Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000618.1 Hibiscus syriacus cultivar Beakdansim tig00001196_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: 80849
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:797 original size:21 final size:18
Alignment explanation
Indices: 753--801 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 18
743 CGGCCAAGAG
753 CATGTATCTTCATTAAAAT
1 CATGTAT-TTCATTAAAAT
772 CATGTACTTTCATTTAAAAGT
1 CATGTA-TTTCA-TTAAAA-T
793 CATGTATTT
1 CATGTATTT
802 TCAAAGGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 7 0.26
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (18 bp):
CATGTATTTCATTAAAAT
Found at i:803 original size:21 final size:19
Alignment explanation
Indices: 753--804 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
743 CGGCCAAGAG
*
753 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
*
772 CATGTACTTTCATTTAAAAGT
1 CATGTATTTTCA-TTAAAA-T
793 CATGTATTTTCA
1 CATGTATTTTCA
805 AAGGAGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:4720 original size:19 final size:21
Alignment explanation
Indices: 4696--4747 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
4686 CGGCCAAGAG
*
4696 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
4715 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
4736 CATGTATTTTCA
1 CATGTATTTTCA
4748 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:7173 original size:9 final size:9
Alignment explanation
Indices: 7159--7188 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
7149 TTTGGAGTGC
7159 AAAAGAAAG
1 AAAAGAAAG
7168 AAAAGAAAG
1 AAAAGAAAG
7177 AAAAGAAA-
1 AAAAGAAAG
7185 AAAA
1 AAAA
7189 TTCAAAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:7373 original size:16 final size:16
Alignment explanation
Indices: 7339--7387 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
7329 GTAAGTTATC
* * *
7339 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
7355 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
7371 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
7388 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:11423 original size:16 final size:16
Alignment explanation
Indices: 11384--11437 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
11374 GAGTTGTAAG
11384 TTATCTTCATTTTCTTA
1 TTAT-TTCATTTTCTTA
*
11401 CTATTTCATTTTCTTA
1 TTATTTCATTTTCTTA
*
11417 TTCTTTCATCTTTTCTTA
1 TTATTTCA--TTTTCTTA
11435 TTA
1 TTA
11438 CATTACCTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 18 0.58
17 3 0.10
18 10 0.32
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTCATTTTCTTA
Found at i:13966 original size:18 final size:18
Alignment explanation
Indices: 13945--13999 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
13935 ACCTTTTGAT
13945 GAAGAGTTGCCATTCCAA
1 GAAGAGTTGCCATTCCAA
* * * *
13963 G-A-AG-TACCTTTTCAC
1 GAAGAGTTGCCATTCCAA
13978 GAAGAGTTGCCATTCCAA
1 GAAGAGTTGCCATTCCAA
13996 GAAG
1 GAAG
14000 TACCTTTTCA
Statistics
Matches: 26, Mismatches: 8, Indels: 6
0.65 0.20 0.15
Matches are distributed among these distances:
15 8 0.31
16 3 0.12
17 3 0.12
18 12 0.46
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (18 bp):
GAAGAGTTGCCATTCCAA
Found at i:13982 original size:33 final size:33
Alignment explanation
Indices: 13933--14010 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
13923 TTGTGAAATC
* *
13933 GTACCTTTTGATGAAGAGTTGCCATTCCAAGAA
1 GTACCTTTTCACGAAGAGTTGCCATTCCAAGAA
13966 GTACCTTTTCACGAAGAGTTGCCATTCCAAGAA
1 GTACCTTTTCACGAAGAGTTGCCATTCCAAGAA
13999 GTACCTTTTCAC
1 GTACCTTTTCAC
14011 AAGGAGCTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (33 bp):
GTACCTTTTCACGAAGAGTTGCCATTCCAAGAA
Found at i:16334 original size:11 final size:12
Alignment explanation
Indices: 16304--16349 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
16294 TTGGTGCTGG
16304 AAACAAGATAAA
1 AAACAAGATAAA
* *
16316 AAATAAGAT-TA
1 AAACAAGATAAA
16327 AAACAAGATAAA
1 AAACAAGATAAA
*
16339 GAA-AAGATAAA
1 AAACAAGATAAA
16350 GGAATTGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:16334 original size:23 final size:22
Alignment explanation
Indices: 16304--16346 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
16294 TTGGTGCTGG
16304 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
16327 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
16347 AAAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:20643 original size:12 final size:12
Alignment explanation
Indices: 20626--20664 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
