Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005747.1 Hibiscus syriacus cultivar Beakdansim tig00013442_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: 63890
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:6171 original size:127 final size:127
Alignment explanation
Indices: 5940--6323 Score: 709
Period size: 127 Copynumber: 3.0 Consensus size: 127
5930 ATCGCCCCCT
*
5940 CTTTGCATGCCGTGACTGCTCCGTTTACTTGATTTAGTCGGTTCTGATCATTGTGATCAAACATA
1 CTTTCCATGCCGTGACTGCTCCGTTTACTTGATTTAGTCGGTTCTGATCATTGTGATCAAACATA
6005 GTAAAAAAAAGCTCACTTGTTTGGATCATTGCTTTTGGTTAACTCATCCTGCATTGATGCTA
66 GTAAAAAAAAGCTCACTTGTTTGGATCATTGCTTTTGGTTAACTCATCCTGCATTGATGCTA
6067 CTTTCCATGCCGTGACTGCTCCGTTTACTTGATTTAGTCGGTTCTGATCATTGTGATCAAACATA
1 CTTTCCATGCCGTGACTGCTCCGTTTACTTGATTTAGTCGGTTCTGATCATTGTGATCAAACATA
* * *
6132 GTAAAAAAAAGCTCACTTGTATGGATCGTTGCTTTTGGTTAACTCATCCTGCATCGATGCTA
66 GTAAAAAAAAGCTCACTTGTTTGGATCATTGCTTTTGGTTAACTCATCCTGCATTGATGCTA
6194 CTTTCCATGCCGTGACTGCTCCGTTTACTTGATTTAGTCGGTTCTGATCATTGTGATCAAACATA
1 CTTTCCATGCCGTGACTGCTCCGTTTACTTGATTTAGTCGGTTCTGATCATTGTGATCAAACATA
*
6259 GT--AAAAAATCTCACTTGTTTGGATCATTGCTTTTGGTTAACTCATCCTGCATTGATGCTA
66 GTAAAAAAAAGCTCACTTGTTTGGATCATTGCTTTTGGTTAACTCATCCTGCATTGATGCTA
6319 CTTTC
1 CTTTC
6324 TGTTTCTTTT
Statistics
Matches: 249, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
125 59 0.24
127 190 0.76
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (127 bp):
CTTTCCATGCCGTGACTGCTCCGTTTACTTGATTTAGTCGGTTCTGATCATTGTGATCAAACATA
GTAAAAAAAAGCTCACTTGTTTGGATCATTGCTTTTGGTTAACTCATCCTGCATTGATGCTA
Found at i:15523 original size:18 final size:18
Alignment explanation
Indices: 15497--15533 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15487 TCTCTCTCCG
15497 CGTGGTCCAACACTTCCT
1 CGTGGTCCAACACTTCCT
* *
15515 CGTGTTCCACCACTTCCT
1 CGTGGTCCAACACTTCCT
15533 C
1 C
15534 AAAATTCGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.43, G:0.14, T:0.30
Consensus pattern (18 bp):
CGTGGTCCAACACTTCCT
Found at i:18545 original size:32 final size:32
Alignment explanation
Indices: 18459--18584 Score: 130
Period size: 32 Copynumber: 3.9 Consensus size: 32
18449 AATCGGATCA
* * * *
18459 GGTCGGGTGATTATTGGATCGGTTG-TTTTCCG
1 GGTCGGGTCAATATCGGATCGGTTGATTTT-TG
* * *
18491 GTTCGGATCAATATCGGGTCGGTTGATTTTTG
1 GGTCGGGTCAATATCGGATCGGTTGATTTTTG
* *
18523 GGTCGGGTTAATACCGGATCGGTTAGA-TTTTG
1 GGTCGGGTCAATATCGGATCGGTT-GATTTTTG
*
18555 GGTTGGGTCAATATCGGATCGGTTGATTTT
1 GGTCGGGTCAATATCGGATCGGTTGATTTT
18585 CGGTTTAAGC
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
31 2 0.03
32 68 0.89
33 6 0.08
ACGTcount: A:0.15, C:0.12, G:0.34, T:0.39
Consensus pattern (32 bp):
GGTCGGGTCAATATCGGATCGGTTGATTTTTG
Found at i:20919 original size:2 final size:2
Alignment explanation
Indices: 20912--20944 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20902 GAGAAACATT
20912 TA 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 T
20945 GATAACCACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22685 original size:26 final size:26
Alignment explanation
Indices: 22656--22705 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
22646 ACTTAATTCT
*
22656 TTTAGTACCTTAACTATCAATTTTGA
