Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008825.1 Hibiscus syriacus cultivar Beakdansim tig00111997_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: 130913
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1212 original size:40 final size:39
Alignment explanation
Indices: 1157--1234 Score: 147
Period size: 40 Copynumber: 2.0 Consensus size: 39
1147 AAGTTAATAT
1157 GAATGCAAAAACTAATGAAATGCATTATAAGTATGCTGCC
1 GAATGCAAAAACTAATGAAATGCATTATAAGTAT-CTGCC
1197 GAATGCAAAAACTAATGAAATGCATTATAAGTATCTGC
1 GAATGCAAAAACTAATGAAATGCATTATAAGTATCTGC
1235 TTGATGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 4 0.11
40 34 0.89
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.26
Consensus pattern (39 bp):
GAATGCAAAAACTAATGAAATGCATTATAAGTATCTGCC
Found at i:4932 original size:22 final size:20
Alignment explanation
Indices: 4907--4946 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4897 CATGTTGTTT
4907 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
4929 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
4947 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:5054 original size:42 final size:42
Alignment explanation
Indices: 4995--5077 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
4985 AGAGTAATAT
4995 GAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGCC
1 GAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGCC
5037 GAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGC
1 GAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGC
5078 TTGATGTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (42 bp):
GAATGCAAATAAACTAATGAAATGCATTATAAGTATGCTGCC
Found at i:5216 original size:15 final size:15
Alignment explanation
Indices: 5193--5228 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5183 AACTATATTC
* *
5193 TTATCATAATATATA
1 TTATAATAACATATA
5208 TTATAATAACATATA
1 TTATAATAACATATA
5223 TTATAA
1 TTATAA
5229 CGCTAATAAT
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:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:11327 original size:24 final size:23
Alignment explanation
Indices: 11282--11327 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
11272 TTTCTTGCTT
*
11282 TTCTTTTGAGTGCTGGATTTTTC
1 TTCTTTTGAGTGCTGGACTTTTC
*
11305 TTCTTTTGGAGTGCTTGACTTTT
1 TTCTTTT-GAGTGCTGGACTTTT
11328 ATTTGCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.09, C:0.13, G:0.22, T:0.57
Consensus pattern (23 bp):
TTCTTTTGAGTGCTGGACTTTTC
Found at i:11366 original size:11 final size:11
Alignment explanation
Indices: 11350--11374 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11340 TTGACTTTCT
11350 TTCACTTGCAC
1 TTCACTTGCAC
11361 TTCACTTGCAC
1 TTCACTTGCAC
11372 TTC
1 TTC
11375 TTTTTGGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:21369 original size:36 final size:35
Alignment explanation
Indices: 21269--21380 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
21259 ATTGGTGGTT
* * * *
21269 TTATAGGCATGAAATGGTGATAGAAGATGGTTAGG
1 TTATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* * * *
21304 ATATAGGCGTGCAATAGTAATGGAAGATGGTGATG
1 TTATAGGCGTGAAATGGTGATGGAAGATGGTGATG
21339 TTATAGGCGTGAAAATGGTGATGGAAGATGGTGATG
1 TTATAGGCGTG-AAATGGTGATGGAAGATGGTGATG
21375 TT-TAGG
1 TTATAGG
21381 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.29
Consensus pattern (35 bp):
TTATAGGCGTGAAATGGTGATGGAAGATGGTGATG
Found at i:27424 original size:23 final size:25
Alignment explanation
Indices: 27398--27452 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
27388 AAATCCATCA
27398 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
27421 AAGAAATTTAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
27446 AAGAAAA
1 AAGAAAA
27453 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.16, T:0.11
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:30235 original size:11 final size:13
Alignment explanation
Indices: 30203--30232 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30193 TGGCCAAAGA
30203 TGAAAAGGTATGT
1 TGAAAAGGTATGT
