Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007412.1 Hibiscus syriacus cultivar Beakdansim tig00020033_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: 97587
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:788 original size:82 final size:83
Alignment explanation
Indices: 637--791 Score: 244
Period size: 82 Copynumber: 1.9 Consensus size: 83
627 TCTGCCTTTG
* * *
637 AATTATTGCCCTCCTTCCCAGGTAGTTGAGATTTTTTTCTATTTTGCCCCGCCTTATTATGTGGT
1 AATTATTGCCCTCCTTCCCAGGCAGTTGAGATTTTTTACTATTTTCCCCCGCCTTATTATGTGGT
702 ATTGGTGCTAGTAGTTAT
66 ATTGGTGCTAGTAGTTAT
720 AATTATTGCCCTCCTTCCCAGGGCA-TTGAGA-TTTTTACTATTTTCCCCCGCCATT-TTATGTG
1 AATTATTGCCCTCCTTCCCA-GGCAGTTGAGATTTTTTACTATTTTCCCCCGCC-TTATTATGTG
782 GTATTGGTGC
64 GTATTGGTGC
792 CGGTAGATAC
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
82 36 0.54
83 28 0.42
84 3 0.04
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.43
Consensus pattern (83 bp):
AATTATTGCCCTCCTTCCCAGGCAGTTGAGATTTTTTACTATTTTCCCCCGCCTTATTATGTGGT
ATTGGTGCTAGTAGTTAT
Found at i:9139 original size:42 final size:42
Alignment explanation
Indices: 9081--9175 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
9071 GAGGTGAATA
* ** *
9081 AGAAGATCTCCGAGCTGGATTCAACGCAGACAGAGGCCAATG
1 AGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCCAATG
*
9123 AGAAGACCTCCAAGCTGGAAGCAACGCAGACAAAGGCCAATG
1 AGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCCAATG
9165 AGAAGATCTCC
1 AGAAGATCTCC
9176 GAGGATGCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.37, C:0.25, G:0.26, T:0.12
Consensus pattern (42 bp):
AGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCCAATG
Found at i:12498 original size:56 final size:57
Alignment explanation
Indices: 12427--12546 Score: 233
Period size: 56 Copynumber: 2.1 Consensus size: 57
12417 TTGAAAGAAG
12427 TTTTTTCTTAACTTCAATTCTTTTGGTTTTATG-TTTCTTTTATTTTCTATGAAATA
1 TTTTTTCTTAACTTCAATTCTTTTGGTTTTATGTTTTCTTTTATTTTCTATGAAATA
12483 TTTTTTCTTAACTTCAATTCTTTTGGTTTTATGTTTTCTTTTATTTTCTATGAAATA
1 TTTTTTCTTAACTTCAATTCTTTTGGTTTTATGTTTTCTTTTATTTTCTATGAAATA
12540 TTTTTTC
1 TTTTTTC
12547 CAGTATGAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 33 0.52
57 30 0.48
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.64
Consensus pattern (57 bp):
TTTTTTCTTAACTTCAATTCTTTTGGTTTTATGTTTTCTTTTATTTTCTATGAAATA
Found at i:12520 original size:31 final size:31
Alignment explanation
Indices: 12429--12522 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 31
12419 GAAAGAAGTT
12429 TTTTCTTAACTTCAATTCTTTTGGTTTTATG
1 TTTTCTTAACTTCAATTCTTTTGGTTTTATG
*** *
12460 -TTTCTT---TT--ATT-TTCTAT-GAAATATT
1 TTTTCTTAACTTCAATTCTT-T-TGGTTTTATG
12485 TTTTCTTAACTTCAATTCTTTTGGTTTTATG
1 TTTTCTTAACTTCAATTCTTTTGGTTTTATG
12516 TTTTCTT
1 TTTTCTT
12523 TTATTTTCTA
Statistics
Matches: 45, Mismatches: 8, Indels: 20
0.62 0.11 0.27
Matches are distributed among these distances:
24 2 0.04
25 8 0.18
26 7 0.16
27 2 0.04
29 2 0.04
30 7 0.16
31 15 0.33
32 2 0.04
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.64
Consensus pattern (31 bp):
TTTTCTTAACTTCAATTCTTTTGGTTTTATG
Found at i:13739 original size:15 final size:15
Alignment explanation
Indices: 13716--13929 Score: 313
Period size: 15 Copynumber: 14.3 Consensus size: 15
13706 AATGATCGAG
* *
