Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003910.1 Hibiscus syriacus cultivar Beakdansim tig00008458_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: 110940
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1223 original size:112 final size:112
Alignment explanation
Indices: 1033--1507 Score: 680
Period size: 112 Copynumber: 4.3 Consensus size: 112
1023 TGTATTGTTC
* * * **
1033 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTG-C-CT--AT-AGAACTG-GGAAA-TTGTTT
1 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGA-AACTGAAAAAAGTTGTTT
* * * *
1091 GTTGACAGCCAGTCACCCCTTCGCTGTAAAGTTGAGCTTGTACTGTCT
65 GTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
* *
1139 CAAGTCTAATATCCTTCGCTGTAAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAGTTGTTTG
1 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAGTTGTTTG
*
1204 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
66 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
* *
1251 CGAGTCTAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAGTTGTTTG
1 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAGTTGTTTG
*
1316 TTGACAGTCAGTAGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
* * *
1363 CGAGTCTAATATCC-TCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTG-AAAAAGTTATTTA
1 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAGTTGTTTG
* *
1426 TTGACAGTCAGCCGCCCTTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
* *
1473 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTG
1508 GATCTAAAAC
Statistics
Matches: 333, Mismatches: 28, Indels: 11
0.90 0.08 0.03
Matches are distributed among these distances:
106 30 0.09
107 1 0.00
108 2 0.01
110 74 0.22
111 58 0.17
112 168 0.50
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (112 bp):
CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAGTTGTTTG
TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
Found at i:13260 original size:23 final size:23
Alignment explanation
Indices: 13234--13315 Score: 137
Period size: 23 Copynumber: 3.6 Consensus size: 23
13224 CTCGTATAAA
*
13234 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
* *
13257 TGCACCGAAGTGCCGTGTAAAAT
1 TGCACCGAAGTGCCGCGTAGAAT
13280 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
13303 TGCACCGAAGTGC
1 TGCACCGAAGTGC
13316 TATATAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:13324 original size:46 final size:46
Alignment explanation
Indices: 13234--13325 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
13224 CTCGTATAAA
* *
13234 TGCACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCGTGTAAAAT
1 TGCACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCATATAAAAT
* *
13280 TGCACCGAAGTGCCGCGTAGAATTGCACCGAAGTGCTATATAAAAT
1 TGCACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCATATAAAAT
13326 GTCCCTGGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.21
Consensus pattern (46 bp):
TGCACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCATATAAAAT
Found at i:16158 original size:20 final size:20
Alignment explanation
Indices: 16133--16180 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
16123 ATTTCATTTC
16133 TTTATTCCATTCTTCCTTTA
1 TTTATTCCATTCTTCCTTTA
16153 TTTATTCCATTCTTCCTTTA
1 TTTATTCCATTCTTCCTTTA
16173 TTTATTCC
1 TTTATTCC
16181 TTATACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATTCCATTCTTCCTTTA
Found at i:18286 original size:23 final size:23
Alignment explanation
Indices: 18260--18303 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
18250 CATCACAGCT
*
18260 CGTATAAATGCACCAAAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCG
* *
18283 CGTAGAATTGCACCGAAGTGC
1 CGTAGAAATGCACCAAAGTGC
18304 TATATAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCG
Found at i:19935 original size:21 final size:21
Alignment explanation
Indices: 19911--19955 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19901 TCTAGTTCGT
* * *
19911 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
19932 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
19953 TTG
1 TTG
19956 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:27462 original size:20 final size:20
Alignment explanation
Indices: 27415--27463 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
27405 TAAGAACAAT
* *
27415 ATCAATATTATTTTATTAGC
1 ATCAATATTATTTTATCAGA
**
27435 ATTGATATTATTTTATCAGA
1 ATCAATATTATTTTATCAGA
27455 ATCAATATT
1 ATCAATATT
27464 TTATCTTCGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (20 bp):
ATCAATATTATTTTATCAGA
Found at i:27587 original size:19 final size:19
Alignment explanation
Indices: 27551--27592 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
