Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006344.1 Hibiscus syriacus cultivar Beakdansim tig00015174_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: 60777
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1938 original size:25 final size:25
Alignment explanation
Indices: 1910--1989 Score: 142
Period size: 25 Copynumber: 3.2 Consensus size: 25
1900 GACACTTGTA
*
1910 TGCACTTAAAAGTGCTTCGTAGAAT
1 TGCACTTAAAAGTGCTTCTTAGAAT
*
1935 TGCACTTAAAAGTGATTCTTAGAAT
1 TGCACTTAAAAGTGCTTCTTAGAAT
1960 TGCACTTAAAAGTGCTTCTTAGAAT
1 TGCACTTAAAAGTGCTTCTTAGAAT
1985 TGCAC
1 TGCAC
1990 CATAGGTGCC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (25 bp):
TGCACTTAAAAGTGCTTCTTAGAAT
Found at i:2102 original size:65 final size:65
Alignment explanation
Indices: 2021--2461 Score: 621
Period size: 65 Copynumber: 6.8 Consensus size: 65
2011 TATCATATAG
* * * ** * *
2021 TCACTCCACCTCATGCATCACAATGGTACATGAGCCATATGAGTGGTCAATACAATATTCAAGTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCTGTACAGTATTCAATTA
** *
2086 TCACTCCACCTCATGCACCATGAAGGTACATGAGTCATATGAGTGGTTTGTACAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCTGTACAGTATTCAATTA
* * * *
2151 TCACTCTACTTCATGCAACACAAAGGAACATGAGTCATATGAGTGGTCTGTACAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCTGTACAGTATTCAATTA
* * * *
2216 TCACTCCACTTCATGCACCACAAAGGTACATGAGTCATATGAGTAGTCTGTACAATTTTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCTGTACAGTATTCAATTA
* * * * *
2281 TCACTCCACCTCATACACCACAAAGGTACATGATTCATATGAGTAGTTTGTATAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCTGTACAGTATTCAATTA
* *
2346 TCACTCCACCTCATGCACCACAAAGATACATGAATCATATGAGTGGTCTGTACAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCTGTACAGTATTCAATTA
* * * *
2411 TTAATCCATCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGT
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCTGT
2462 GTCGTATCAT
Statistics
Matches: 334, Mismatches: 42, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 334 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (65 bp):
TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCTGTACAGTATTCAATTA
Found at i:2955 original size:109 final size:110
Alignment explanation
Indices: 2827--3053 Score: 393
Period size: 112 Copynumber: 2.1 Consensus size: 110
2817 TAATATTCAA
* *
2827 TTTATATCCATATTAATTATTTTCACATTATATCCAATC-TAATGCATTAACTTTACATAATTGT
1 TTTATATCCATATAAATTATTTTCACATTATATCCAATCATAATACATTAACTTTACATAATTGT
2891 CATTTCACCACCAACTTTCCTAAAACTTACGAACTGGATCTCTAT
66 CATTTCACCACCAACTTTCCTAAAACTTACGAACTGGATCTCTAT
*
2936 TTTATGTCCATATAAATTATTTTCACATTATATCCAATCTAATAATACATTAACTTTACATAATT
1 TTTATATCCATATAAATTATTTTCACATTATATCCAATC--ATAATACATTAACTTTACATAATT
*
3001 TTCATTTCACCACCAACTTTCCTAAAACTTACGAACTGGATCTCTAT
64 GTCATTTCACCACCAACTTTCCTAAAACTTACGAACTGGATCTCTAT
3048 TTTATA
1 TTTATA
3054 CAACTTCCCA
Statistics
Matches: 110, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
109 37 0.34
112 73 0.66
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (110 bp):
TTTATATCCATATAAATTATTTTCACATTATATCCAATCATAATACATTAACTTTACATAATTGT
CATTTCACCACCAACTTTCCTAAAACTTACGAACTGGATCTCTAT
Found at i:3614 original size:20 final size:22
Alignment explanation
Indices: 3591--3632 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
3581 AATTTCACAC
3591 TCTAGCATC-AAATT-CAACAT
