Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009105.1 Hibiscus syriacus cultivar Beakdansim tig00112570_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: 137275
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:697 original size:15 final size:15
Alignment explanation
Indices: 677--714 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
667 TACTTAACTA
* *
677 ATATTATCATAATAT
1 ATATTATAATAACAT
692 ATATTATAATAACAT
1 ATATTATAATAACAT
707 ATA-TATAA
1 ATATTATAA
715 AGCTAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATTATAATAACAT
Found at i:4692 original size:22 final size:20
Alignment explanation
Indices: 4667--4706 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4657 ATGTTTGTTT
4667 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
4689 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
4707 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:6062 original size:13 final size:13
Alignment explanation
Indices: 6040--6077 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
6030 TTTCATCATC
6040 CATCCATCATCAA
1 CATCCATCATCAA
*
6053 CATCCTTCATCAA
1 CATCCATCATCAA
*
6066 GA-CCATCATCAA
1 CATCCATCATCAA
6078 TTCCATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.24
Consensus pattern (13 bp):
CATCCATCATCAA
Found at i:6131 original size:17 final size:19
Alignment explanation
Indices: 6099--6143 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
6089 TGTAGCCATC
6099 TCTA-TCATTTCTTTAT-T
1 TCTATTCATTTCTTTATCT
6116 TCTATTCATTTC-TTATCT
1 TCTATTCATTTCTTTATCT
6134 T-TATT-ATTTC
1 TCTATTCATTTC
6144 AATTATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 12 0.46
18 9 0.35
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTATTCATTTCTTTATCT
Found at i:13336 original size:13 final size:13
Alignment explanation
Indices: 13318--13343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13308 AACACCTCTC
13318 ACATACCTTTTCA
1 ACATACCTTTTCA
13331 ACATACCTTTTCA
1 ACATACCTTTTCA
13344 TCTTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:19654 original size:33 final size:33
Alignment explanation
Indices: 19610--19677 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
19600 CATCACCATA
*
19610 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
19643 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
19676 TT
1 TT
19678 TATTCATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.31, C:0.35, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:22112 original size:15 final size:15
Alignment explanation
Indices: 22092--22127 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
22082 ATTATTAGCT
*
22092 TTATAATATATGTTA
1 TTATAATATATATTA
22107 TTATAATATATATTA
1 TTATAATATATATTA
*
22122 TGATAA
1 TTATAA
22128 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:29419 original size:22 final size:23
Alignment explanation
Indices: 29382--29431 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
29372 ACAATCTGTC
* *
29382 CATCACCATTATCACGCCTATAT
1 CATCACCATTATCACGCCAATAA
29405 CATCACCA-TATCACGCCAATAA
1 CATCACCATTATCACGCCAATAA
29427 CATCA
1 CATCA
29432 TCCTTCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.36, C:0.36, G:0.04, T:0.24
Consensus pattern (23 bp):
CATCACCATTATCACGCCAATAA
Found at i:31202 original size:33 final size:32
Alignment explanation
Indices: 31138--31202 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
31128 CTTGTTGATG
*
31138 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
31170 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
31203 GATGGTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:31214 original size:13 final size:13
Alignment explanation
Indices: 31196--31242 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
31186 TATTGGCGTG
*
31196 ATATGGTGATGGT
1 ATATGGTGATGAT
31209 ATATGGTGATGAT
1 ATATGGTGATGAT
*
31222 ATA-GGCG-TGAT
1 ATATGGTGATGAT
31233 A-ATGGTGATG
1 ATATGGTGATG
31243 GACAGATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 1 0.03
11 8 0.28
12 5 0.17
13 15 0.52
