Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002970.1 Hibiscus syriacus cultivar Beakdansim tig00006145_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: 66726
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1371 original size:19 final size:20
Alignment explanation
Indices: 1347--1385 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1337 CAGCAATCAA
1347 ACTTTACTTACAATC-CCAT
1 ACTTTACTTACAATCTCCAT
1366 ACTTTACTTACAATCTCCAT
1 ACTTTACTTACAATCTCCAT
1386 CTGTATTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (20 bp):
ACTTTACTTACAATCTCCAT
Found at i:4256 original size:21 final size:20
Alignment explanation
Indices: 4223--4266 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
4213 AAATGTAATT
*
4223 TAATAAATGTTAT-TTCATTA
1 TAATAAATATTATATTCA-TA
4243 TAATAAAATATTATATTCATA
1 TAAT-AAATATTATATTCATA
4264 TAA
1 TAA
4267 GAGTAAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
TAATAAATATTATATTCATA
Found at i:7606 original size:26 final size:28
Alignment explanation
Indices: 7576--7637 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
7566 AAAAATTTTT
7576 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCTGCAGAGTTTTCGAGTCGAGTCG
*
7602 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-C--TGCAGAGTTTTCGAGTCGAGTCG
7633 AGCTC
1 AGCTC
7638 AGCAATATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCTGCAGAGTTTTCGAGTCGAGTCG
Found at i:11521 original size:18 final size:20
Alignment explanation
Indices: 11494--11544 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
11484 ATAAAGTTCT
*
11494 TAAAAATTATTATTAT-C-A
1 TAAAATTTATTATTATACTA
11512 TAAAATTTATTGA-TATACTA
1 TAAAATTTATT-ATTATACTA
*
11532 TAAGATTTATTAT
1 TAAAATTTATTAT
11545 ATTTCTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 13 0.48
19 3 0.11
20 11 0.41
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
TAAAATTTATTATTATACTA
Found at i:16029 original size:14 final size:15
Alignment explanation
Indices: 16010--16040 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
16000 AGTGGTTAAG
16010 TATTTTATAT-TTCA
1 TATTTTATATGTTCA
16024 TATTTTATATGTTCA
1 TATTTTATATGTTCA
16039 TA
1 TA
16041 GTTAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (15 bp):
TATTTTATATGTTCA
Found at i:19478 original size:3 final size:3
Alignment explanation
Indices: 19470--19499 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19460 ACGGGAAGTC
19470 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19500 CAAGTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19929 original size:26 final size:26
Alignment explanation
Indices: 19893--19942 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
19883 TATTTTTATT
* *
19893 TTCCTAGAATTTTATAAGTCTATCCA
1 TTCCTAAAATTTTAAAAGTCTATCCA
*
19919 TTCCTAAAATTTTAAAAGTTTATC
1 TTCCTAAAATTTTAAAAGTCTATC
19943 TTAGGGGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (26 bp):
TTCCTAAAATTTTAAAAGTCTATCCA
Found at i:20050 original size:15 final size:15
Alignment explanation
Indices: 20029--20071 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
20019 TTTCGCACCT
20029 CTGAATGATTCAGTG
1 CTGAATGATTCAGTG
*
20044 TTGAATGATTCAGTG
1 CTGAATGATTCAGTG
*
20059 CTAAATGATTCAG
1 CTGAATGATTCAG
20072 CATCAAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (15 bp):
CTGAATGATTCAGTG
Found at i:20148 original size:15 final size:15
Alignment explanation
Indices: 20126--20161 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
20116 ATGTCACATT
20126 CAGAGCTAATTCATA
1 CAGAGCTAATTCATA
*
20141 CCGAGCTAATTCATA
1 CAGAGCTAATTCATA
20156 CAGAGC
1 CAGAGC
20162 CTCTGAATCA
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:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (15 bp):
CAGAGCTAATTCATA
Found at i:20473 original size:56 final size:55
Alignment explanation
Indices: 20383--20487 Score: 158
Period size: 56 Copynumber: 1.9 Consensus size: 55
20373 CGCTACCTAT
* *
20383 ATATATGTGTTTTGATATTATAAGACTACGGCATGTAAATGTAACCCTAGGTATAC
1 ATATATATGTTTTGATATCATAAGACTACGGCATGT-AATGTAACCCTAGGTATAC