1 TCTAGCATCTAAATTCCAACAT
*
3611 TCTAGCTTCTAAATTCCAACAT
1 TCTAGCATCTAAATTCCAACAT
3633 ATTACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (22 bp):
TCTAGCATCTAAATTCCAACAT
Found at i:13322 original size:20 final size:20
Alignment explanation
Indices: 13299--13366 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
13289 TTTGTGCATT
*
13299 TAGTATCGCTATTGTTCATA
1 TAGTATCGATATTGTTCATA
* *
13319 TAGTATCGATAATGTTCGTCA
1 TAGTATCGATATTGTTCAT-A
*
13340 -AGTA-CTGATATTGTTCTTA
1 TAGTATC-GATATTGTTCATA
13359 TAGTATCG
1 TAGTATCG
13367 TTAAGAGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 2 0.05
20 35 0.90
21 2 0.05
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (20 bp):
TAGTATCGATATTGTTCATA
Found at i:14000 original size:2 final size:2
Alignment explanation
Indices: 13889--13990 Score: 66
Period size: 2 Copynumber: 51.5 Consensus size: 2
13879 TGACACATAC
* * *
13889 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT TT AT AC AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * **
13930 TT CAC AT AT AT -T TT TT AGT -T AC AT AT TT CC AT AT AT AT AT AT
1 AT -AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
13972 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
13991 CTCTTATATA
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
1 3 0.04
2 74 0.95
3 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15572 original size:27 final size:25
Alignment explanation
Indices: 15522--15572 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
15512 TAGACTTGAT
*
15522 TGGATGTTTTTTTATTTTTCTGTTG
1 TGGATGTTTTTTCATTTTTCTGTTG
15547 TGGATGTTCATTTTCATATTTT-TGTT
1 TGGATGTT--TTTTCAT-TTTTCTGTT
15573 ATGGCTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 8 0.36
27 10 0.45
28 4 0.18
ACGTcount: A:0.12, C:0.06, G:0.18, T:0.65
Consensus pattern (25 bp):
TGGATGTTTTTTCATTTTTCTGTTG
Found at i:29028 original size:23 final size:23
Alignment explanation
Indices: 29001--29060 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
28991 AGGAAAATCG
*
29001 TGCTAACAAGCAGAGATGGATCA
1 TGCTAAAAAGCAGAGATGGATCA
29024 TGCTAAAAAGCAGAGATGGATCA
1 TGCTAAAAAGCAGAGATGGATCA
29047 TGCTAAAAAGCAGA
1 TGCTAAAAAGCAGA
29061 AGTCGTGCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.17
Consensus pattern (23 bp):
TGCTAAAAAGCAGAGATGGATCA
Found at i:29071 original size:19 final size:22
Alignment explanation
Indices: 29001--29081 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 22
28991 AGGAAAATCG
*
29001 TGCTAACAAGCAGAGATGGATCA
1 TGCTAAAAAGCAGAGA-GGATCA
29024 TGCTAAAAAGCAGAGATGGATCA
1 TGCTAAAAAGCAGAGA-GGATCA
*
29047 TGCTAAAAAGCAGA-A-G-TCG
1 TGCTAAAAAGCAGAGAGGATCA
*
29066 TGCTAACAAGCAGAGA
1 TGCTAAAAAGCAGAGA
29082 AAGGTCGTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
19 15 0.28
20 2 0.04
22 1 0.02
23 36 0.67
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (22 bp):
TGCTAAAAAGCAGAGAGGATCA
Found at i:29417 original size:10 final size:10
Alignment explanation
Indices: 29399--29437 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
29389 TTTTACAAAT
*
29399 ATTTTAAAAA
1 ATTTAAAAAA
29409 ATTTAAAAAA
1 ATTTAAAAAA
29419 ATTT-AAAAA
1 ATTTAAAAAA
*
29428 TTTTAAAAAA
1 ATTTAAAAAA
29438 TATATTATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATTTAAAAAA
Found at i:29425 original size:19 final size:19