27541 GGCAAAAATT
*
27551 TAAATTATTTAATATTATA
1 TAAATTATTAAATATTATA
*
27570 TAAATTTATTAAAT-TTATT
1 TAAA-TTATTAAATATTATA
27589 TAAA
1 TAAA
27593 ATAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAATTATTAAATATTATA
Found at i:27591 original size:10 final size:10
Alignment explanation
Indices: 27548--27592 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
27538 TATGGCAAAA
27548 ATTTAAA-TT
1 ATTTAAATTT
27557 ATTT-AATATT
1 ATTTAAAT-TT
*
27567 ATATAAATTT
1 ATTTAAATTT
27577 A-TTAAATTT
1 ATTTAAATTT
27586 ATTTAAA
1 ATTTAAA
27593 ATAAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 2 0.07
9 12 0.40
10 13 0.43
11 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:29778 original size:21 final size:21
Alignment explanation
Indices: 29734--29777 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
29724 AAATTACACA
*
29734 TTTAGTATCTAAACTATTAAT
1 TTTAGTATCTAAACTATCAAT
29755 TTTAGTATCTAAACT-TCAAT
1 TTTAGTATCTAAACTATCAAT
29775 TTT
1 TTT
29778 TTTTCTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTAGTATCTAAACTATCAAT
Found at i:40176 original size:2 final size:2
Alignment explanation
Indices: 40165--40202 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
40155 ATTGGTAAAT
40165 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40203 TATTTGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49647 original size:17 final size:17
Alignment explanation
Indices: 49620--49658 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
49610 AATTTACAAT
49620 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
49636 TAATTATAAATAATATC
1 TAATTATAAATAATATC
49653 TAATTA
1 TAATTA
49659 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:53882 original size:14 final size:15
Alignment explanation
Indices: 53850--53884 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
53840 AAAATTTAAA
53850 TATTTTATTAATGTTG
1 TATTTTATTAA-GTTG
53866 TATTTTATTAA-TTG
1 TATTTTATTAAGTTG
53880 TATTT
1 TATTT
53885 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
16 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (15 bp):
TATTTTATTAAGTTG
Found at i:57832 original size:11 final size:11
Alignment explanation
Indices: 57816--57842 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
57806 TGTTTATGTT
57816 ATTTAATTTTC
1 ATTTAATTTTC
57827 ATTTAATTTTC
1 ATTTAATTTTC
57838 ATTTA
1 ATTTA
57843 CTTTCAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTAATTTTC
Found at i:58171 original size:3 final size:3
Alignment explanation
Indices: 58157--58209 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
58147 TCACTATCTC
* * *
58157 CAT CAT CGT CAT CAT CAT CAT CAT CAT CAA CAT CAT CAT CAT CAC CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
58205 CAT CA
1 CAT CA
58210 GGAGCAGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.36, G:0.02, T:0.28
Consensus pattern (3 bp):
CAT
Found at i:60431 original size:22 final size:22
Alignment explanation
Indices: 60406--60451 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
60396 TTTGAATGAA
60406 GAGGGGATGGGGGTATTTATAG
1 GAGGGGATGGGGGTATTTATAG
60428 GAGGGGATGGGGGTATTTATAG
1 GAGGGGATGGGGGTATTTATAG
60450 GA
1 GA
60452 AGAGATGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.50, T:0.26
Consensus pattern (22 bp):
GAGGGGATGGGGGTATTTATAG
Found at i:60458 original size:22 final size:22
Alignment explanation
Indices: 60411--60463 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
60401 ATGAAGAGGG
* *
60411 GATGGGGGTATTTATAGGAGGG
1 GATGGGGGTATTTATAGGAAGA
60433 GATGGGGGTATTTATAGGAAGA
1 GATGGGGGTATTTATAGGAAGA
*
60455 GATGAGGGT
1 GATGGGGGT
60464 TAGTCGGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.47, T:0.26
Consensus pattern (22 bp):
GATGGGGGTATTTATAGGAAGA
Found at i:61198 original size:16 final size:16
Alignment explanation
Indices: 61174--61217 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
61164 TTCAAATCAA
*
61174 AATTAAAAAAAATATT
1 AATTTAAAAAAATATT
*
61190 -ATTTTAAAAAATATT
1 AATTTAAAAAAATATT
*
61205 AATTTATAAAAAT
1 AATTTAAAAAAAT
61218 TGTATGGTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTTAAAAAAATATT
Found at i:61200 original size:15 final size:15
Alignment explanation
Indices: 61180--61217 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
61170 TCAAAATTAA
*
61180 AAAAAATATTATTTT
1 AAAAAATATTAATTT
61195 AAAAAATATTAATTT
1 AAAAAATATTAATTT
61210 ATAAAAAT
1 A-AAAAAT
61218 TGTATGGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAAATATTAATTT
Found at i:61764 original size:24 final size:26
Alignment explanation
Indices: 61722--61769 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