13716 GAAGGTGAAAATTCT
1 GAAGATGAAAATCCT
*
13731 GAAGATGAAAATTCT
1 GAAGATGAAAATCCT
*
13746 GAAGATG-AAATACT
1 GAAGATGAAAATCCT
* *
13760 GAAGGTGAAAATTCT
1 GAAGATGAAAATCCT
*
13775 GAAGATGAAAATTCT
1 GAAGATGAAAATCCT
13790 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
*
13805 GAAGATGGAAATCCT
1 GAAGATGAAAATCCT
13820 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
13835 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
13850 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
13865 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
*
13880 GAAGGTGAAAATCCT
1 GAAGATGAAAATCCT
*
13895 AAAGATGAAAATCCT
1 GAAGATGAAAATCCT
* *
13910 GTAGATGAAAATTCT
1 GAAGATGAAAATCCT
13925 GAAGA
1 GAAGA
13930 AGATCAAAGC
Statistics
Matches: 183, Mismatches: 15, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
14 12 0.07
15 171 0.93
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.22
Consensus pattern (15 bp):
GAAGATGAAAATCCT
Found at i:14632 original size:14 final size:14
Alignment explanation
Indices: 14613--14651 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
14603 TTCGTGATCT
14613 ATATATATTTGT-A
1 ATATATATTTGTAA
14626 A-ATATATTTGTAA
1 ATATATATTTGTAA
14639 ATATATATTTGTA
1 ATATATATTTGTA
14652 GTGGAAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.42
13 3 0.12
14 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (14 bp):
ATATATATTTGTAA
Found at i:14642 original size:10 final size:12
Alignment explanation
Indices: 14615--14644 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
14605 CGTGATCTAT
14615 ATATATTTGTAA
1 ATATATTTGTAA
14627 ATATATTTGTAA
1 ATATATTTGTAA
14639 ATATAT
1 ATATAT
14645 ATTTGTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATATTTGTAA
Found at i:20335 original size:181 final size:177
Alignment explanation
Indices: 20035--20394 Score: 621
Period size: 181 Copynumber: 2.0 Consensus size: 177
20025 TGCGACTTTT
*
20035 GGATAGAATACTACTATCCCTTTATGTGTTGTATAGACTAGGATCACACTATGTTTTACTTTTGG
1 GGATAGAATACTACTATCCCTTTATGTGTTGAATAGACTAGGATCACACTATGTTTTACTTTTGG
*
20100 AAAGGCTTATGCATGCCTTAAGCTGGGATTTTGTAATATTGGATTTGTATTATTATTATTTGGCT
66 AAAGGCTTATGCATGCCTTAAGCTGGGATTTCGTAATATTGGATTTGTATTATTATTATTTGGCT
20165 AAAAATGTATAGTTTATCTTGTTGGTTGTGAATTTCATTCTTCAACA
131 AAAAATGTATAGTTTATCTTGTTGGTTGTGAATTTCATTCTTCAACA
*
20212 GGATAGAATACTGCTATCCCTTTATGTGTTGAATAGACTAGGATCACACTATGTTTTACTTACTT
1 GGATAGAATACTACTATCCCTTTATGTGTTGAATAGACTAGGATCACACTATG--TT--TTACTT
*
20277 TTGGAAAGGCTTATGCATGCCTTAAGCTGGGATTTCGTAATATTGGATTTTTATTATTATTATTT
62 TTGGAAAGGCTTATGCATGCCTTAAGCTGGGATTTCGTAATATTGGATTTGTATTATTATTATTT
* * *
20342 GTCTAAAAATGTATAGTTTATTTTGTTGTTTGTGAATTTCATTCTTCAACA
127 GGCTAAAAATGTATAGTTTATCTTGTTGGTTGTGAATTTCATTCTTCAACA
20393 GG
1 GG
20395 GACGATTCCT
Statistics
Matches: 172, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
177 51 0.30
179 2 0.01
181 119 0.69
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (177 bp):
GGATAGAATACTACTATCCCTTTATGTGTTGAATAGACTAGGATCACACTATGTTTTACTTTTGG
AAAGGCTTATGCATGCCTTAAGCTGGGATTTCGTAATATTGGATTTGTATTATTATTATTTGGCT
AAAAATGTATAGTTTATCTTGTTGGTTGTGAATTTCATTCTTCAACA
Found at i:27955 original size:2 final size:2
Alignment explanation
Indices: 27948--27999 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
27938 CGGCGTTTTG