1 TTTAGTACCTAAACTATCAATTTTGA
* *
22682 TTTAGTACCTAAACTTTTAATTTT
1 TTTAGTACCTAAACTATCAATTTT
22706 TTTTCAAAAC
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:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (26 bp):
TTTAGTACCTAAACTATCAATTTTGA
Found at i:25903 original size:39 final size:41
Alignment explanation
Indices: 25854--25946 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 41
25844 TTCGGTTTGC
25854 AAAAAA-CCAGTTTTAAAAAAAAAACGGA-TTTTTTCGGAT
1 AAAAAATCCAGTTTTAAAAAAAAAACGGATTTTTTTCGGAT
** *
25893 -AAAAATCCAGTTTTTTAAAAAAACCGGATTTTTTTCGGAT
1 AAAAAATCCAGTTTTAAAAAAAAAACGGATTTTTTTCGGAT
25933 AAAAAAT-CAGTTTT
1 AAAAAATCCAGTTTT
25947 TTATCCGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
38 5 0.10
39 19 0.40
40 18 0.38
41 6 0.12
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (41 bp):
AAAAAATCCAGTTTTAAAAAAAAAACGGATTTTTTTCGGAT
Found at i:25926 original size:40 final size:40
Alignment explanation
Indices: 25854--25949 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 40
25844 TTCGGTTTGC
**
25854 AAAAAA-CCAGTTTTAAAAAAAAAACGGATTTTTTCGGAT
1 AAAAAATCCAGTTTTTTAAAAAAAACGGATTTTTTCGGAT
*
25893 -AAAAATCCAGTTTTTTAAAAAAACCGGATTTTTTTCGGAT
1 AAAAAATCCAGTTTTTTAAAAAAAACGGA-TTTTTTCGGAT
25933 AAAAAAT-CAGTTTTTTA
1 AAAAAATCCAGTTTTTTA
25950 TCCGGTTTGA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
38 5 0.10
39 19 0.37
40 21 0.41
41 6 0.12
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (40 bp):
AAAAAATCCAGTTTTTTAAAAAAAACGGATTTTTTCGGAT
Found at i:25986 original size:24 final size:23
Alignment explanation
Indices: 25908--25989 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 23
25898 TCCAGTTTTT
*
25908 TAAAAAAACCGGATTTTT-TTCGG
1 TAAAAAAACCGG-TTTTTATCCGG
* * *
25931 ATAAAAAATCAGTTTTTTATCCGG
1 -TAAAAAAACCGGTTTTTATCCGG
*
25955 TTTGAAAAAACCGGTTTTTAATCCGG
1 --TAAAAAAACCGGTTTTT-ATCCGG
25981 TAAAAAAAC
1 TAAAAAAAC
25990 GGTCGTTCAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
23 5 0.11
24 21 0.47
25 13 0.29
26 6 0.13
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (23 bp):
TAAAAAAACCGGTTTTTATCCGG
Found at i:29950 original size:38 final size:37
Alignment explanation
Indices: 29884--30087 Score: 135
Period size: 38 Copynumber: 5.4 Consensus size: 37
29874 ACGTTTAAAA
29884 AAAACATTTTAGAAAA--TATATATAATATATAATTTTT
1 AAAACATTTT-GAAAACTTATATAT-ATATATAATTTTT
29921 AAAATCATTTTGAAAACTTATATATATATATATATATAGTTTTT
1 AAAA-CATTTTGAAAAC---T-TATATATATATATA-A-TTTTT
* * *
29965 GAAAACGTTTATGAAAAC--ATATATAT-TATAGTTTTG
1 -AAAACATTT-TGAAAACTTATATATATATATAATTTTT
*
30001 AAAACATTTTGAAAACATT-TATATATTATATAGTTTTT
1 AAAACATTTTGAAAAC-TTATATATA-TATATAATTTTT
*
30039 AAAACGTTTTTGAAAA-TT-TATA-ATAT-T--TTTTT
1 AAAAC-ATTTTGAAAACTTATATATATATATAATTTTT
*
30071 GAAAACATGTTGAAAAC
1 -AAAACATTTTGAAAAC
30088 AGGCGTATAT
Statistics
Matches: 140, Mismatches: 8, Indels: 42
0.74 0.04 0.22
Matches are distributed among these distances:
32 13 0.09
33 5 0.04
34 8 0.06
35 11 0.08
36 11 0.08
37 16 0.11
38 24 0.17
39 17 0.12
42 7 0.05
43 8 0.06
44 9 0.06
45 11 0.08
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (37 bp):
AAAACATTTTGAAAACTTATATATATATATAATTTTT
Found at i:29980 original size:45 final size:43
