Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006134.1 Hibiscus syriacus cultivar Beakdansim tig00014546_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: 73481
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:15895 original size:36 final size:36
Alignment explanation
Indices: 15855--15932 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
15845 TAAGCCATAA
15855 AGCTTCTTTTGCAGCTTCAACCGCTGCCATGTATTC
1 AGCTTCTTTTGCAGCTTCAACCGCTGCCATGTATTC
* * *
15891 AGCTTCTTTTGTAGCTTCAGCCGCTGCTATGTATTC
1 AGCTTCTTTTGCAGCTTCAACCGCTGCCATGTATTC
15927 AGCTTC
1 AGCTTC
15933 AGTTGTAGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.38
Consensus pattern (36 bp):
AGCTTCTTTTGCAGCTTCAACCGCTGCCATGTATTC
Found at i:15939 original size:36 final size:36
Alignment explanation
Indices: 15867--15940 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
15857 CTTCTTTTGC
**
15867 AGCTTCAACCGCTGCCATGTATTCAGCTTCTTTTGT
1 AGCTTCAACCGCTGCCATGTATTCAGCTTCAGTTGT
* *
15903 AGCTTCAGCCGCTGCTATGTATTCAGCTTCAGTTGT
1 AGCTTCAACCGCTGCCATGTATTCAGCTTCAGTTGT
15939 AG
1 AG
15941 ATAATGCCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (36 bp):
AGCTTCAACCGCTGCCATGTATTCAGCTTCAGTTGT
Found at i:20937 original size:10 final size:10
Alignment explanation
Indices: 20902--20944 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
20892 ATCATTTAAA
*
20902 TTTAGGTTTG
1 TTTATGTTTG
* *
20912 TTTATATTTA
1 TTTATGTTTG
20922 TTTATGTTTG
1 TTTATGTTTG
*
20932 TTTATGTTCG
1 TTTATGTTTG
20942 TTT
1 TTT
20945 GTACTAGGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.14, C:0.02, G:0.16, T:0.67
Consensus pattern (10 bp):
TTTATGTTTG
Found at i:27305 original size:6 final size:6
Alignment explanation
Indices: 27283--27331 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
27273 GTAAACACTA
* * *
27283 ATTTTT -TTTTT -TTTTT ATTTTT ATTATT ATTTTT ATTATT ATTATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
27329 ATT
1 ATT
27332 AAATATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:27309 original size:3 final size:3
Alignment explanation
Indices: 27297--27352 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
27287 TTTTTTTTTT
* * *
27297 TTA TTT TTA TTA TTA TTT TTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
27343 TTA -TA TTA TT
1 TTA TTA TTA TT
27353 TACAAACAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27407 original size:26 final size:26
Alignment explanation
Indices: 27359--27413 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
27349 TATTTACAAA
* * *
27359 CAGTTACAAACCAAACTGGACCGGCC
1 CAGTTACAAACCAAAATGAACCGACC
27385 CAGTTACAAA-CAAAATAGAACCGACC
1 CAGTTACAAACCAAAAT-GAACCGACC
27411 CAG
1 CAG
27414 ACCAACCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.42, C:0.31, G:0.16, T:0.11
Consensus pattern (26 bp):
CAGTTACAAACCAAAATGAACCGACC
Found at i:29057 original size:23 final size:22
Alignment explanation
Indices: 29011--29057 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
29001 ATTATAAAAA
* * *
29011 AAATTATATTTTAATTTTTTTT
1 AAATTATATATTAATATTTATT
29033 AAATTATTATATTAATATTTATT
1 AAATTA-TATATTAATATTTATT
29056 AA
1 AA
29058 TATCGAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTATATATTAATATTTATT
Found at i:29131 original size:23 final size:26
Alignment explanation
Indices: 29105--29159 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
29095 CCTTTTCTAA
29105 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTCTAAATATATATAAATTATTT
*
29128 TATTTATAAATATATATAAATTATTT
1 TATTTCTAAATATATATAAATTATTT
29154 T-TTTCT
1 TATTTCT
29160 CATAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 9 0.33
26 6 0.22
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTCTAAATATATATAAATTATTT
Found at i:31730 original size:14 final size:14
Alignment explanation
Indices: 31694--31732 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