27948 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
27990 AT AT AT AT AT
1 AT AT AT AT AT
28000 CTCAATAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29787 original size:9 final size:9
Alignment explanation
Indices: 29773--29871 Score: 99
Period size: 10 Copynumber: 10.3 Consensus size: 9
29763 GCTGCTGGAA
29773 ACCGGTTTG
1 ACCGGTTTG
*
29782 ACCGGTTTTCA
1 ACCGG-TTT-G
29793 ACCGGTTCTG
1 ACCGGTT-TG
29803 ACCGGTTTG
1 ACCGGTTTG
*
29812 ACCGGTTTCA
1 ACCGGTTT-G
*
29822 ACCGGTTCG
1 ACCGGTTTG
29831 AACCGGTTTG
1 -ACCGGTTTG
29841 ACCGGTTTG
1 ACCGGTTTG
*
29850 AATCGGTTTG
1 -ACCGGTTTG
*
29860 ACCGGTCTG
1 ACCGGTTTG
29869 ACC
1 ACC
29872 CGACCCGACC
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.47
11 6 0.08
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:29817 original size:19 final size:18
Alignment explanation
Indices: 29773--29871 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 18
29763 GCTGCTGGAA
*
29773 ACCGGTTTGACCGGTTTTCA
1 ACCGGTTTGACCGG-TTT-G
29793 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTTTG
* *
29812 ACCGGTTTCAACCGGTTCG
1 ACCGGTTT-GACCGGTTTG
29831 AACCGGTTTGACCGGTTTG
1 -ACCGGTTTGACCGGTTTG
* *
29850 AATCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTTTG
29869 ACC
1 ACC
29872 CGACCCGACC
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.04
19 40 0.59
20 18 0.26
21 7 0.10
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:29835 original size:29 final size:28
Alignment explanation
Indices: 29773--29871 Score: 135
Period size: 29 Copynumber: 3.4 Consensus size: 28
29763 GCTGCTGGAA
29773 ACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
29803 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
29831 AACCGGTTTGACCGGTTTGAATCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
29860 ACCGGTCTGACC
1 ACCGGTTTGACC
29872 CGACCCGACC
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
28 12 0.19
29 38 0.59
30 14 0.22
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:29894 original size:22 final size:22
Alignment explanation
Indices: 29868--29910 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
29858 TGACCGGTCT
*
29868 GACCCGACCCGACCGTTGACCC
1 GACCCAACCCGACCGTTGACCC
29890 GACCCAACCCGACCGTTGACC
1 GACCCAACCCGACCGTTGACC
29911 GTTGACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.09
Consensus pattern (22 bp):
GACCCAACCCGACCGTTGACCC
Found at i:30870 original size:32 final size:31
Alignment explanation
Indices: 30786--30862 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
30776 CTAATGTGAC
* *
30786 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
30817 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
30849 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
30863 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:30888 original size:63 final size:63
Alignment explanation
Indices: 30786--30909 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
30776 CTAATGTGAC
* ** * *
30786 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
30849 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAAT-TATTCTCGGGTAGGCCCTCAGGCCCTAAGATGT
30910 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.94
64 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:34425 original size:23 final size:23
