTTTCATT
1 TTTCATTTTTCAGTCTTTTTCATT
72560 TTT
1 TTT
72563 TTTCAGGCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTCATTTTTCAGTCTTTTTCATT
Found at i:77288 original size:3 final size:3
Alignment explanation
Indices: 77266--77324 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
77256 ATATTATAAA
*
77266 TAT TAAT TA- TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
77311 TAA TATT TAT TAT T
1 TAT TA-T TAT TAT T
77325 TTACATTTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.86
4 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:78861 original size:4 final size:4
Alignment explanation
Indices: 78852--78885 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
78842 TTTTAACTTG
78852 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
78886 TTTTTTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:79154 original size:2 final size:2
Alignment explanation
Indices: 79149--79212 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
79139 ATATTGTGTG
79149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
79190 TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
79213 TTAAAGTATA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92245 original size:55 final size:55
Alignment explanation
Indices: 92153--92534 Score: 339
Period size: 55 Copynumber: 7.1 Consensus size: 55
92143 GTGAAGCAAA
* * * *
92153 TGAAGATTGTTCGAGTCTTATACTCTCTGAACAAATAGAGAGCAGACACGATTGT
1 TGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * *
92208 TGAAGATTGTTCAAGTCTCATACTCTCTTAAGCAATAGGGAGCAGACATGAATAT
1 TGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * *
92263 TGAAAATTGTTCGAGTCTAATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
1 TGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * *
92318 TGAAAATTATTCGAGTCTTATACTCTCTGAAGGAATAGGGGGCAGACAC-ATTTGT
1 TGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
* * *
92373 TGAAGA----TCAAGTC-CTATACTTTCTGAAGGAATAGGGAG-AGGACACGTTTGT
1 TGAAGATTGTTCAAGTCTC-ATACTCTCTGAAGAAATAGGGAGCA-GACACGATTGT
* * *
92424 TGAAGGTTTTTTAAG--TCATACTCTCTGAA-AAATAGGGAGCAGACACG-TTGAT
1 TGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG-T
* * *
92476 TGAAGATTG----AGTC-CTATACTCTCTGAAGGAATGGGGAGCGGACAC-ATTTGT
1 TGAAGATTGTTCAAGTCTC-ATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
92527 TGAAGATT
1 TGAAGATT
92535 TAGTCATATA
Statistics
Matches: 274, Mismatches: 36, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
48 2 0.01
49 1 0.00
50 13 0.05
51 67 0.24
52 26 0.09
53 12 0.04
54 2 0.01
55 151 0.55
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (55 bp):
TGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
Found at i:92417 original size:51 final size:51
Alignment explanation
Indices: 92282--92560 Score: 273
Period size: 51 Copynumber: 5.4 Consensus size: 51
92272 TTCGAGTCTA
* * * *
92282 ATACTCTCTGAAGAAATAGGGAGCAGACACGA-ATGTTGAAAATTATTCGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCAGACAC-ATTTGTTGAAGATTA----AGTCCT
* *
92337 ATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTAAGTCCT
* * *
92388 ATACTTTCTGAAGGAATAGGGAG-AGGACACGTTTGTTGAAGGTTTTTTAAGT-C-
1 ATACTCTCTGAAGGAATAGGGAGCA-GACACATTTGTTGAA-G---ATTAAGTCCT
* * *
92441 ATACTCTCTGAA-AAATAGGGAGCAGACAC-GTTGATTGAAGATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTG-TTGAAGATTAAGTCCT
* * * *
92491 ATACTCTCTGAAGGAATGGGGAGCGGACACATTTGTTGAAGATTTAGTCAT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTAAGTCCT
92542 ATACTCTCTGAAGGAATAG
1 ATACTCTCTGAAGGAATAG
92561 AGAACAAACT
Statistics
Matches: 189, Mismatches: 23, Indels: 28
0.79 0.10 0.12
Matches are distributed among these distances:
48 5 0.03
49 1 0.01
50 13 0.07
51 90 0.48
52 23 0.12
53 12 0.06
54 2 0.01
55 43 0.23
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (51 bp):
ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTAAGTCCT
Found at i:92495 original size:103 final size:104
Alignment explanation
Indices: 92337--92531 Score: 286
Period size: 103 Copynumber: 1.9 Consensus size: 104
92327 TTCGAGTCTT
* * * *
92337 ATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCCTATACTTTCTGAAGG
1 ATACTCTCTGAAGAAATAGGGAGCAGACACAGTTGTTGAAGATCAAGTCCTATACTCTCTGAAGG
*
92402 AATAGGGAGAGGACACGTTTGTTGAAGGTTTTTTAAGTC
66 AATAGGGAGAGGACACATTTGTTGAAGGTTTTTTAAGTC
**
92441 ATACTCTCTGAA-AAATAGGGAGCAGACAC-GTTGATTGAAGATTGAGTCCTATACTCTCTGAAG
1 ATACTCTCTGAAGAAATAGGGAGCAGACACAGTTG-TTGAAGATCAAGTCCTATACTCTCTGAAG
* *
92504 GAATGGGGAGCGGACACATTTGTTGAAG
65 GAATAGGGAGAGGACACATTTGTTGAAG
92532 ATTTAGTCAT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
102 3 0.04
103 66 0.81
104 12 0.15
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (104 bp):
ATACTCTCTGAAGAAATAGGGAGCAGACACAGTTGTTGAAGATCAAGTCCTATACTCTCTGAAGG
AATAGGGAGAGGACACATTTGTTGAAGGTTTTTTAAGTC
Found at i:92599 original size:154 final size:158
Alignment explanation
Indices: 92262--92607 Score: 386
Period size: 154 Copynumber: 2.2 Consensus size: 158
92252 GACATGAATA
* * *
92262 TTGAAAATTGTTCGAGTCTAATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAAATTA
1 TTGAAGATTGTTTGAGT-TAATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTG-AAATGA
* *
92327 TTCGAGTCTTATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCCTATAC
64 TTCGAGTCCTATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCATATAC
* ** *
92392 TTTCTGAAGGAATAGGGAGAGGACACGTTTG
129 TCTCTGAAGGAATA-GGAGAACAAACGTTTG
* * * * *
92423 TTGAAGGTTTTTTAAG-TCATACTCTCTGAA-AAATAGGGAGCAGACACG-TTGATTG-AA-GAT
1 TTGAAGATTGTTTGAGTTAATACTCTCTGAAGAAATAGGGAGCAGACACGAATG-TTGAAATGAT
* **
92483 T-GAGTCCTATACTCTCTGAAGGAAT-GGGGAGCGGACACATTTGTTGAAGATTTAGTCATATAC
65 TCGAGTCCTATACTCTCTGAAGGAATAGGGG-GCAGACACATTTGTTGAAGATCAAGTCATATAC
*
92546 TCTCTGAAGGAATA-GAGAACAAAC-TTGTT
129 TCTCTGAAGGAATAGGAGAACAAACGTT-TG
* *
92575 TTGAAGATTGTTTGAGTTTTATACTCCCTGAAG
1 TTGAAGATTGTTTGAG-TTAATACTCTCTGAAG
92608 CAAAAAAGAG
Statistics
Matches: 156, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
151 2 0.01
152 21 0.13
153 4 0.03
154 77 0.49
155 3 0.02
156 2 0.01
157 2 0.01
158 21 0.13
159 13 0.08
161 11 0.07
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (158 bp):
TTGAAGATTGTTTGAGTTAATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAATGATT
CGAGTCCTATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCATATACTC
TCTGAAGGAATAGGAGAACAAACGTTTG
Done.