ACGTcount: A:0.28, C:0.02, G:0.36, T:0.34
Consensus pattern (13 bp):
ATATGGTGATGAT
Found at i:35248 original size:17 final size:16
Alignment explanation
Indices: 35226--35260 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
35216 TGTAGGAGTC
35226 TTTTCTTTTCTCTTTTG
1 TTTTCTTTT-TCTTTTG
*
35243 TTTTCTTTTTTTTTTG
1 TTTTCTTTTTCTTTTG
35259 TT
1 TT
35261 GCTTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTG
Found at i:35670 original size:33 final size:33
Alignment explanation
Indices: 35606--35706 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
35596 CTTGTTGATG
* * *
35606 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
35638 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
35671 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
35707 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:39558 original size:33 final size:33
Alignment explanation
Indices: 39514--39582 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
39504 CATCACCATA
*
39514 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
39547 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
39580 TTC
1 TTC
39583 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:46075 original size:17 final size:17
Alignment explanation
Indices: 46053--46120 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
46043 AATTAAGAGT
46053 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* **
46070 TAGTTTGATTTATGAAC
1 TAGTTTAATAAATGAAC
*
46087 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
46104 TAACTTTATTAAATGAA
1 T-AGTTTAATAAATGAA
46121 ATAGATGCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 30 0.71
18 12 0.29
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:46904 original size:16 final size:16
Alignment explanation
Indices: 46883--46915 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
46873 CACATTCCAT
46883 CCTTCTTTGGTACCAA
1 CCTTCTTTGGTACCAA
46899 CCTTCTTTGGTACCAA
1 CCTTCTTTGGTACCAA
46915 C
1 C
46916 ATCACTGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.33, G:0.12, T:0.36
Consensus pattern (16 bp):
CCTTCTTTGGTACCAA
Found at i:49775 original size:23 final size:24
Alignment explanation
Indices: 49726--49778 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
49716 TTCTTTGCTT
* *
49726 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
49749 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
49772 TTTCTTT
1 TTTCTTT
49779 TTCTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:60604 original size:20 final size:24
Alignment explanation
Indices: 60578--60629 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
60568 TAAATGGATT
60578 AATGAAAT-AAT-AAATGA-AAGA
1 AATGAAATAAATGAAATGATAAGA
60599 AA-GAAATGAAATGAAATGATAAGA
1 AATGAAAT-AAATGAAATGATAAGA
60623 AATGAAA
1 AATGAAA
60630 GGGATTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.19
21 2 0.08
22 3 0.12
23 6 0.23
24 6 0.23
25 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (24 bp):
AATGAAATAAATGAAATGATAAGA
Found at i:60611 original size:5 final size:5
Alignment explanation
Indices: 60578--60629 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
60568 TAAATGGATT
60578 AATGA AAT-- AAT-A AATGA AA-GA AA-GA AATGA AATGA AATGA TAA-GA
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA -AATGA
60623 AATGA AA
1 AATGA AA
60630 GGGATTGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.07
4 13 0.31
5 24 0.57
6 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (5 bp):
AATGA
Found at i:62089 original size:61 final size:62
Alignment explanation
Indices: 62015--62140 Score: 227
Period size: 61 Copynumber: 2.0 Consensus size: 62
62005 AAGCAAAAGC
*
62015 ACTTATTTGCCAAAGGTGACAAGAAATATCAACATT-GACCAATCCTAAAGAAGTTTTCAAG
1 ACTTATTTGCCAAAGGTGACAAGAAATATCAACATTCAACCAATCCTAAAGAAGTTTTCAAG
62076 ACTTATTTGCCAAAGGTGACAAGAAATATCAACATTCCAACCAATCCTAAAGAAGTTTTCAAG
1 ACTTATTTGCCAAAGGTGACAAGAAATATCAACATT-CAACCAATCCTAAAGAAGTTTTCAAG
62139 AC
1 AC
62141 CTTTGATTGT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 36 0.58