Alignment explanation
Indices: 34382--34426 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34372 AGGAGTGAAT
* **
34382 TTATAATATTTTAAGGGATAAAC
1 TTATAAAATTTTAAGAAATAAAC
34405 TTATAAAATTTTAAGAAATAAA
1 TTATAAAATTTTAAGAAATAAA
34427 AATAAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (23 bp):
TTATAAAATTTTAAGAAATAAAC
Found at i:34481 original size:29 final size:29
Alignment explanation
Indices: 34445--34506 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
34435 ATCAATAGAA
34445 AATACAAAAAATTACTTAGATAATACAAT
1 AATACAAAAAATTACTTAGATAATACAAT
*
34474 AATACAAAAAATTACTTAGATAATACGAT
1 AATACAAAAAATTACTTAGATAATACAAT
34503 AATA
1 AATA
34507 TGAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (29 bp):
AATACAAAAAATTACTTAGATAATACAAT
Found at i:35149 original size:22 final size:22
Alignment explanation
Indices: 35121--35180 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
35111 TTTTATATAC
35121 AATTATTTAAATAAATCAATGA
1 AATTATTTAAATAAATCAATGA
35143 AATTATTTAAATAAATCAATGA
1 AATTATTTAAATAAATCAATGA
35165 AATTATTTAAATAAAT
1 AATTATTTAAATAAAT
35181 ATAAAAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (22 bp):
AATTATTTAAATAAATCAATGA
Found at i:37954 original size:18 final size:18
Alignment explanation
Indices: 37931--37975 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
37921 GTTTTGATGT
*
37931 TGGGTTGGGT-TCTGTATC
1 TGGGTTGGGTCT-TGTAAC
*
37949 TGGGTTAGGTCTTGTAAC
1 TGGGTTGGGTCTTGTAAC
37967 TGGGTTGGG
1 TGGGTTGGG
37976 CTTTAGGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.42, T:0.40
Consensus pattern (18 bp):
TGGGTTGGGTCTTGTAAC
Found at i:38031 original size:3 final size:3
Alignment explanation
Indices: 38023--38082 Score: 93
Period size: 3 Copynumber: 19.3 Consensus size: 3
38013 ATTAAAATGT
38023 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
38069 TAA TTAA AAA TAA T
1 TAA -TAA TAA TAA T
38083 TAAAAAAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40224 original size:42 final size:42
Alignment explanation
Indices: 40177--40276 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
40167 GGAAGCGGTG
* *
40177 AATGAGAAGATCTCCAAGCTGGATTCAACGCAGACAGAGGCC
1 AATGAGAAGATCTCCAAGCTGGAATCAACGCAGACAAAGGCC
*
40219 AATGAGAAGATCTCCAAGCTGGAATCCACGCAGACAAAGGCC
1 AATGAGAAGATCTCCAAGCTGGAATCAACGCAGACAAAGGCC
40261 AATGAGAAGATCTCCA
1 AATGAGAAGATCTCCA
40277 TGGAGGCTGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (42 bp):
AATGAGAAGATCTCCAAGCTGGAATCAACGCAGACAAAGGCC
Found at i:45033 original size:24 final size:24
Alignment explanation
Indices: 45005--45052 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
44995 AAATTCCATA
45005 AAAGATCAAGGCAATTCTTCAACT
1 AAAGATCAAGGCAATTCTTCAACT
45029 AAAGATCAAGGCAATTCTTCAACT
1 AAAGATCAAGGCAATTCTTCAACT
45053 TCTATCTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (24 bp):
AAAGATCAAGGCAATTCTTCAACT
Found at i:53510 original size:9 final size:9
Alignment explanation
Indices: 53481--53547 Score: 62
Period size: 9 Copynumber: 7.0 Consensus size: 9
53471 TGGAAAACCG
53481 GGTTTGACC
1 GGTTTGACC
*
53490 AGTTTCGAACC
1 GGTTT-G-ACC
53501 GGTTTGACC
1 GGTTTGACC
*
53510 GGTCTGAACC
1 GGTTTG-ACC
53520 GGTTTGACC
1 GGTTTGACC
*
53529 GGTCTGAACC
1 GGTTTG-ACC
*
53539 GGGTTGACC
1 GGTTTGACC