61712 ATTATAAAAC
61722 TTTAAAAGAATAAAATT-AATTATTT
1 TTTAAAAGAATAAAATTAAATTATTT
* *
61747 TTTAAAA-AATATATTTAAATTAT
1 TTTAAAAGAATAAAATTAAATTAT
61770 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
TTTAAAAGAATAAAATTAAATTATTT
Found at i:61794 original size:19 final size:18
Alignment explanation
Indices: 61749--61802 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
61739 AATTATTTTT
*
61749 TAAAAAATATATTTAAATTA
1 TAAAAAA-A-ATTAAAATTA
*
61769 TATAAAAAATTAAAATCTA
1 TAAAAAAAATTAAAAT-TA
*
61788 TAAAAAAAAATAAAA
1 TAAAAAAAATTAAAA
61803 ACCGCATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAAAATTAAAATTA
Found at i:66294 original size:2 final size:2
Alignment explanation
Indices: 66287--66344 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
66277 GTTATCGTTC
66287 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
66329 AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT A
66345 GAGAGAGAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66445 original size:36 final size:36
Alignment explanation
Indices: 66366--66498 Score: 169
Period size: 40 Copynumber: 3.5 Consensus size: 36
66356 ATATGTGTGC
*
66366 ATGTATGTATGTATCCCAACATATATATATTATAGAT-G
1 ATGTATGTATGTATCCC-A-ATATATATA-GATAGATAG
66404 AATGTATGTATGTATCCCAATATATATAGATAGATAG
1 -ATGTATGTATGTATCCCAATATATATAGATAGATAG
66441 ATGTATGCATGCATGTATCCCAATATATATAGATAGATAG
1 ATGTATG--T--ATGTATCCCAATATATATAGATAGATAG
*
66481 ATGTATGCATGTATCCCA
1 ATGTATGTATGTATCCCA
66499 TGTCCCCATG
Statistics
Matches: 87, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
36 23 0.26
37 10 0.11
38 2 0.02
39 17 0.20
40 35 0.40
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (36 bp):
ATGTATGTATGTATCCCAATATATATAGATAGATAG
Found at i:66457 original size:40 final size:40
Alignment explanation
Indices: 66374--66491 Score: 175
Period size: 40 Copynumber: 3.0 Consensus size: 40
66364 GCATGTATGT
* * * * * *
66374 ATGTATCCCAACATATATATAT-TATAGATGAATGTATGT
1 ATGTATCCCAATATATATAGATAGATAGATGTATGCATGC
66413 ATGTATCCCAATATATATAGATAGATAGATGTATGCATGC
1 ATGTATCCCAATATATATAGATAGATAGATGTATGCATGC
66453 ATGTATCCCAATATATATAGATAGATAGATGTATGCATG
1 ATGTATCCCAATATATATAGATAGATAGATGTATGCATG
66492 TATCCCATGT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 20 0.28
40 52 0.72
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (40 bp):
ATGTATCCCAATATATATAGATAGATAGATGTATGCATGC
Found at i:75387 original size:38 final size:38
Alignment explanation
Indices: 75336--75412 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
75326 GATATTCGTA
75336 ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
1 ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
75374 ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
1 ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
75412 A
1 A
75413 ACTGATGACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (38 bp):
ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
Found at i:81991 original size:2 final size:2
Alignment explanation
Indices: 81984--82011 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
81974 AAGATTATGA
81984 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
82012 GATTAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82368 original size:14 final size:14
Alignment explanation
Indices: 82349--82414 Score: 86
Period size: 14 Copynumber: 5.0 Consensus size: 14
82339 GTGAACATTC
82349 GGTTATGTTCGTTT
1 GGTTATGTTCGTTT
82363 GGTTATGTTCGTTT
1 GGTTATGTTCGTTT
82377 GGTTATGTTCG--T
1 GGTTATGTTCGTTT
*
82389 --TTATGTTCGTTC
1 GGTTATGTTCGTTT
*
82401 GATTATGTTCGTTT
1 GGTTATGTTCGTTT
82415 ATATTCATTC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
10 9 0.20
12 1 0.02
14 36 0.78
ACGTcount: A:0.09, C:0.09, G:0.26, T:0.56
Consensus pattern (14 bp):
GGTTATGTTCGTTT
Found at i:82392 original size:24 final size:24
Alignment explanation
Indices: 82365--82433 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
82355 GTTCGTTTGG
* *
82365 TTATGTTCGTTTGGTTATGTTCGT
1 TTATGTTCGTTCGATTATGTTCGT
82389 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTCGT
* *
82413 TTATATTCATTC-ATTTATGTT
1 TTATGTTCGTTCGA-TTATGTT
82434 TAACCCAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.14, C:0.10, G:0.17, T:0.58
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTCGT
Found at i:83179 original size:16 final size:16
Alignment explanation
Indices: 83158--83224 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
83148 GTCTCCAACG
83158 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
83174 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
83190 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