*
20439 ATATATATGTTTTGGTATCATAAGACTA-GAGCATGTAATGTAACCCTAG
1 ATATATATGTTTTGATATCATAAGACTACG-GCATGTAATGTAACCCTAG
20488 CTAGCTAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
55 14 0.31
56 31 0.69
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (55 bp):
ATATATATGTTTTGATATCATAAGACTACGGCATGTAATGTAACCCTAGGTATAC
Found at i:28326 original size:59 final size:61
Alignment explanation
Indices: 28254--28371 Score: 186
Period size: 62 Copynumber: 2.0 Consensus size: 61
28244 AATTCCCCCT
* *
28254 TACTCGTAATTATTTTGTCATTTTAAG-TATA-TTTTTTATCAAAGTTAAATCACATGTTA
1 TACTCGTAATTATTTTATCATTTGAAGATATATTTTTTTATCAAAGTTAAATCACATGTTA
*
28313 TACTCGTAATTATTTTATCGTTTGAAGTATATATTTTTTTATCAAAGTTAAATCACATG
1 TACTCGTAATTATTTTATCATTTGAAG-ATATATTTTTTTATCAAAGTTAAATCACATG
28372 CTATTGTAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 24 0.45
61 4 0.08
62 25 0.47
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.48
Consensus pattern (61 bp):
TACTCGTAATTATTTTATCATTTGAAGATATATTTTTTTATCAAAGTTAAATCACATGTTA
Found at i:30350 original size:14 final size:14
Alignment explanation
Indices: 30331--30370 Score: 57
Period size: 12 Copynumber: 3.0 Consensus size: 14
30321 GGATCATTGT
*
30331 AAGCATACGAAGAA
1 AAGCATAAGAAGAA
30345 AAGCATAAGAAG--
1 AAGCATAAGAAGAA
30357 AAGCATAAGAAGAA
1 AAGCATAAGAAGAA
30371 GCATGGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.60, C:0.10, G:0.23, T:0.07
Consensus pattern (14 bp):
AAGCATAAGAAGAA
Found at i:30362 original size:12 final size:12
Alignment explanation
Indices: 30340--30374 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
30330 TAAGCATACG
30340 AAGAA-AAGCAT
1 AAGAAGAAGCAT
30351 AAGAAGAAGCAT
1 AAGAAGAAGCAT
30363 AAGAAGAAGCAT
1 AAGAAGAAGCAT
30375 GGGTTTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.60, C:0.09, G:0.23, T:0.09
Consensus pattern (12 bp):
AAGAAGAAGCAT
Found at i:36520 original size:37 final size:37
Alignment explanation
Indices: 36461--36573 Score: 171
Period size: 35 Copynumber: 3.2 Consensus size: 37
36451 ATCCCATTAT
* *
36461 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
*
36497 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
36533 CA-TTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
36568 CATTTT
1 CATTTT
36574 AATACTTTCA
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
35 35 0.49
36 16 0.23
37 20 0.28
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.32
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
Found at i:36536 original size:21 final size:21
Alignment explanation
Indices: 36512--36572 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
36502 TTCAAAGAAA
36512 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
36533 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
36547 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
36568 CATTT
1 CATTT
36573 TAATACTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:37705 original size:12 final size:12
Alignment explanation
Indices: 37688--37713 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37678 TGGCATCTGG
37688 TAAAACCACTGC
1 TAAAACCACTGC
37700 TAAAACCACTGC
1 TAAAACCACTGC
37712 TA
1 TA
37714 CTCATGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (12 bp):
TAAAACCACTGC
Found at i:41121 original size:37 final size:36
Alignment explanation
Indices: 41062--41181 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
41052 ATCCCATTAT
* *
41062 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
41098 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
41134 CA-TTTTCAAATAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
41169 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
41182 TTGGTTACCA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 28 0.37
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:41137 original size:21 final size:21
Alignment explanation
Indices: 41113--41173 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
41103 TTCAAAGAAA
41113 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