Alignment explanation
Indices: 29899--29994 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 43
29889 ATTTTAGAAA
*
29899 ATATATATAATATATAATTTTTAAAATCATTTTGAAAACTTAT
1 ATATATATAATATATAATTTTTAAAATCATTTTGAAAACATAT
* *
29942 ATATATATATATATATAGTTTTTGAAAA-CGTTTATGAAAACATAT
1 ATATATATA-ATATATAATTTTT-AAAATCATTT-TGAAAACATAT
29987 ATAT-TATA
1 ATATATATA
29995 GTTTTGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
43 9 0.19
44 20 0.43
45 18 0.38
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (43 bp):
ATATATATAATATATAATTTTTAAAATCATTTTGAAAACATAT
Found at i:30012 original size:11 final size:11
Alignment explanation
Indices: 29996--30020 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29986 TATATTATAG
29996 TTTTGAAAACA
1 TTTTGAAAACA
30007 TTTTGAAAACA
1 TTTTGAAAACA
30018 TTT
1 TTT
30021 ATATATTATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:30084 original size:71 final size:72
Alignment explanation
Indices: 29945--30138 Score: 207
Period size: 71 Copynumber: 2.7 Consensus size: 72
29935 AACTTATATA
* ** *
29945 TATATATATATATAGTTTTTGAAAACGTTTATGAAAACATAT-ATATTATAGTTTTGAAAACATT
1 TATATAT-TATATAGTTTTT-AAAACGTTTTTGAAAATTTATAATATTAT--TTTTGAAAACATG
**
30009 TTGAAAACATT
62 TTGAAAACAGG
30020 TATATATTATATAGTTTTTAAAACGTTTTTGAAAATTTATAATATT-TTTTTGAAAACATGTTGA
1 TATATATTATATAGTTTTTAAAACGTTTTTGAAAATTTATAATATTATTTTTGAAAACATGTTGA
30084 AAACAGG
66 AAACAGG
** ** *
30091 CGTATATTATATAGTTTAAAAAAAAC-ATTTTGAAAATTTAT-ATATTAT
1 TATATATTATATAGTTT--TTAAAACGTTTTTGAAAATTTATAATATTAT
30139 ATGTTTTTGA
Statistics
Matches: 104, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
71 41 0.39
72 15 0.14
73 24 0.23
74 17 0.16
75 7 0.07
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (72 bp):
TATATATTATATAGTTTTTAAAACGTTTTTGAAAATTTATAATATTATTTTTGAAAACATGTTGA
AAACAGG
Found at i:30178 original size:3 final size:3
Alignment explanation
Indices: 30170--30237 Score: 52
Period size: 3 Copynumber: 21.3 Consensus size: 3
30160 TATATATATA
30170 TAT TAT TATT TAT T-T T-T GTAT ATAT ATAT TATT TAT TAT TAT TATT
1 TAT TAT TA-T TAT TAT TAT -TAT -TAT -TAT TA-T TAT TAT TAT TA-T
30216 TAT TAT TAT TATT TAT T-T TAT T
1 TAT TAT TAT TA-T TAT TAT TAT T
30238 GTTTTGGTCT
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
2 5 0.09
3 32 0.56
4 20 0.35
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:30191 original size:26 final size:25
Alignment explanation
Indices: 30162--30234 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 25
30152 TATTTATGTA
30162 TATATATATATTATTATTTATTTTT
1 TATATATATATTATTATTTATTTTT
*
30187 GTATATATATATTATT-TATTA-TTAT
1 -TATATATATATTATTAT-TTATTTTT
*
30212 TATTTAT-TATTATTATTTATTTT
1 TATATATATATTATTATTTATTTT
30235 ATTGTTTTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.24
24 9 0.22
25 4 0.10
26 18 0.44
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (25 bp):
TATATATATATTATTATTTATTTTT
Found at i:31480 original size:22 final size:22
Alignment explanation
Indices: 31455--31497 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31445 AACTTTAATC
*
31455 TTTT-TTTTATCTATTTTTATTA
1 TTTTATTTTAT-TATTGTTATTA
31477 TTTTATTTTATTATTGTTATT
1 TTTTATTTTATTATTGTTATT