31684 TTCATACATG
31694 CATTTT-CATTTTA
1 CATTTTGCATTTTA
*
31707 CATCTTTGCATTTTT
1 CAT-TTTGCATTTTA
31722 CATTTTGCATT
1 CATTTTGCATT
31733 CATACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (14 bp):
CATTTTGCATTTTA
Found at i:36010 original size:114 final size:114
Alignment explanation
Indices: 35810--36022 Score: 347
Period size: 114 Copynumber: 1.9 Consensus size: 114
35800 TCGTAATAGG
* * *
35810 AATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAA
1 AATAAGGAGACCCAATAGAATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGTATAA
*
35875 ACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGA
66 ACCCCAAAACCAATCATTGGATTAGAAAGATGAATTTGCTCATAGTAGA
35924 AATAAGGAGACCCAATAGAATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AG
1 AATAAGGAGACCCAATAGAATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGTATA-
** *
35988 AACCTTAAAACCAATCATTGGATTAGGAAGATGAA
65 AACCCCAAAACCAATCATTGGATTAGAAAGATGAA
36023 CTGCATGATC
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 1 0.01
114 90 0.99
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (114 bp):
AATAAGGAGACCCAATAGAATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGGTATAA
ACCCCAAAACCAATCATTGGATTAGAAAGATGAATTTGCTCATAGTAGA
Found at i:37050 original size:76 final size:77
Alignment explanation
Indices: 36918--37080 Score: 183
Period size: 76 Copynumber: 2.2 Consensus size: 77
36908 TTTGGGCAGA
* * * * *
36918 CTGAAAGCCCATTTCAATTAGAATCAGAAATATTGATGTATCCTGGACGTTTATATCAG-CAAAA
1 CTGAAAGCCCATTTCAATCAGAATAAGAAATATTGATGTATCCTGAACGCTCATATCAGCCAAAA
36982 TGCTAGGGCATG
66 TGCTAGGGCATG
* * **
36994 CTGAAAGCCCCTTTCAATCAGAATGAAG-AATGTTGATGTATTTTGAACGCTCATATCAGCCAAA
1 CTGAAAGCCCATTTCAATCAGAAT-AAGAAATATTGATGTATCCTGAACGCTCATATCAGCCAAA
37058 AT--T-GGGTCATG
65 ATGCTAGGG-CATG
*
37069 TTGAAAGCCCAT
1 CTGAAAGCCCAT
37081 ATTATCCTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
74 3 0.04
75 15 0.21
76 47 0.64
77 8 0.11
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (77 bp):
CTGAAAGCCCATTTCAATCAGAATAAGAAATATTGATGTATCCTGAACGCTCATATCAGCCAAAA
TGCTAGGGCATG
Found at i:38320 original size:22 final size:22
Alignment explanation
Indices: 38289--38343 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
38279 TATCTACTTC
*
38289 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
38311 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
38333 TTCAAAGATGA
1 TTCAAAGATGA
38344 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:39001 original size:76 final size:76
Alignment explanation
Indices: 38921--40015 Score: 2012
Period size: 76 Copynumber: 14.4 Consensus size: 76
38911 CTATTTCCCA
* *
38921 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
38986 AGCCTTTGGGT
66 AGCCTTCGGGT
38997 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
39062 AACCTTCGGGT
66 AGCCTTCGGGT
*
39073 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39138 AGCCTTCGGGT
66 AGCCTTCGGGT
39149 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
39214 AACCTTCGGGT
66 AGCCTTCGGGT
*
39225 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39290 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
39301 CATCTGTAAGACCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39366 AGCCTTCGGGT
66 AGCCTTCGGGT
39377 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
39442 AACCTTCGGGT
66 AGCCTTCGGGT
*
39453 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39518 AGCCTTCGGGT
66 AGCCTTCGGGT
39529 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
39594 AACCTTCGGGT
66 AGCCTTCGGGT
*
39605 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39670 AGCCTTCGGGT
66 AGCCTTCGGGT
39681 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39746 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
39757 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39822 AGCCTTCGGGT