41134 CATTT-TCAAA---T--AAA-
1 CATTTACCAAACTTTGAAAAC
41148 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
41169 CATTT
1 CATTT
41174 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
17 1 0.03
18 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:44270 original size:22 final size:22
Alignment explanation
Indices: 44245--44309 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
44235 TGTTCCCTTA
44245 GAATGTGTATGAGTCAGCTTTG
1 GAATGTGTATGAGTCAGCTTTG
* * **
44267 GAATGCGCA-GAGCTTTTGC-TTG
1 GAATGTGTATGAG--TCAGCTTTG
44289 GAATGTGTATGAGTCAGCTTT
1 GAATGTGTATGAGTCAGCTTT
44310 ATAAACCTCC
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
21 6 0.19
22 19 0.61
23 6 0.19
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (22 bp):
GAATGTGTATGAGTCAGCTTTG
Found at i:46234 original size:14 final size:14
Alignment explanation
Indices: 46217--46243 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46207 GATCATGTAA
46217 GGAGGATTGAGGCT
1 GGAGGATTGAGGCT
46231 GGAGGATTGAGGC
1 GGAGGATTGAGGC
46244 CGCAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.52, T:0.19
Consensus pattern (14 bp):
GGAGGATTGAGGCT
Found at i:47125 original size:12 final size:11
Alignment explanation
Indices: 47096--47137 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
47086 GTTGTTGTTT
47096 TATTTTTAAAA
1 TATTTTTAAAA
*
47107 T-TTTTTAAATG
1 TATTTTTAAA-A
47118 TATTTTTAAAA
1 TATTTTTAAAA
47129 TATATTTTA
1 TAT-TTTTA
47138 CACGTGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.31
11 5 0.19
12 13 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:47436 original size:20 final size:20
Alignment explanation
Indices: 47413--47479 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
47403 GTTTCCAAAT
47413 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* *
47433 TCGCAACGTGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
* * *
47453 TCGCAACTCGAATTTGTAAT
1 TCGCAACGCGAATATGTAAA
47473 TCGCAAC
1 TCGCAAC
47480 ACAGAAGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:47492 original size:20 final size:20
Alignment explanation
Indices: 47469--47507 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
47459 CTCGAATTTG
47469 TAATTCGCAACACAGAAGTT
1 TAATTCGCAACACAGAAGTT
*
47489 TAATTCGCAACACATAAGT
1 TAATTCGCAACACAGAAGT
47508 CAAATTCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.26
Consensus pattern (20 bp):
TAATTCGCAACACAGAAGTT
Found at i:47497 original size:40 final size:40
Alignment explanation
Indices: 47410--47499 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 40
47400 TCAGTTTCCA
**
47410 AATTCGCAACGCGAATATGTAAATCGCAACGTGAATCTGT
1 AATTCGCAACGCGAATATGTAAATCGCAACCAGAATCTGT
* * * *
47450 AAATCGCAACTCGAATTTGTAATTCGCAACACAGAAGT-T-T
1 AATTCGCAACGCGAATATGTAAATCGCAAC-CAGAA-TCTGT
47490 AATTCGCAAC
1 AATTCGCAAC
47500 ACATAAGTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
40 36 0.88
41 4 0.10
42 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (40 bp):
AATTCGCAACGCGAATATGTAAATCGCAACCAGAATCTGT
Found at i:47513 original size:20 final size:20
Alignment explanation
Indices: 47470--47515 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
47460 TCGAATTTGT
**
47470 AATTCGCAACACAGAAGTTT
1 AATTCGCAACACAGAAGTCA
*
47490 AATTCGCAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
47510 AATTCG
1 AATTCG
47516 TAAAACGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:48145 original size:41 final size:42
Alignment explanation
Indices: 48096--48189 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
48086 TGCAACTCAA
**
48096 TTTCCAAATTCACAACGCGAATATGTAAA-TCGCATTGCGAT
1 TTTCCAAATTCACAACGCGAATATCCAAATTCGCATTGCGAT
* ** * *
48137 TTTCCAAATTCGCATTGCGATTTTCCAAATTCGCATTGCGAT
1 TTTCCAAATTCACAACGCGAATATCCAAATTCGCATTGCGAT
48179 TTTCCAAATTC
1 TTTCCAAATTC
48190 GCGTTGCGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.49
42 23 0.51
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (42 bp):
TTTCCAAATTCACAACGCGAATATCCAAATTCGCATTGCGAT
Found at i:48151 original size:21 final size:21