63 26 0.42
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.25
Consensus pattern (62 bp):
ACTTATTTGCCAAAGGTGACAAGAAATATCAACATTCAACCAATCCTAAAGAAGTTTTCAAG
Found at i:66608 original size:19 final size:20
Alignment explanation
Indices: 66570--66612 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
66560 GAAACCCATT
*
66570 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
66590 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
66609 TGAA
1 TGAA
66613 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:69998 original size:16 final size:16
Alignment explanation
Indices: 69979--70017 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
69969 TGAAAATAAC
69979 AATTGA-AAGAAATGGA
1 AATTGATAAGAAAT-GA
*
69995 AATTGATAAGGAATGA
1 AATTGATAAGAAATGA
70011 AATTGAT
1 AATTGAT
70018 GTGATCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (16 bp):
AATTGATAAGAAATGA
Found at i:71884 original size:35 final size:35
Alignment explanation
Indices: 71843--71959 Score: 171
Period size: 35 Copynumber: 3.3 Consensus size: 35
71833 ATGGTAAGGG
* *
71843 GATGGTGATGATATAGGCACGAAATGGTGATAGAA
1 GATGGTGATGATATAGGCAAGAAATGGTGATGGAA
* * *
71878 GATGGTGATAATATAGGCAAGCAATGATGATGGAA
1 GATGGTGATGATATAGGCAAGAAATGGTGATGGAA
*
71913 GATGGTGATGATATAGGCATGAAAATGGTGATGGAA
1 GATGGTGATGATATAGGCAAG-AAATGGTGATGGAA
71949 GATGGTGATGA
1 GATGGTGATGA
71960 ACAGATAGTA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 49 0.68
36 23 0.32
ACGTcount: A:0.37, C:0.04, G:0.35, T:0.24
Consensus pattern (35 bp):
GATGGTGATGATATAGGCAAGAAATGGTGATGGAA
Found at i:74452 original size:47 final size:47
Alignment explanation
Indices: 74387--74480 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
74377 GGCACTACAA
*
74387 AAACAACCCATGTGCGTGACCAGCAAGGCAAGATGCTTGTCTCCACT
1 AAACAACCCATGTGCGTGACCAGCAAAGCAAGATGCTTGTCTCCACT
* * *
74434 AAACAACCCATGTGCGTGACCAGCAAAGCAAGGTGTTTTTCTCCACT
1 AAACAACCCATGTGCGTGACCAGCAAAGCAAGATGCTTGTCTCCACT
74481 TAAGCATCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (47 bp):
AAACAACCCATGTGCGTGACCAGCAAAGCAAGATGCTTGTCTCCACT
Found at i:75019 original size:5 final size:5
Alignment explanation
Indices: 75011--75035 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
75001 GATAAGATAA
75011 GAAAT GAAAT GAAAT GAAAT GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT
75036 AAAGAAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
GAAAT
Found at i:77292 original size:21 final size:21
Alignment explanation
Indices: 77267--77318 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
77257 AAATGGTTGA
77267 AGATAAGGAAAATGAAGGTAT
1 AGATAAGGAAAATGAAGGTAT
77288 AGATAAGGAAAATGAAGGTAT
1 AGATAAGGAAAATGAAGGTAT
*
77309 AGAAAAGGAA
1 AGATAAGGAA
77319 GAGGTGACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (21 bp):
AGATAAGGAAAATGAAGGTAT
Found at i:77478 original size:14 final size:15
Alignment explanation
Indices: 77449--77485 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
77439 TTGGCTTGCT
77449 TTCTTTTTGACTTTTC
1 TTCTTTTT-ACTTTTC
77465 TTCTTTTT-CTTTTC
1 TTCTTTTTACTTTTC
77479 TT-TTTTT
1 TTCTTTTT
77486 TTCTGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 8 0.38
16 8 0.38
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (15 bp):
TTCTTTTTACTTTTC
Found at i:82444 original size:19 final size:18
Alignment explanation
Indices: 82411--82464 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
82401 TTGCTTTCCC
82411 TTTTGAATTTCTTTTCTTCT
1 TTTTG-ATTT-TTTTCTTCT
82431 TTTCTGATTTTTTTCTTCT
1 TTT-TGATTTTTTTCTTCT
*
82450 TTTTG-TCTTTTTCTT
1 TTTTGATTTTTTTCTT
82465 TTCTTTTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 9 0.28
18 2 0.06
19 12 0.38
20 7 0.22
21 2 0.06
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTGATTTTTTTCTTCT
Found at i:82468 original size:19 final size:20
Alignment explanation
Indices: 82418--82473 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
82408 CCCTTTTGAA
82418 TTTCTTTTCTTCTTT-TCTGAT
1 TTTCTTTTCTT-TTTGTCT-AT
*
82439 TTTTTTCTTCTTTTTGTCT-T