30216 TGAAAAGGTATG-
1 TGAAAAGGTATGT
30228 TGAAA
1 TGAAA
30233 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:35481 original size:23 final size:23
Alignment explanation
Indices: 35455--35499 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
35445 AAATCCAGTA
35455 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
35478 AAGAAATTGAAAGCACTCAAAA
1 AAGAAAATCAAAGCACTCAAAA
35500 AGAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.16, G:0.13, T:0.11
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:39774 original size:22 final size:22
Alignment explanation
Indices: 39725--39777 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 22
39715 AAAATCCAGT
39725 AAAGAAAATCAAAGCACTCAAA
1 AAAGAAAATCAAAGCACTCAAA
* *
39747 AGAAGAAATTGAAAGCACTCAAA
1 A-AAGAAAATCAAAGCACTCAAA
39770 AAAGAAAA
1 AAAGAAAA
39778 GAAAGAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.64, C:0.13, G:0.13, T:0.09
Consensus pattern (22 bp):
AAAGAAAATCAAAGCACTCAAA
Found at i:48801 original size:26 final size:23
Alignment explanation
Indices: 48772--48819 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
48762 GTGCTACAAC
48772 AACAAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAAG-AA-AAGAAA-AAGAA
*
48798 AACAAAAGAGAAAAGAAAAAGA
1 AACAAAAAAGAAAAGAAAAAGA
48820 CTCCTACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 2 0.10
26 9 0.43
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (23 bp):
AACAAAAAAGAAAAGAAAAAGAA
Found at i:48866 original size:14 final size:14
Alignment explanation
Indices: 48843--48888 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
48833 TTTGGAGTGC
48843 AAAAGAAAGAAAAGA
1 AAAAG-AAGAAAAGA
**
48858 AAAAGAAGAAAATC
1 AAAAGAAGAAAAGA
48872 AAAAG-A-AAAAGA
1 AAAAGAAGAAAAGA
48884 AAAAG
1 AAAAG
48889 TGAAGCAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 9 0.33
13 1 0.04
14 12 0.44
15 5 0.19
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Found at i:60169 original size:51 final size:49
Alignment explanation
Indices: 60114--60222 Score: 148
Period size: 49 Copynumber: 2.2 Consensus size: 49
60104 AATGTGCTGG
* *
60114 AATGAATGCATTATAATATAATGAGCTGA-CGTGCATGTGTACATCAACTAA
1 AATGAATGCATTACAATAT--TGAACT-ACCGTGCATGTGTACATCAACTAA
* *
60165 AATGAATGTATTACAATATTGAACTACCGTGCATGTGTGCATCAACTAA
1 AATGAATGCATTACAATATTGAACTACCGTGCATGTGTACATCAACTAA
60214 AATGAATGC
1 AATGAATGC
60223 CATGTGTGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 1 0.02
49 34 0.65
51 17 0.33
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (49 bp):
AATGAATGCATTACAATATTGAACTACCGTGCATGTGTACATCAACTAA
Found at i:63903 original size:19 final size:20
Alignment explanation
Indices: 63856--63906 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
63846 GAAACCCCTT
**
63856 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
63876 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
63895 TGAAGATACATG
1 TGAAAATACATG
63907 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:64821 original size:30 final size:31
Alignment explanation
Indices: 64782--64841 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
64772 TCATGCTTCC
*
64782 ATGATATCT-AAATGATATGCAAACATAATAA
1 ATGATATCTAAAACG-TATGCAAACATAATAA
*
64813 ATGA-ATCTAAAACGTATGTAAACATAATA
1 ATGATATCTAAAACGTATGCAAACATAATA
64842 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACGTATGCAAACATAATAA
Found at i:65903 original size:24 final size:24
Alignment explanation
Indices: 65876--65956 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
65866 ATGATCACAA
*
65876 CTTTTGGCACTTCAAGTGACATAT
1 CTTTTGGAACTTCAAGTGACATAT
* * *
65900 CTTTTTGAACTTCAAGTGGCATAA
1 CTTTTGGAACTTCAAGTGACATAT
* * *
65924 CTGTTGGAACGTCAAAG-GACATGT
1 CTTTTGGAACTTC-AAGTGACATAT
*
65948 CTTGTGGAA
1 CTTTTGGAA
65957 ACACCGAAGG
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
24 41 0.93
25 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (24 bp):
CTTTTGGAACTTCAAGTGACATAT
Found at i:67537 original size:17 final size:17
Alignment explanation