Alignment explanation
Indices: 29401--29437 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29391 TTACAAATAT
29401 TTTAAAAAATTTAAAAAAA
1 TTTAAAAAATTTAAAAAAA
*
29420 TTTAAAAATTTTAAAAAA
1 TTTAAAAAATTTAAAAAA
29438 TATATTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAAAAATTTAAAAAAA
Found at i:29438 original size:10 final size:10
Alignment explanation
Indices: 29387--29438 Score: 63
Period size: 9 Copynumber: 5.3 Consensus size: 10
29377 CGGATGATTT
29387 AATTTTACAAA
1 AATTTTA-AAA
*
29398 TATTTTAAAA
1 AATTTTAAAA
29408 AA-TTTAAAA
1 AATTTTAAAA
*
29417 AAATTT-AAA
1 AATTTTAAAA
29426 AATTTTAAAA
1 AATTTTAAAA
29436 AAT
1 AAT
29439 ATATTATCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 17 0.47
10 13 0.36
11 6 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
AATTTTAAAA
Found at i:30716 original size:3 final size:3
Alignment explanation
Indices: 30701--30743 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
30691 AAAAAATATA
*
30701 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
30744 CATATGTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 29 0.83
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:32544 original size:2 final size:2
Alignment explanation
Indices: 32508--32573 Score: 66
Period size: 2 Copynumber: 33.5 Consensus size: 2
32498 CTGTCATTTG
* * *
32508 TA TA TA T- TA TA TCA TA T- TA T- TCA TA TA TG TG TA TA TA TA CA
1 TA TA TA TA TA TA T-A TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
32549 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
32574 TAATTTACCC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
1 3 0.05
2 49 0.89
3 3 0.05
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34893 original size:13 final size:13
Alignment explanation
Indices: 34852--34894 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
34842 GGATCAACAT
34852 TTTTGCATCTGCA
1 TTTTGCATCTGCA
*
34865 -TTTGCGTCTTTGCA
1 TTTTGCATC--TGCA
34879 TTTTGCATCTGCA
1 TTTTGCATCTGCA
34892 TTT
1 TTT
34895 CATTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 7 0.28
13 7 0.28
14 4 0.16
15 7 0.28
ACGTcount: A:0.12, C:0.21, G:0.16, T:0.51
Consensus pattern (13 bp):
TTTTGCATCTGCA
Found at i:36218 original size:44 final size:43
Alignment explanation
Indices: 36136--36218 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
36126 ATCTAATCAG
* *
36136 AACAAAAAAAAAGAGAAAAAGAGAAAGCAAAATGAAAAGAAAA
1 AACAAAAAAAAACAGAAAAAGAGAAAGCAAAATAAAAAGAAAA
36179 AACAAAGAAAAAATCAGAAAAA-AGAAAAGC-AAATAAAAAG
1 AACAAA-AAAAAA-CAGAAAAAGAG-AAAGCAAAATAAAAAG
36219 GGACAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
43 6 0.17
44 17 0.49
45 12 0.34
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (43 bp):
AACAAAAAAAAACAGAAAAAGAGAAAGCAAAATAAAAAGAAAA
Found at i:37861 original size:124 final size:124
Alignment explanation
Indices: 37704--38053 Score: 553
Period size: 124 Copynumber: 2.8 Consensus size: 124
37694 CATATGAACT
*
37704 GTGTTATCACCCTTAGATGGCCAAGA-TTCATCATAGTATGAGCAGTGTCATCCCTGACCAGATC
1 GTGTTATCACCCTTAGATGGCCAAGACTT-ATCATAGTATGAGCAGTGTCATCCCCGACCAGATC
*
37768 TCCTCATCACGTAGGAGCCGTGTCAACCCTGGATAACCAATATTCATCATAGTATGAGCA
65 TCCTCATCACGTAGGAGCCGTGTCAACCCTGGATAACCAAGATTCATCATAGTATGAGCA
*
37828 GTGTTATCACCCTTAGATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCCCCGACTAGATCT
1 GTGTTATCACCCTTAGATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCCCCGACCAGATCT
*
37893 CCTCATCACGTAGGAGCCGTGTCAACCATGGATAACCAAGATTCATCATAGTATGAGCA
66 CCTCATCACGTAGGAGCCGTGTCAACCCTGGATAACCAAGATTCATCATAGTATGAGCA
* * * * *
37952 GTTTTATCACCCTTAGATGGCTAAGACTTATCATAGTATGAGTAATGTCATCCCCGACCAG-CCG
1 GTGTTATCACCCTTAGATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCCCCGACCAGATC-
* * *
38016 TCCTCATCACGTAGGAACCGTGTCATCCC-CGATAACCA
65 TCCTCATCACGTAGGAGCCGTGTCAACCCTGGATAACCA
38054 GCCGTCCTCA
Statistics
Matches: 210, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
123 9 0.04
124 199 0.95
125 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (124 bp):
GTGTTATCACCCTTAGATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCCCCGACCAGATCT
CCTCATCACGTAGGAGCCGTGTCAACCCTGGATAACCAAGATTCATCATAGTATGAGCA
Found at i:40279 original size:393 final size:392
Alignment explanation
Indices: 39491--40282 Score: 1415
Period size: 391 Copynumber: 2.0 Consensus size: 392
39481 TTTTGGTCAC
39491 TAATGAAGTTTATTTTCTTGTGATTTGGGTATGTAATTTTTATTTTATTTATTTTGGTCTTAACT
1 TAATGAAGTTTATTTTCTTGTGATTTGGGTATGTAATTTTTATTTTATTTATTTTGGTCTTAACT
*
39556 ACTTCCTTCTTCCTTCTTACATCTTATCTATGTCTTTATTATTTTGGTATGGTAATTTATTTCCT
66 A------TCTTCCTTCTTACATCTTATCTATGTATTTATTATTTTGGTATGGTAATTTATTTCCT
* *
39621 ATTGTTATGTATTTCTGGGATTTGTTATATTTACTTTCACACGTAATAGTATGATAATACTTATA
125 ATTGTTATCTATTTCTGGGATTCGTTATATTTACTTTCACACGTAATAGTATGATAATACTTATA
* *
39686 TATTTATTACCTTTAATATTTGGATATATTTAGTATATAAGTATATATTATTTATATAGCATGAA
190 TATTTATTACCATTAATATTTGGATATATTTAGTATATAAGTATATATTATTTATATAGCACGAA
39751 TATGTGTTTATTAAATACTATAACTTTAATTTCATTTCTAATTTTATTTTGGTTTCCTTTTTTTA
255 TATGTGTTTATTAAATACTATAACTTTAATTTCATTTCTAATTTTATTTTGGTTTCCTTTTTTTA
*
39816 TTTTTCTATATTCGATGAATTGATTCACTTTTCATATATCTTGAAGGCATCTTTTAAAGTTCCCC
320 TTTTTCTATATTCGATGAATTGATTCACTTTTCATACATCTTGAAGGCATCTTTTAAAGTTCCCC
39881 TAAGATTT
385 TAAGATTT
* *
39889 TAATGAAGTTTATTTTCTTGTGATTTGGTTATGTAATTTTTATTTTGTTTATTTTGGTCTTAACT
1 TAATGAAGTTTATTTTCTTGTGATTTGGGTATGTAATTTTTATTTTATTTATTTTGGTCTTAACT
*
39954 A-CTTCCTTCTTACCTCTTATCTATGTATTTATTATTTTGGTATGGTAATTTATTTCCTATTGTT
66 ATCTTCCTTCTTACATCTTATCTATGTATTTATTATTTTGGTATGGTAATTTATTTCCTATTGTT
40018 ATCTATTTCTGGGATTCGTTATATTTACTTTCACACGTAATAGTATGATAATACTTATATATTTA
131 ATCTATTTCTGGGATTCGTTATATTTACTTTCACACGTAATAGTATGATAATACTTATATATTTA
40083 TTACCATTAATATTTGGATATATTTAGTATATAAGTATATATTATTTATATAGCACGAATATGTG
196 TTACCATTAATATTTGGATATATTTAGTATATAAGTATATATTATTTATATAGCACGAATATGTG
*
40148 TTTATATTAAATACTATAACTTTAATTTCATTTCTAATTTTATTTTGGTTTCTTTTTTTTATTTT
261 -TT-TATTAAATACTATAACTTTAATTTCATTTCTAATTTTATTTTGGTTTCCTTTTTTTATTTT
40213 TCTATATTCGATGAATTGATTCACTTTTCATACATCTTGAAGGCATCTTTTAAAGTTCCCCTAAG
324 TCTATATTCGATGAATTGATTCACTTTTCATACATCTTGAAGGCATCTTTTAAAGTTCCCCTAAG
40278 ATTT
389 ATTT
40282 T
1 T
40283 GGTTGCATTT
Statistics
Matches: 382, Mismatches: 10, Indels: 9
0.95 0.02 0.02
Matches are distributed among these distances:
391 187 0.49
392 2 0.01
393 129 0.34
398 64 0.17
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (392 bp):
TAATGAAGTTTATTTTCTTGTGATTTGGGTATGTAATTTTTATTTTATTTATTTTGGTCTTAACT
ATCTTCCTTCTTACATCTTATCTATGTATTTATTATTTTGGTATGGTAATTTATTTCCTATTGTT
ATCTATTTCTGGGATTCGTTATATTTACTTTCACACGTAATAGTATGATAATACTTATATATTTA
TTACCATTAATATTTGGATATATTTAGTATATAAGTATATATTATTTATATAGCACGAATATGTG