1 TTTCTT-TTCTTTTTGTCTAT
82459 TTTCTTTTCTTTTTG
1 TTTCTTTTCTTTTTG
82474 CACTCCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 9 0.29
20 6 0.19
21 8 0.26
22 8 0.26
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTCTTTTCTTTTTGTCTAT
Found at i:85179 original size:31 final size:30
Alignment explanation
Indices: 85105--85203 Score: 180
Period size: 30 Copynumber: 3.3 Consensus size: 30
85095 GAAAACATGT
*
85105 ATGAGCTAGAAAAAAGATGCATACATGCAG
1 ATGAGCTAGAAAAAAGATGCATACATGCAA
85135 ATGAGCTAGAAAAAAGATGCATACATGCAA
1 ATGAGCTAGAAAAAAGATGCATACATGCAA
85165 ATGAGCTAGAAAAAAAGATGCATACATGCAA
1 ATGAGCTAG-AAAAAAGATGCATACATGCAA
85196 ATGAGCTA
1 ATGAGCTA
85204 AAGATCATGG
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
30 38 0.57
31 29 0.43
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.17
Consensus pattern (30 bp):
ATGAGCTAGAAAAAAGATGCATACATGCAA
Found at i:90420 original size:19 final size:20
Alignment explanation
Indices: 90379--90429 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
90369 GAAACCCCTT
*
90379 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
90399 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
90418 TGAAGATACATG
1 TGAAAATACATG
90430 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:92382 original size:15 final size:15
Alignment explanation
Indices: 92362--92391 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
92352 TATCACAATC
92362 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
92377 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
92392 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:108971 original size:5 final size:6
Alignment explanation
Indices: 108928--108969 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
108918 GTGCTGCAAC
*
108928 AAAAAG CAACAAG AAAGAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG -AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
108970 GACTCCTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 21 0.66
7 11 0.34
ACGTcount: A:0.79, C:0.05, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:112838 original size:24 final size:26
Alignment explanation
Indices: 112811--112859 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
112801 ATGTTGGGAT
112811 AAACTT-GCTGTTTT-TTTTCTTTTG
1 AAACTTCGCTGTTTTGTTTTCTTTTG
* *
112835 AAACTTCTCTTTTTTGTTTTCTTTT
1 AAACTTCGCTGTTTTGTTTTCTTTT
112860 TTTTGAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 6 0.29
26 9 0.43
ACGTcount: A:0.12, C:0.14, G:0.08, T:0.65
Consensus pattern (26 bp):
AAACTTCGCTGTTTTGTTTTCTTTTG
Found at i:125348 original size:26 final size:26
Alignment explanation
Indices: 125282--125349 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
125272 ATGAACCCAC
*
125282 ATGCAAGGCACATGGGGGCTGGTCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
* *
125308 ATGCAAGGAACATGGGGGTTGATCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
* *
125334 ATGCAAAGCATATGGG
1 ATGCAAGGCACATGGG
125350 TGTTCTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (26 bp):
ATGCAAGGCACATGGGGGCTGATCAT
Found at i:128301 original size:23 final size:23
Alignment explanation
Indices: 128275--128318 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
128265 TTTCTTTTCT
128275 TTTTTC-TTCTTTTTGAGTGCTGG
1 TTTTTCTTTC-TTTTGAGTGCTGG
128298 TTTTTCTTTCTTTTGAGTGCT
1 TTTTTCTTTCTTTTGAGTGCT
128319 TCACTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.05, C:0.14, G:0.18, T:0.64
Consensus pattern (23 bp):
TTTTTCTTTCTTTTGAGTGCTGG
Found at i:129126 original size:26 final size:26
Alignment explanation
Indices: 129090--129147 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
129080 ATGAACCCAC
*
129090 ATGCAAGGCACATGGGGGCTGGTCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
129116 ATGCAAGGCACATGGGGGCTGATCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
129142 ATGCAA
1 ATGCAA
129148 AACATGGGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.34, T:0.19
Consensus pattern (26 bp):
ATGCAAGGCACATGGGGGCTGATCAT
Done.