Indices: 67517--67552 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
67507 TAATATAAGT
67517 AATGAAATAAAAAAAAG
1 AATGAAATAAAAAAAAG
* *
67534 AATGAAATGAAATAAAG
1 AATGAAATAAAAAAAAG
67551 AA
1 AA
67553 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (17 bp):
AATGAAATAAAAAAAAG
Found at i:68949 original size:30 final size:31
Alignment explanation
Indices: 68910--68969 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
68900 TCATGCTTCC
**
68910 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
68941 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
68970 TAAATCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:69349 original size:150 final size:146
Alignment explanation
Indices: 69083--69373 Score: 530
Period size: 150 Copynumber: 2.0 Consensus size: 146
69073 ATGCTCATAA
69083 TATATAGTGCATAAATGAGTAATATATAAAGTAAGGTATAACTCCTATATTGAGCATGATGAATT
1 TATATAGTGCATAAATGAGTAATATATAAAGTAAGGTATAACTCCTATATTGAGCATGATGAATT
69148 TCAATGATGTGAGTGTGTTATGAAGAAAGTTAGTGCTAGACATGATCACATCATCCT-CCCTTCT
66 TCAATGATGTGAGTGTGTTATGAAGAAAGTTAGTGCTAGACATGATCACATCATCCTCCCCTTCT
69212 TTTAGGCGATTAATAG
131 TTTAGGCGATTAATAG
69228 TATATAGTGCATAAATGAGTAAAATATATAAAGTAAGGTATAACTCCCTTATATTGAGCATGATG
1 TATATAGTGCATAAATGAGT--AATATATAAAGTAAGGTATAACT-CC-TATATTGAGCATGATG
69293 AATTTTCAATGATGTGAGTGTGTTATGAAGAAAGTTAGTGCTAGACATGATCACATCATCCTCCC
62 AA-TTTCAATGATGTGAGTGTGTTATGAAGAAAGTTAGTGCTAGACATGATCACATCATCCTCCC
69358 CTTCTTTTAGGCGATT
126 CTTCTTTTAGGCGATT
69374 TGTCCTCAAA
Statistics
Matches: 140, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
145 20 0.14
147 23 0.16
148 2 0.01
149 18 0.13
150 59 0.42
151 18 0.13
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (146 bp):
TATATAGTGCATAAATGAGTAATATATAAAGTAAGGTATAACTCCTATATTGAGCATGATGAATT
TCAATGATGTGAGTGTGTTATGAAGAAAGTTAGTGCTAGACATGATCACATCATCCTCCCCTTCT
TTTAGGCGATTAATAG
Found at i:70154 original size:24 final size:24
Alignment explanation
Indices: 70126--70182 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
70116 GAACTTGGAG
*
70126 CTTCAA-TGATCACAACTTTTTGCA
1 CTTCAAGTGA-CACAACTTTTTGAA
* *
70150 CTTCAAGTGACATATCTTTTTGAA
1 CTTCAAGTGACACAACTTTTTGAA
70174 CTTCAAGTG
1 CTTCAAGTG
70183 GCATAACTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (24 bp):
CTTCAAGTGACACAACTTTTTGAA
Found at i:70187 original size:24 final size:24
Alignment explanation
Indices: 70141--70187 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
70131 ATGATCACAA
*
70141 CTTTTTGCACTTCAAGTGACATAT
1 CTTTTTGAACTTCAAGTGACATAT
*
70165 CTTTTTGAACTTCAAGTGGCATA
1 CTTTTTGAACTTCAAGTGACATA
70188 ACTGTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (24 bp):
CTTTTTGAACTTCAAGTGACATAT
Found at i:70198 original size:24 final size:24
Alignment explanation
Indices: 70149--70203 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
70139 AACTTTTTGC
* * *
70149 ACTTCAAGTGACATATCTTTTTGA
1 ACTTCAAGTGACATAACTGTTGGA
*
70173 ACTTCAAGTGGCATAACTGTTGGA
1 ACTTCAAGTGACATAACTGTTGGA
*
70197 ACGTCAA
1 ACTTCAA
70204 AGACATGTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (24 bp):
ACTTCAAGTGACATAACTGTTGGA
Found at i:72178 original size:19 final size:20
Alignment explanation
Indices: 72140--72187 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
72130 AACCCCTTTG
**
72140 AAATACATGATTTTTTATGA
1 AAATACATGATTTTAAATGA
72160 AAATACATGA-TTTAAATGA
1 AAATACATGATTTTAAATGA
*
72179 AGATACATG
1 AAATACATG
72188 CTCTTGGCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
AAATACATGATTTTAAATGA
Found at i:72569 original size:10 final size:10
Alignment explanation
Indices: 72554--72584 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
72544 GTCTTCTCAG
72554 CTCCCAGCTA
1 CTCCCAGCTA
72564 CTCCCAGCTA
1 CTCCCAGCTA
72574 CTCCCAGCTA
1 CTCCCAGCTA
72584 C
1 C
72585 CTTTAGTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.10, T:0.19
Consensus pattern (10 bp):
CTCCCAGCTA
Found at i:73126 original size:30 final size:30
Alignment explanation
Indices: 73087--73145 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