31498 TCTTTCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTATTTTATTATTGTTATTA
Found at i:31485 original size:13 final size:14
Alignment explanation
Indices: 31469--31498 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
31459 TTTTATCTAT
31469 TTTTATTATT-TTA
1 TTTTATTATTGTTA
31482 TTTTATTATTGTTA
1 TTTTATTATTGTTA
31496 TTT
1 TTT
31499 CTTTCCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTATTATTGTTA
Found at i:33493 original size:19 final size:19
Alignment explanation
Indices: 33469--33514 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
33459 ATTTAGACAT
33469 TTTGCATTTCATTATTTTC
1 TTTGCATTTCATTATTTTC
**
33488 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCATTATTTTC
*
33507 TTTACATT
1 TTTGCATT
33515 CACATTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.15, C:0.13, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTGCATTTCATTATTTTC
Found at i:37105 original size:84 final size:81
Alignment explanation
Indices: 36847--37317 Score: 524
Period size: 84 Copynumber: 5.7 Consensus size: 81
36837 TTTAAAACAA
* * * * *
36847 ATCATTTACAGCATAACTCAAGGCTAA-AAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTC-AAGAAGGGCTATC--TG-CCAAAAGACCTTCGAGTTCGAC
36911 TACGCTCAGCTC-AACGGCAC
62 TACGCTCAGCTCTAA-GGCAC
* * * * * *
36931 ATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAAGACC-CCGAGTTCGATTACA
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGACTACG
*
36994 CTCAGCTTCCAAGGCAC
66 CTCAGC-TCTAAGGCAC
* *
37011 ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTG-C--CAAAAGACCTTCGAGTTCGACT
*
37076 ACGCTTAGCTCTAAGGCAC
63 ACGCTCAGCTCTAAGGCAC
* *
37095 ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTG-C--CAAAAGACCTTCGAGTTCGACT
37160 ACGCTCAGCTCTAAGGCAC
63 ACGCTCAGCTCTAAGGCAC
* * * * * *
37179 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAACACC-CCGAGTTCGATTACA
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGACTACG
* *
37242 CTCAGCTTCGAGGGCAC
66 CTCAGC-TCTAAGGCAC
* * *
37259 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CTAAAGACCTTCGAGTTCGA
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGA
37318 TTATATTCAA
Statistics
Matches: 342, Mismatches: 34, Indels: 25
0.85 0.08 0.06
Matches are distributed among these distances:
79 36 0.11
80 107 0.31
81 15 0.04
82 2 0.01
83 3 0.01
84 162 0.47
85 17 0.05
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (81 bp):
ATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCTAAGGCAC
Found at i:37118 original size:164 final size:161
Alignment explanation
Indices: 36847--37320 Score: 562
Period size: 164 Copynumber: 2.9 Consensus size: 161
36837 TTTAAAACAA
* * * * *
36847 ATCATTTACAGCATAACTCAAGGCTAA-AAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTC-AAGAAGGGTTATCTG-CA-CAAAAGACCTTCGAGTTCGAC
*
36911 TACGCTCAGCTCAACGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
63 TACGCTCAGCTCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
*
36976 ACC-CCGAGTTCGATTACACTCAGCTTCCAAGGCAC
127 ACCTTCGAGTTCGATTACACTCAGC-TCCAAGGCAC
*
37011 ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTG-C-ACAAAAGACCTTCGAGTTCGACT
* * * * *
37076 ACGCTTAGCTCTAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAA
64 ACGCTCAGCTC-AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-A
* * *
37141 AAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCAC
124 AAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCAC
* * * * * *
37179 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC-C-AAACACC-CCGAGTTCGATTAC
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCACAAAAGACCTTCGAGTTCGACTAC
* * *
37241 ACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAAAGAC
66 GCTCAGC-TC-AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
37306 CTTCGAGTTCGATTA
129 CTTCGAGTTCGATTA
37321 TATTCAACTT
Statistics
Matches: 267, Mismatches: 34, Indels: 22
0.83 0.11 0.07
Matches are distributed among these distances:
160 20 0.07
163 20 0.07
164 151 0.57
165 5 0.02
167 2 0.01
168 51 0.19
169 18 0.07
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (161 bp):
ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCACAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCT
TCGAGTTCGATTACACTCAGCTCCAAGGCAC
Found at i:37290 original size:248 final size:244
Alignment explanation
Indices: 36847--37317 Score: 721
Period size: 248 Copynumber: 1.9 Consensus size: 244
36837 TTTAAAACAA
** * *
36847 ATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
* *
36912 ACGCTCAGCTCAACGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAACA
*
36977 CCCCGAGTTCGATTACACTCAGCTTCCAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
131 CCCCGAGTTCGATTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGG
*
37042 GTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTTAGCTCTAAGGCAC
196 GCTATCTG----CAAAAGACCTTCGAGTTCGACTACGCTTAGCTCTAAGGCAC
* * * *
37095 ATCATTTGCAGTATAACTTAAGTC-AAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGAC
1 ATCATTTACAGCATAACTCAAGGCTAA-AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGAC
37159 TACGCTCAGCTCTAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
65 TACGCTCAGCTC-AACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
* * * *
37223 CACCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
129 CACCCCGAGTTCGATTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAA
*
37288 GGGCTATCTGCTAAAGACCTTCGAGTTCGA
194 GGGCTATCTGCAAAAGACCTTCGAGTTCGA
37318 TTATATTCAA
Statistics
Matches: 204, Mismatches: 17, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
244 19 0.09
247 2 0.01
248 181 0.89
249 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (244 bp):
ATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAACA
CCCCGAGTTCGATTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGG
GCTATCTGCAAAAGACCTTCGAGTTCGACTACGCTTAGCTCTAAGGCAC
Found at i:37377 original size:82 final size:80
Alignment explanation
Indices: 36956--37379 Score: 201
Period size: 84 Copynumber: 5.2 Consensus size: 80
36946 GCTTAAGTCG
* * ** * * * *
36956 AGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTCCAAGGCACATCATTTGCA
1 AGAAGGGCTATCTGCCAAACACCCCGAGTTCGATTACACTCAACTTAGAGGGCAAATCACTTACA
* * * *
37021 GTATAACTTAAGTCA
66 GAATAGCTCAAGGCA
* * * * * * * *
37036 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTTAGCTCTA-A-GGCACATCA
1 AGAAGGGCTATCTG-C--C-AAACACC-CCGAGTTCGATTACACTCAACT-TAGAGGGCAAATCA
* * * * * *