TTTATTAAATACTATAACTTTAATTTCATTTCTAATTTTATTTTGGTTTCCTTTTTTTATTTTTC
TATATTCGATGAATTGATTCACTTTTCATACATCTTGAAGGCATCTTTTAAAGTTCCCCTAAGAT
TT
Found at i:47580 original size:15 final size:15
Alignment explanation
Indices: 47560--47597 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
47550 TACAAGTCAT
47560 GTACAAATGTACTAA
1 GTACAAATGTACTAA
47575 GTACAAATGTACTAA
1 GTACAAATGTACTAA
*
47590 ATACAAAT
1 GTACAAAT
47598 TCATAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (15 bp):
GTACAAATGTACTAA
Found at i:53971 original size:18 final size:19
Alignment explanation
Indices: 53950--53985 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53940 ATTTAAATGG
*
53950 TTTGG-AATTATTAATTTT
1 TTTGGAAATTAATAATTTT
53968 TTTGGAAATTAATAATTT
1 TTTGGAAATTAATAATTT
53986 AATTTTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTGGAAATTAATAATTTT
Found at i:54315 original size:19 final size:21
Alignment explanation
Indices: 54273--54315 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
54263 TCAATTTCCT
54273 TTTCTCTTTTATTAATTCTTG
1 TTTCTCTTTTATTAATTCTTG
*
54294 TTTC-CTTTTCTTAATT-TTG
1 TTTCTCTTTTATTAATTCTTG
54313 TTT
1 TTT
54316 TTCAATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTCTCTTTTATTAATTCTTG
Found at i:58671 original size:23 final size:23
Alignment explanation
Indices: 58644--58689 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
58634 AAATATTTAT
58644 AATGAATAATAATAAGTTTCATA
1 AATGAATAATAATAAGTTTCATA
58667 AATGAATAATAATAAGTTTCATA
1 AATGAATAATAATAAGTTTCATA
58690 GCTTAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (23 bp):
AATGAATAATAATAAGTTTCATA
Found at i:58810 original size:24 final size:25
Alignment explanation
Indices: 58783--58860 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 25
58773 AATTTTTATA
58783 TATTCTT-TTTTATAAGAGCATA-TT
1 TATTCTTATTTTATAAG-GCATATTT
* *
58807 TATT-TTATTTTATATGGCTTATTT
1 TATTCTTATTTTATAAGGCATATTT
* *
58831 TATTCTTATTTTATTATGCATATATT
1 TATTCTTATTTTATAAGGCATAT-TT
58857 TATT
1 TATT
58861 TTCTTTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
23 6 0.14
24 18 0.41
25 14 0.32
26 6 0.14
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (25 bp):
TATTCTTATTTTATAAGGCATATTT
Found at i:58867 original size:25 final size:25
Alignment explanation
Indices: 58802--58867 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
58792 TTATAAGAGC
*
58802 ATATTTATTTTATTTTATATGGCTT
1 ATATTTATTTTATTTTATATGGCAT
58827 AT-TTTATTCTTATTTTATTAT-GCAT
1 ATATTTATT-TTATTTTA-TATGGCAT
*
58852 ATATTTATTTTCTTTT
1 ATATTTATTTTATTTT
58868 TATTCGAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 6 0.17
25 21 0.58
26 9 0.25
ACGTcount: A:0.23, C:0.06, G:0.05, T:0.67
Consensus pattern (25 bp):
ATATTTATTTTATTTTATATGGCAT
Found at i:59474 original size:54 final size:54
Alignment explanation
Indices: 59391--59498 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
59381 ACTGGGGACT
*
59391 GGTTAGAGAGTTAGACCATTAATCGCTTATATGTTGTCATAGTGGTAAAAATTG
1 GGTTAGAGAGTTAGACCATTAATCGCTTATACGTTGTCATAGTGGTAAAAATTG
* * * *
59445 GGTTAGAGAGTTAGGCCATTAATCTCTTATACGTTGTCGTAGTGGTGAAAATTG
1 GGTTAGAGAGTTAGACCATTAATCGCTTATACGTTGTCATAGTGGTAAAAATTG
59499 TGAATTCGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (54 bp):
GGTTAGAGAGTTAGACCATTAATCGCTTATACGTTGTCATAGTGGTAAAAATTG
Done.