20616 AAATTTTGGC
20626 TTTTTTT-GTTT
1 TTTTTTTGGTTT
*
20637 TTTTTTTGGCTT
1 TTTTTTTGGTTT
20649 TTTTTTTGGTTT
1 TTTTTTTGGTTT
20661 TTTT
1 TTTT
20665 GTTTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 7 0.28
12 18 0.72
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.85
Consensus pattern (12 bp):
TTTTTTTGGTTT
Found at i:20643 original size:21 final size:21
Alignment explanation
Indices: 20619--20677 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
20609 TTTTTTGAAA
20619 TTTTGGCTTTTTTTGTTTTTT
1 TTTTGGCTTTTTTTGTTTTTT
*
20640 TTTTGGCTTTTTTT-TTGGTTT
1 TTTTGGCTTTTTTTGTT-TTTT
20661 TTTT-G--TTTTTTGTTTTT
1 TTTTGGCTTTTTTTGTTTTT
20678 AAAAAAATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 3 0.09
21 21 0.62
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.81
Consensus pattern (21 bp):
TTTTGGCTTTTTTTGTTTTTT
Found at i:20676 original size:12 final size:11
Alignment explanation
Indices: 20626--20676 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
20616 AAATTTTGGC
20626 TTTTTTTGTTT
1 TTTTTTTGTTT
*
20637 TTTTTTTGGCTT
1 TTTTTTT-GTTT
*
20649 TTTTTTTG--G
1 TTTTTTTGTTT
20658 TTTTTTTGTTT
1 TTTTTTTGTTT
20669 TTTGTTTT
1 TTT-TTTT
20677 TAAAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 8 0.24
11 11 0.33
12 14 0.42
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:21035 original size:11 final size:12
Alignment explanation
Indices: 21005--21050 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
20995 TTGGTGCTGG
21005 AAACAAGATAAA
1 AAACAAGATAAA
* *
21017 AAATAAGAT-TA
1 AAACAAGATAAA
21028 AAACAAGATAAA
1 AAACAAGATAAA
*
21040 GAA-AAGATAAA
1 AAACAAGATAAA
21051 GGAATTGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:21035 original size:23 final size:22
Alignment explanation
Indices: 21005--21047 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
20995 TTGGTGCTGG
21005 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
21028 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
21048 AAAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:22154 original size:25 final size:29
Alignment explanation
Indices: 22125--22179 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
22115 CATATATAAA
22125 AAATAT-ATC-CATATTAT-AATA-AATC
1 AAATATGATCACATATTATGAATATAATC
*
22150 AAATATGATCATATATTATGAATATAATC
1 AAATATGATCACATATTATGAATATAATC
22179 A
1 A
22180 TCATAAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 6 0.24
26 3 0.12
27 7 0.28
28 4 0.16
29 5 0.20
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (29 bp):
AAATATGATCACATATTATGAATATAATC
Found at i:33448 original size:44 final size:44
Alignment explanation
Indices: 33377--33465 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
33367 TCGGCTATAA
* *
33377 TGGATGAACATCTCCCTTAGCCAAATGGTCTTGTGATGATTCAT
1 TGGATGAACATCTCCATTAGCCAAATGGTCTTATGATGATTCAT
* **
33421 TGGATGAACATCTCCATTGGCTGAATGGTCTTATGATGATTCAT
1 TGGATGAACATCTCCATTAGCCAAATGGTCTTATGATGATTCAT
33465 T
1 T
33466 TTGGCCCCGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (44 bp):
TGGATGAACATCTCCATTAGCCAAATGGTCTTATGATGATTCAT
Found at i:38014 original size:23 final size:23
Alignment explanation
Indices: 37987--38033 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
37977 GAGTGGAGCA
37987 TCATCATTTTTTTGGAGTGATCG
1 TCATCATTTTTTTGGAGTGATCG
38010 TCATCATTTTTTTGGAGTGATCG
1 TCATCATTTTTTTGGAGTGATCG
38033 T
1 T
38034 GAGGATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.49
Consensus pattern (23 bp):
TCATCATTTTTTTGGAGTGATCG
Found at i:40109 original size:36 final size:36
Alignment explanation
Indices: 40062--40166 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
40052 GATACAATCT
*
40062 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
40098 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
40134 TTCCATCACTA-TATCACGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
40167 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.30, C:0.34, G:0.05, T:0.31
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:40582 original size:24 final size:24
Alignment explanation
Indices: 40542--40588 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
40532 AGAGTGCTAC
40542 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
40567 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
40589 CTCCTACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:40644 original size:14 final size:15
Alignment explanation
Indices: 40610--40656 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
40600 AATTTGGAGT