37099 TTTGCAGTATAACTTAAGTCA
60 CTTACAGAATAGCTCAAGGCA
* * * * * * *
37120 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTA-A-GGCACATCA
1 AGAAGGGCTATCTG-C--C-AAACACC-CCGAGTTCGATTACACTCAACT-TAGAGGGCAAATCA
* * * * * *
37183 TTTGCAGCATAGCTTAAGTCG
60 CTTACAGAATAGCTCAAGGCA
* * * * *
37204 AGAAGGGCTATCTGCCAAACACCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
1 AGAAGGGCTATCTGCCAAACACCCCGAGTTCGATTACACTCAACTTAGAGGGCAAATCACTTACA
* * * *
37269 GCATAGCTTAAGTCG
66 GAATAGCTCAAGGCA
* * * * *
37284 AGAAGGGCTATCTGCTAAAGACCTTCGAGTTCGATTATATTCAACTTAGA-GGCAAATCAAGCTT
1 AGAAGGGCTATCTGCCAAACACC-CCGAGTTCGATTACACTCAACTTAGAGGGCAAATC-A-CTT
37348 ACAGAATAGCTCAAGGCA
63 ACAGAATAGCTCAAGGCA
37366 AGAAGGGCTATCTG
1 AGAAGGGCTATCTG
37380 TCAATAAAAC
Statistics
Matches: 303, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
78 1 0.00
79 20 0.07
80 77 0.25
81 24 0.08
82 29 0.10
83 2 0.01
84 130 0.43
85 19 0.06
86 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (80 bp):
AGAAGGGCTATCTGCCAAACACCCCGAGTTCGATTACACTCAACTTAGAGGGCAAATCACTTACA
GAATAGCTCAAGGCA
Found at i:38046 original size:38 final size:37
Alignment explanation
Indices: 37980--38246 Score: 195
Period size: 38 Copynumber: 7.2 Consensus size: 37
37970 GTTTTAAAAA
*
37980 AAAACATTTTAGAAAA--TATATATAATATATAATTTTT
1 AAAACATTTT-GAAAACTTATATAT-ATATATAGTTTTT
38017 AAAATCATTTTGAAAACTTATATATATATATAGTTTTT
1 AAAA-CATTTTGAAAACTTATATATATATATAGTTTTT
* *
38055 GAAAACGTTTATGAAAAC--ATATATAT-TATAGTTTTG
1 -AAAACATTT-TGAAAACTTATATATATATATAGTTTTT
38091 AAAACATTTTGAAAACATT-TATATATTATATAGTTTTT
1 AAAACATTTTGAAAAC-TTATATATA-TATATAGTTTTT
*
38129 AAAACGTTTTTGAAAA-TT-TATA-ATAT-T--TTTTT
1 AAAAC-ATTTTGAAAACTTATATATATATATAGTTTTT
* *** **
38161 GAAAACATGTTGAAAACAGGCGTATAT-TATATAGTTTAAAA
1 -AAAACATTTTGAAAAC--TTATATATATATATAGTTT--TT
*
38202 AAAACATTTTGAAAATTTATATAT-TATAT-GTTTTT
1 AAAACATTTTGAAAACTTATATATATATATAGTTTTT
*
38237 GAAAATATTT
1 -AAAACATTT
38247 ATGTATATAT
Statistics
Matches: 187, Mismatches: 20, Indels: 47
0.74 0.08 0.19
Matches are distributed among these distances:
32 13 0.07
33 5 0.03
34 8 0.04
35 11 0.06
36 31 0.17
37 29 0.16
38 46 0.25
39 30 0.16
40 14 0.07
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
AAAACATTTTGAAAACTTATATATATATATAGTTTTT
Found at i:38102 original size:11 final size:11
Alignment explanation
Indices: 38086--38110 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38076 TATATTATAG
38086 TTTTGAAAACA
1 TTTTGAAAACA
38097 TTTTGAAAACA
1 TTTTGAAAACA
38108 TTT
1 TTT
38111 ATATATTATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:38174 original size:71 final size:73
Alignment explanation
Indices: 37980--38246 Score: 242
Period size: 73 Copynumber: 3.6 Consensus size: 73
37970 GTTTTAAAAA
* *
37980 AAAACATTTTAGAAAATATATATAATATATAATTTTT-AAAATCATTTTGAAAAC--TTATATAT
1 AAAACGTTTTTGAAAAT-T-TATAATATAT-ATTTTTGAAAA-CATTTTGAAAACATTTATATAT
38042 ATATATAGTTTTT
62 -TATATAGTTTTT
* ** *
38055 GAAAACGTTTATGAAAACATAT-ATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATTA
1 -AAAACGTTTTTGAAAATTTATAATA-TATATTTTTGAAAACATTTTGAAAACATTTATATATTA
38119 TATAGTTTTT
64 TATAGTTTTT
* ****
38129 AAAACGTTTTTGAAAATTTATAATAT-T-TTTTTGAAAACATGTTGAAAACAGGCGTATATTATA