83206 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
83220 TTTAT
1 TTTAT
83225 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:83197 original size:32 final size:32
Alignment explanation
Indices: 83156--83216 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
83146 GGGTCTCCAA
83156 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
83188 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
83217 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:83307 original size:16 final size:16
Alignment explanation
Indices: 83286--83318 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
83276 AAAAAAAATT
83286 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
83302 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
83318 T
1 T
83319 TTATTTATTA
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:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:88741 original size:15 final size:15
Alignment explanation
Indices: 88721--88754 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
88711 CCACAAACGG
88721 TTATTAGTGTTTTTC
1 TTATTAGTGTTTTTC
88736 TTATTAGTGTTTTTC
1 TTATTAGTGTTTTTC
88751 TTAT
1 TTAT
88755 AAATGTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (15 bp):
TTATTAGTGTTTTTC
Found at i:88761 original size:15 final size:15
Alignment explanation
Indices: 88728--88761 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
88718 CGGTTATTAG
* *
88728 TGTTTTTCTTATTAG
1 TGTTTTTCTTATAAA
88743 TGTTTTTCTTATAAA
1 TGTTTTTCTTATAAA
88758 TGTT
1 TGTT
88762 ATAAGGAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65
Consensus pattern (15 bp):
TGTTTTTCTTATAAA
Found at i:97070 original size:9 final size:8
Alignment explanation
Indices: 97048--97098 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
97038 TGTTTCAACA
97048 TTTTGGAT
1 TTTTGGAT
97056 ATTTTGGAT
1 -TTTTGGAT
97065 TGTTT-GAT
1 T-TTTGGAT
97073 TTTGTGGAT
1 TTT-TGGAT
*
97082 TGTTGGA-
1 TTTTGGAT
97089 TTTTGGAT
1 TTTTGGAT
97097 TT
1 TT
97099 ATGAATGGCG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:97082 original size:17 final size:17
Alignment explanation
Indices: 97050--97093 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
97040 TTTCAACATT
97050 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
97067 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
97084 TTGGATTTTG
1 TTGGATTTTG
97094 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:104005 original size:3 final size:3
Alignment explanation
Indices: 103997--104085 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
103987 CAAACAAACG
103997 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
104045 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
104086 GTCTTGCTAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:106008 original size:21 final size:20
Alignment explanation
Indices: 105961--106009 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
105951 CAATAACATA
* *
105961 AAATAAAATAAAATTTAAAT
1 AAATAAAAAAAAATTAAAAT
*
105981 ATTATAAATAAAAAATTAAAAT
1 A-AATAAA-AAAAAATTAAAAT
106003 AAATAAA
1 AAATAAA
106010 CCTAGATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 10 0.43
22 12 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAAAAAAAATTAAAAT
Found at i:108717 original size:22 final size:22
Alignment explanation
Indices: 108687--108728 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
108677 ACAGAATTCC
108687 ATTTGTAATT-TATAAGTTAACA
1 ATTTGTAATTATATAA-TTAACA
*
108709 ATTTTTAATTATATAATTAA
1 ATTTGTAATTATATAATTAA
108729 AAATACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTTGTAATTATATAATTAACA
Found at i:110668 original size:3 final size:3
Alignment explanation
Indices: 110660--110937 Score: 425
Period size: 3 Copynumber: 95.0 Consensus size: 3
110650 CAAACTCTTA
110660 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
110708 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
110756 CCT TCT TCT TC- TCT TCT TCT T-T TCT TCT TCT TCT TC- TCT CTCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT
110799 TCT TCT T-T TCT TCT TC- TCT TCT TCT TCT T-T TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
110844 TCCT TCT TCT TCT TCT TCT TC- TCT TCT TC- TCT TCCT TCT CTCT T-T
1 T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT -TCT TCT
110889 TCT TCT TCT TC- TCT TCT TCT TCT TCT TCT TCT T-T TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
110935 TCT
1 TCT
110938 CTT
Statistics
Matches: 256, Mismatches: 4, Indels: 30
0.88 0.01 0.10
Matches are distributed among these distances:
2 22 0.09
3 222 0.87
4 12 0.05
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Done.