73077 ACATGCTTCC
**
73087 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATG-AAACATAATAA
*
73118 ATGA-ATCTAAAACATATGTAACATAATA
1 ATGATATCTAAAACATATGAAACATAATA
73146 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 12 0.48
31 4 0.16
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (30 bp):
ATGATATCTAAAACATATGAAACATAATAA
Found at i:75629 original size:51 final size:49
Alignment explanation
Indices: 75574--75679 Score: 133
Period size: 49 Copynumber: 2.1 Consensus size: 49
75564 GTGCTGGAAT
**
75574 GAATGCATTATAATATAATGAGTTGA-CGTGCATGTGTGCATCAACTAAAAC
1 GAATGCATTAT-A-ATAATGAACT-ACCGTGCATGTGTGCATCAACTAAAAC
* * *
75625 GAATGTATTATAATAGTGAACTACCGTGCATGTGTGCATCAACTAAAAT
1 GAATGCATTATAATAATGAACTACCGTGCATGTGTGCATCAACTAAAAC
75674 GAATGC
1 GAATGC
75680 CATGTGTGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 1 0.02
49 36 0.75
50 1 0.02
51 10 0.21
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (49 bp):
GAATGCATTATAATAATGAACTACCGTGCATGTGTGCATCAACTAAAAC
Found at i:75747 original size:51 final size:53
Alignment explanation
Indices: 75685--75791 Score: 164
Period size: 56 Copynumber: 2.0 Consensus size: 53
75675 AATGCCATGT
*
75685 GTGAATT-A-AAAATAAATGATATCATGCTATTTGAATGTGAATGCACGTGAA
1 GTGAATTAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
75736 GTGAATTAAAAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
1 GTGAATT---AAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
75792 TGACATAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
51 7 0.14
55 1 0.02
56 42 0.84
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (53 bp):
GTGAATTAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
Found at i:88386 original size:8 final size:8
Alignment explanation
Indices: 88375--88399 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
88365 GAGAAAAACC
88375 AGAAAAGA
1 AGAAAAGA
88383 AGAAAAGA
1 AGAAAAGA
88391 AGAAAAGA
1 AGAAAAGA
88399 A
1 A
88400 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:88409 original size:16 final size:16
Alignment explanation
Indices: 88358--88409 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
88348 TTGGAGTGAA
88358 AAAAGAAGAGAAAAACCAG
1 AAAAGAAGA-AAAAA--AG
*
88377 AAAAGAAGAAAAGAAG
1 AAAAGAAGAAAAAAAG
88393 AAAAGAA-AAGAAAAAG
1 AAAAGAAGAA-AAAAAG
88409 A
1 A
88410 GAAGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
18 4 0.13
19 9 0.30
ACGTcount: A:0.75, C:0.04, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:92689 original size:19 final size:20
Alignment explanation
Indices: 92665--92704 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
92655 TATCCTTTCT
92665 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
92684 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
92704 T
1 T
92705 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:95998 original size:15 final size:16
Alignment explanation
Indices: 95955--96000 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
95945 TATGAAATAA
*
95955 GAAATGGAAGAAGAATG
1 GAAATGG-AGAAGAAAG
*
95972 GAAAT-GATAAGAAAG
1 GAAATGGAGAAGAAAG
95987 GAAATGGA-AAGAAA
1 GAAATGGAGAAGAAA
96001 TGATATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 18 0.69
16 3 0.12
17 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (16 bp):
GAAATGGAGAAGAAAG
Found at i:102692 original size:6 final size:6
Alignment explanation
Indices: 102681--102705 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
102671 TGTAGGAGTC
102681 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
102706 CTTTTTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:104923 original size:19 final size:20
Alignment explanation
Indices: 104876--104926 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
104866 GAAACCCCTT
**
104876 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
104896 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
104915 TGAACATACATG
1 TGAAAATACATG
104927 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:105843 original size:30 final size:31
Alignment explanation