40610 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
40625 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
40639 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
40656 G
1 G
40657 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:44494 original size:13 final size:12
Alignment explanation
Indices: 44475--44535 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
44465 CACGCCTATA
44475 TCATCACCATAT
1 TCATCACCATAT
44487 TCCATCACC--AT
1 T-CATCACCATAT
*
44498 T-ATCACGCCTAT
1 TCATCAC-CATAT
44510 ATCATCACCATAT
1 -TCATCACCATAT
44523 TCCATCACCATAT
1 T-CATCACCATAT
44536 CACGCCTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
9 5 0.12
10 1 0.02
11 3 0.07
12 4 0.10
13 23 0.56
14 5 0.12
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.31
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:44508 original size:36 final size:36
Alignment explanation
Indices: 44461--44554 Score: 163
Period size: 36 Copynumber: 2.6 Consensus size: 36
44451 TTTATAAGAT
44461 TTATCACGCCTATATCATCACCATATTCCATCACCA
1 TTATCACGCCTATATCATCACCATATTCCATCACCA
44497 TTATCACGCCTATATCATCACCATATTCCATCACCA
1 TTATCACGCCTATATCATCACCATATTCCATCACCA
* *
44533 -TATCACGCCTATTTTATCACCA
1 TTATCACGCCTATATCATCACCA
44555 ACTTATAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 20 0.36
36 36 0.64
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (36 bp):
TTATCACGCCTATATCATCACCATATTCCATCACCA
Found at i:57026 original size:16 final size:16
Alignment explanation
Indices: 57000--57055 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
56990 GTAAGTTATC
57000 TTCATTTTTCTTACTAT
1 TTCATTTTTCTTA-TAT
*
57017 TTCA-TTTTCTTATTCT
1 TTCATTTTTCTTA-TAT
*
57033 TTCATCTTTTCTTATTT
1 TTCAT-TTTTCTTATAT
57050 TTCATT
1 TTCATT
57056 ACTTTATCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 15 0.44
17 11 0.32
18 8 0.24
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCATTTTTCTTATAT
Found at i:60130 original size:16 final size:16
Alignment explanation
Indices: 60096--60144 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
60086 GTAAGTTATC
* * *
60096 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
60112 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
60128 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
60145 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:65347 original size:18 final size:18
Alignment explanation
Indices: 65324--65372 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
65314 AATTGGAGTG
65324 CAAAAAGAA-AAGAAAAGA
1 CAAAAAGAAGAA-AAAAGA
**
65342 CAAAAAGAAGAAAAAATT
1 CAAAAAGAAGAAAAAAGA
65360 CAAAAAGAAGAAA
1 CAAAAAGAAGAAA
65373 GGAAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 26 0.93
19 2 0.07
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
CAAAAAGAAGAAAAAAGA
Found at i:65373 original size:25 final size:25
Alignment explanation
Indices: 65325--65398 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
65315 ATTGGAGTGC
* * *
65325 AAAAAGAAAAGAAAAGACAA-AAAG
1 AAAAAGAAAATAAAAAAGAAGAAAG
* *
65349 AAGAAA-AAATTCAAAAAGAAGAAAGG
1 AA-AAAGAAAATAAAAAAGAAGAAA-G
65375 AAAAAGAAAATAAAAAAG-AGAAAG
1 AAAAAGAAAATAAAAAAGAAGAAAG
65399 CAAGCCAAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
24 12 0.31
25 14 0.36
26 13 0.33
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.04
Consensus pattern (25 bp):
AAAAAGAAAATAAAAAAGAAGAAAG
Found at i:65378 original size:21 final size:20
Alignment explanation
Indices: 65324--65378 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 20
65314 AATTGGAGTG
65324 CAAAAAG-A-AAAGAAAAGA
1 CAAAAAGAAGAAAGAAAAGA
**
65342 CAAAAAGAAG-AA-AAAATT
1 CAAAAAGAAGAAAGAAAAGA
65360 CAAAAAGAAGAAAGGAAAA
1 CAAAAAGAAGAAA-GAAAA
65379 AGAAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 21 0.70
19 5 0.17
21 4 0.13
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (20 bp):
CAAAAAGAAGAAAGAAAAGA
Found at i:73791 original size:36 final size:35
Alignment explanation
Indices: 73697--73802 Score: 133
Period size: 35 Copynumber: 3.0 Consensus size: 35
73687 ATTGGTGGTT
* * * *
73697 ATATAGGCATGAAATGGTGATAGAATATGGTAATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* *
73732 ATATAGGCGTGCAATGGTAATGGAAGATGGTGAT-
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
73766 ATTATAGGCGTGAAAATGGTGATGGAAGATGGTGATG
1 A-TATAGGCGTG-AAATGGTGATGGAAGATGGTGATG
73803 TTTACGTAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.02
35 38 0.63
36 21 0.35
ACGTcount: A:0.35, C:0.04, G:0.34, T:0.27
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
Done.