66 AGCCTTCGGGT
39833 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
39898 AGCCTTCGGGT
66 AGCCTTCGGGT
*
39909 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAACCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
39974 AAGCCTTAGGGT
65 AAGCCTTCGGGT
39986 CATCTGTAAGT-CTTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTT-CAGTGCATGATGTTT
40016 TTAGGACCTC
Statistics
Matches: 989, Mismatches: 28, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
76 921 0.93
77 68 0.07
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:40175 original size:15 final size:15
Alignment explanation
Indices: 40145--40191 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
40135 GTAAACACTA
40145 ATTTTT-TTATTT-TT
1 ATTTTTATT-TTTATT
40159 ATTTTTATTTTTATT
1 ATTTTTATTTTTATT
*
40174 ATTTTTATTATTATT
1 ATTTTTATTTTTATT
40189 ATT
1 ATT
40192 ATTAAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 9 0.30
15 21 0.70
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTTATTTTTATT
Found at i:40184 original size:3 final size:3
Alignment explanation
Indices: 40151--40215 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
40141 ACTAATTTTT
* * * *
40151 TTA TTT TTA TTT TTA TTT TTA TTA TTT TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
40197 ATA TTA TTA TTA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
40216 TACAAACAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:41921 original size:23 final size:22
Alignment explanation
Indices: 41875--41919 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
41865 TTATAAAAAA
*
41875 AAATTATATTTTAATTTTATTT
1 AAATTATATATTAATTTTATTT
41897 AAATTATTATATTAATATTTATT
1 AAATTA-TATATTAAT-TTTATT
41920 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTATATATTAATTTTATTT
Found at i:41995 original size:23 final size:26
Alignment explanation
Indices: 41969--42023 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
41959 CATTTTCTAA
41969 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTCTAAATATATATAAATTATTT
*
41992 TATTTATAAATATATATAAATTATTT
1 TATTTCTAAATATATATAAATTATTT
42018 T-TTTCT
1 TATTTCT
42024 CATAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 9 0.33
26 6 0.22
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTCTAAATATATATAAATTATTT
Found at i:44577 original size:25 final size:25
Alignment explanation
Indices: 44543--44604 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
44533 ATCACTAGTA
44543 AAGACTAAGGTAGTGAAAGATAACC
1 AAGACTAAGGTAGTGAAAGATAACC
44568 AAGACTAAGGTAGTGAAAGATAACC
1 AAGACTAAGGTAGTGAAAGATAACC
*
44593 AAGGCTAAGGTA
1 AAGACTAAGGTA
44605 ATAGTGACCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.26, T:0.16
Consensus pattern (25 bp):
AAGACTAAGGTAGTGAAAGATAACC
Found at i:47749 original size:20 final size:20
Alignment explanation
Indices: 47724--47767 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
47714 TAAGATGATG
47724 ACACAAGATAAATTCTGGAA
1 ACACAAGATAAATTCTGGAA
47744 ACACAAGATAAATTCTGGAA
1 ACACAAGATAAATTCTGGAA
47764 ACAC
1 ACAC
47768 CGAAAAACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (20 bp):
ACACAAGATAAATTCTGGAA
Found at i:49042 original size:32 final size:30
Alignment explanation
Indices: 48973--49075 Score: 143
Period size: 32 Copynumber: 3.3 Consensus size: 30
48963 GAAGGACCTA
* * *
48973 TCCATATGTTCCGAAGAACATAGGTAACTG
1 TCCATATGTCCCAAAGGACATAGGTAACTG
49003 TCCATATGTCCCAAAGGACATAGGTAATCTTG
1 TCCATATGTCCCAAAGGACATAGGTAA-C-TG
*
49035 TCCATATGTCCCAAAGGACATAGGTAAACTA
1 TCCATATGTCCCAAAGGACATAGGT-AACTG
49066 TCCATATGTC
1 TCCATATGTC
49076 TCGTAAGATA
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
30 24 0.36
31 12 0.18
32 28 0.42
33 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (30 bp):
TCCATATGTCCCAAAGGACATAGGTAACTG
Found at i:51336 original size:21 final size:21
Alignment explanation