Indices: 105804--105863 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
105794 TCATGCTTCC
**
105804 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
105835 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
105864 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:106924 original size:24 final size:24
Alignment explanation
Indices: 106897--106978 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
106887 ATGATCACAA
*
106897 CTTTTGGCACTTCAAGTGACATAT
1 CTTTTGGAACTTCAAGTGACATAT
* * *
106921 CTTTTTGAACTTCAAGTGGCATAA
1 CTTTTGGAACTTCAAGTGACATAT
* * *
106945 CTGTTGGAACGTCAAAG-GACATGT
1 CTTTTGGAACTTC-AAGTGACATAT
*
106969 CTTGTGGAAC
1 CTTTTGGAAC
106979 ACCAAAGGTC
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
24 42 0.93
25 3 0.07
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (24 bp):
CTTTTGGAACTTCAAGTGACATAT
Found at i:109034 original size:19 final size:21
Alignment explanation
Indices: 108990--109041 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
108980 GAAACCCCTT
**
108990 TGAAAATACATGATTTGTTTA
1 TGAAAATACATGATTTGTAAA
109011 TGAAAATACATGA-TT-TAAA
1 TGAAAATACATGATTTGTAAA
109030 TGAAAATACATG
1 TGAAAATACATG
109042 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 14 0.48
20 2 0.07
21 13 0.45
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTGTAAA
Found at i:109978 original size:30 final size:31
Alignment explanation
Indices: 109939--109998 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
109929 TCATGCTTCC
**
109939 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
109970 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
109999 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:111045 original size:24 final size:24
Alignment explanation
Indices: 111017--111073 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
111007 GAACTTGGAG
*
111017 CTTCAA-TGATCACAACTTTTTGCA
1 CTTCAAGTGA-CACAACTTTTTGAA
* *
111041 CTTCAAGTGACATATCTTTTTGAA
1 CTTCAAGTGACACAACTTTTTGAA
111065 CTTCAAGTG
1 CTTCAAGTG
111074 GCATAACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (24 bp):
CTTCAAGTGACACAACTTTTTGAA
Found at i:111078 original size:24 final size:24
Alignment explanation
Indices: 111032--111078 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
111022 ATGATCACAA
*
111032 CTTTTTGCACTTCAAGTGACATAT
1 CTTTTTGAACTTCAAGTGACATAT
*
111056 CTTTTTGAACTTCAAGTGGCATA
1 CTTTTTGAACTTCAAGTGACATA
111079 ACTATTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (24 bp):
CTTTTTGAACTTCAAGTGACATAT
Found at i:111089 original size:24 final size:24
Alignment explanation
Indices: 111040--111094 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
111030 AACTTTTTGC
* * *
111040 ACTTCAAGTGACATATCTTTTTGA
1 ACTTCAAGTGACATAACTATTGGA
*
111064 ACTTCAAGTGGCATAACTATTGGA
1 ACTTCAAGTGACATAACTATTGGA
*
111088 ACGTCAA
1 ACTTCAA
111095 AGGACATGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (24 bp):
ACTTCAAGTGACATAACTATTGGA
Found at i:113160 original size:19 final size:20
Alignment explanation
Indices: 113113--113163 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
113103 GAAACCCCTT
**
113113 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
113133 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
113152 TGAAGATACATG
1 TGAAAATACATG
113164 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:116734 original size:51 final size:53
Alignment explanation
Indices: 116672--116778 Score: 155
Period size: 56 Copynumber: 2.0 Consensus size: 53
116662 AATGCCATGT
* *
116672 GTGAATT-A-AAAATAAATGATATCATGCTATTTGAATGTGAATGCATGTGAA
1 GTGAATTAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
116723 GTGAATTAAAAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
1 GTGAATT---AAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
116779 TGACATAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
51 7 0.14
55 1 0.02
56 41 0.84
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (53 bp):
GTGAATTAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
Done.