1 AAAACGTTTTTGAAAATTTATAATATATATTTTTGAAAACATTTTGAAAACATTTATATATTATA
**
38192 TAGTTTAAAA
66 TAGTTT--TT
* * *
38202 AAAAC-ATTTTGAAAATTTATATATTATATGTTTTTGAAAATATTT
1 AAAACGTTTTTGAAAATTTATA-A-TATATATTTTTGAAAACATTT
38247 ATGTATATAT
Statistics
Matches: 160, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
71 36 0.22
72 16 0.10
73 45 0.28
74 28 0.17
75 9 0.06
76 26 0.16
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (73 bp):
AAAACGTTTTTGAAAATTTATAATATATATTTTTGAAAACATTTTGAAAACATTTATATATTATA
TAGTTTTT
Found at i:38274 original size:29 final size:32
Alignment explanation
Indices: 38251--38309 Score: 88
Period size: 29 Copynumber: 1.9 Consensus size: 32
38241 ATATTTATGT
*
38251 ATATATATATTA-TTATTA-T-TTATTTTTGT
1 ATATATATATTATTTATTATTATTATTTATGT
38280 ATATATATATTATTTATTATTATTATTTAT
1 ATATATATATTATTTATTATTATTATTTAT
38310 TTTATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
30 6 0.23
31 1 0.04
32 7 0.27
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (32 bp):
ATATATATATTATTTATTATTATTATTTATGT
Found at i:39569 original size:22 final size:22
Alignment explanation
Indices: 39544--39586 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39534 AACTTTAATC
*
39544 TTTT-TTTTATCTATTTTTATTA
1 TTTTATTTTAT-TATTGTTATTA
39566 TTTTATTTTATTATTGTTATT
1 TTTTATTTTATTATTGTTATT
39587 TCTTTCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTATTTTATTATTGTTATTA
Found at i:39574 original size:13 final size:14
Alignment explanation
Indices: 39558--39587 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39548 TTTTATCTAT
39558 TTTTATTATT-TTA
1 TTTTATTATTGTTA
39571 TTTTATTATTGTTA
1 TTTTATTATTGTTA
39585 TTT
1 TTT
39588 CTTTCCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTATTATTGTTA
Found at i:41930 original size:20 final size:20
Alignment explanation
Indices: 41905--41947 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41895 TCTAAAGGCC
41905 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
41925 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
41945 CAT
1 CAT
41948 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:49670 original size:21 final size:21
Alignment explanation
Indices: 49646--49686 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
49636 ACGTTTTCAC
*
49646 CTTTCACTTTCTATCTTTTTA
1 CTTTCACTTTCTATCATTTTA
*
49667 CTTTTACTTTCTATCATTTT
1 CTTTCACTTTCTATCATTTT
49687 CTTCTCCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (21 bp):
CTTTCACTTTCTATCATTTTA
Found at i:51549 original size:15 final size:16
Alignment explanation
Indices: 51529--51559 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
51519 CCCTTTCACT
51529 TAGAGTG-TGGGATGA
1 TAGAGTGATGGGATGA
51544 TAGAGTGATGGGATGA
1 TAGAGTGATGGGATGA
51560 CTCCCCTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (16 bp):
TAGAGTGATGGGATGA
Found at i:51980 original size:20 final size:20
Alignment explanation
Indices: 51955--51997 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
51945 TCTAAAGGCC
51955 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
51975 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
51995 CAT
1 CAT
51998 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Done.