Alignment explanation
Indices: 48125--48203 Score: 149
Period size: 21 Copynumber: 3.8 Consensus size: 21
48115 AATATGTAAA
48125 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
48146 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
48167 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
48188 TCGCGTTGCGATTTTC
1 TCGCATTGCGATTTTC
48204 ATTTTCAGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:49553 original size:21 final size:20
Alignment explanation
Indices: 49523--49562 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49513 TTAACTTTGG
49523 CAACGCGAAAAATCAAATTCA
1 CAACGCG-AAAATCAAATTCA
* *
49544 CAACGTGAAAGTCAAATTC
1 CAACGCGAAAATCAAATTC
49563 GCGTTACGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.47, C:0.23, G:0.12, T:0.17
Consensus pattern (20 bp):
CAACGCGAAAATCAAATTCA
Found at i:55380 original size:2 final size:2
Alignment explanation
Indices: 55373--55397 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55363 ATTTGGAAAT
55373 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 T
55398 CAATTGTGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55466 original size:2 final size:2
Alignment explanation
Indices: 55459--55491 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55449 GTGATCCAAC
55459 AT AT AT AT 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 AT AT AT AT A
55492 CATTTAACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58716 original size:36 final size:36
Alignment explanation
Indices: 58666--58889 Score: 340
Period size: 36 Copynumber: 6.2 Consensus size: 36
58656 TGAATAAGAA
* * * *
58666 GAACGAAAGAAAGCATCGGTACTTCCGATTCAAGTT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
*
58702 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
*
58738 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
*
58774 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
* * * *
58810 GAACGGAAGGAAACATCGACACTTCCGATTCAGGTT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
*
58846 GAACGGAATGAAGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
58882 GAACGGAA
1 GAACGGAA
58890 AGATGTATCA
Statistics
Matches: 169, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 169 1.00
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
Found at i:59878 original size:14 final size:14
Alignment explanation
Indices: 59859--59888 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
59849 TTTGTTAAGC
59859 CTAACAGACTCTAA
1 CTAACAGACTCTAA
59873 CTAACAGACTCTAA
1 CTAACAGACTCTAA
59887 CT
1 CT
59889 GAATCTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (14 bp):
CTAACAGACTCTAA
Found at i:63358 original size:18 final size:18
Alignment explanation
Indices: 63337--63425 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 18
63327 ATTATCGTAA
*
63337 GAAGCACGATGATCATTG
1 GAAGCACGATTATCATTG
* *
63355 GAAGCACGATTATCGTAG
1 GAAGCACGATTATCATTG
* ** *
63373 GAAGGACGACGACCATTG
1 GAAGCACGATTATCATTG
*
63391 GAAACACGATTATCATTG
1 GAAGCACGATTATCATTG
63409 GAAGCACGATTATCATT
1 GAAGCACGATTATCATT
63426 TGTGACACAG
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (18 bp):
GAAGCACGATTATCATTG
Found at i:63366 original size:36 final size:36
Alignment explanation
Indices: 63326--63425 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 36
63316 TAGGAAGTCT
* *
63326 GATTATCGTAAGAAGCACGATGATCATTGGAAGCAC
1 GATTATCGTAGGAAGCACGATGATCATTGGAAACAC
* * *
63362 GATTATCGTAGGAAGGACGACGACCATTGGAAACAC
1 GATTATCGTAGGAAGCACGATGATCATTGGAAACAC
* * *
63398 GATTATCATTGGAAGCACGATTATCATT
1 GATTATCGTAGGAAGCACGATGATCATT
63426 TGTGACACAG
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (36 bp):
GATTATCGTAGGAAGCACGATGATCATTGGAAACAC
Found at i:64491 original size:14 final size:14
Alignment explanation
Indices: 64472--64501 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
64462 TTTGTTAAGC
64472 CTAACAGACTCTAA
1 CTAACAGACTCTAA
64486 CTAACAGACTCTAA
1 CTAACAGACTCTAA
64500 CT
1 CT
64502 GAATCTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (14 bp):
CTAACAGACTCTAA
Done.