Indices: 51310--51356 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
51300 TGATCAAGTT
51310 GGTGATTCCTTACAGACCTAA
1 GGTGATTCCTTACAGACCTAA
51331 GGTGATTCCTTACAGACCTAA
1 GGTGATTCCTTACAGACCTAA
*
51352 TGTGA
1 GGTGA
51357 CACCTTGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (21 bp):
GGTGATTCCTTACAGACCTAA
Found at i:51362 original size:21 final size:21
Alignment explanation
Indices: 51317--51362 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
51307 GTTGGTGATT
**
51317 CCTTACAGACCTAAGGTGATT
1 CCTTACAGACCTAAGGTGACA
*
51338 CCTTACAGACCTAATGTGACA
1 CCTTACAGACCTAAGGTGACA
51359 CCTT
1 CCTT
51363 GGATCGGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (21 bp):
CCTTACAGACCTAAGGTGACA
Found at i:62339 original size:22 final size:22
Alignment explanation
Indices: 62314--62358 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
62304 TATCTAAAAG
62314 GTGATTTGAAGACGAGAAAATA
1 GTGATTTGAAGACGAGAAAATA
62336 GTGATTTGAAGACGAGAAAATA
1 GTGATTTGAAGACGAGAAAATA
62358 G
1 G
62359 CAATATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.29, T:0.22
Consensus pattern (22 bp):
GTGATTTGAAGACGAGAAAATA
Found at i:62367 original size:22 final size:22
Alignment explanation
Indices: 62320--62367 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
62310 AAAGGTGATT
** *
62320 TGAAGACGAGAAAATAGTGATT
1 TGAAGACGAGAAAATAGCAATA
62342 TGAAGACGAGAAAATAGCAATA
1 TGAAGACGAGAAAATAGCAATA
62364 TGAA
1 TGAA
62368 ACTACTCGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (22 bp):
TGAAGACGAGAAAATAGCAATA
Found at i:70301 original size:19 final size:19
Alignment explanation
Indices: 70277--70330 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
70267 ATAAGACTCA
70277 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
70296 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
*
70315 GTGCATCGGTGCACTA
1 GTGCATCGGTACACTA
70331 ATTACATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.20, C:0.22, G:0.35, T:0.22
Consensus pattern (19 bp):
GTGCATCGGTACACTAGGG
Found at i:70368 original size:46 final size:45
Alignment explanation
Indices: 70315--70412 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 45
70305 TACACTAGGG
* * * *
70315 GTGCATCGGTGCACTAATTACATTTGATGTTTCAA-ACAAGCCTAGA
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAATA-AAGCCT-GA
* *
70361 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAATCCTGA
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAATAAAGCCTGA
70406 GTGCATC
1 GTGCATC
70413 TATGCATGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 9 0.20
46 35 0.78
47 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (45 bp):
GTGCATCGGTACACAAAATACATTCGATGTTTCAATAAAGCCTGA
Found at i:73108 original size:23 final size:22
Alignment explanation
Indices: 73080--73158 Score: 97
Period size: 23 Copynumber: 3.6 Consensus size: 22
73070 GCCAGCAAAG
73080 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* * * *
73103 TACATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
73124 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
73146 TGCATCGATGCAC
1 TGCATCGATGCAC
73159 TGTCTAGTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 16 0.36
22 12 0.27
23 17 0.38
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:73135 original size:21 final size:21
Alignment explanation
Indices: 73106--73177 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
73096 CAAGGAATAC
*
73106 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACCTTCATGGTGT
* * *
73127 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACCTTCATGG-TGT
*
73149 ATCGATGCA-CTGTC-TAGTGT
1 ATCGATGCACCT-TCATGGTGT
73169 ATCGATGCA
1 ATCGATGCA
73178 TTATGCACTA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 11 0.27
21 17 0.41
22 13 0.32
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (21 bp):
ATCGATGCACCTTCATGGTGT
Done.