53548 CGACCCGACT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 23 0.49
10 17 0.36
11 7 0.15
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.27
Consensus pattern (9 bp):
GGTTTGACC
Found at i:53520 original size:19 final size:19
Alignment explanation
Indices: 53476--53547 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
53466 GCTGCTGGAA
* *
53476 AACCGGGTTTGACCAGTTTCG
1 AACC-GGTTTGACCGGTCT-G
53497 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
53516 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
53535 AACCGGGTTGACC
1 AACCGGTTTGACC
53548 CGACCCGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 32 0.67
20 12 0.25
21 4 0.08
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:53566 original size:17 final size:17
Alignment explanation
Indices: 53541--53603 Score: 108
Period size: 17 Copynumber: 3.7 Consensus size: 17
53531 TCTGAACCGG
53541 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
53558 GTGGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
53575 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
53592 GTTGACCCGACC
1 GTTGACCCGACC
53604 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.17, C:0.43, G:0.25, T:0.14
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:53598 original size:12 final size:12
Alignment explanation
Indices: 53583--53610 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53573 CTGTTGACCC
53583 GACCCGACCGTT
1 GACCCGACCGTT
53595 GACCCGACCGTT
1 GACCCGACCGTT
53607 GACC
1 GACC
53611 GTTGACCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:53610 original size:7 final size:7
Alignment explanation
Indices: 53588--53649 Score: 87
Period size: 7 Copynumber: 9.4 Consensus size: 7
53578 GACCCGACCC
53588 GACCGTT
1 GACCGTT
*
53595 GACC--C
1 GACCGTT
53600 GACCGTT
1 GACCGTT
53607 GACCGTT
1 GACCGTT
53614 GACCG-T
1 GACCGTT
53620 GACCGTT
1 GACCGTT
53627 GACCG-T
1 GACCGTT
53633 GACCGTT
1 GACCGTT
53640 GACCGTT
1 GACCGTT
53647 GAC
1 GAC
53650 TTTCTTTGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
5 4 0.08
6 12 0.24
7 33 0.67
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:53624 original size:13 final size:13
Alignment explanation
Indices: 53600--53645 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
53590 CCGTTGACCC
53600 GACCGTTGACCGTT
1 GACCG-TGACCGTT
53614 GACCGTGACCGTT
1 GACCGTGACCGTT
53627 GACCGTGACCGTT
1 GACCGTGACCGTT
53640 GACCGT
1 GACCGT
53646 TGACTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 27 0.84
14 5 0.16
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:53625 original size:20 final size:20
Alignment explanation
Indices: 53588--53649 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
53578 GACCCGACCC
*
53588 GACCGTTGACC-CGACCGTT
1 GACCGTTGACCGTGACCGTT
53607 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
53627 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
53647 GAC
1 GAC
53650 TTTCTTTGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
19 17 0.43
20 23 0.57
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:60253 original size:9 final size:9
Alignment explanation
Indices: 60221--60290 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
60211 CTGCTGGAAA
60221 ACCGGTTTG
1 ACCGGTTTG
*
60230 ACCAGTTTCG
1 ACCGGTTT-G
60240 AACCGGTTTG
1 -ACCGGTTTG
*
60250 ACCGGTCTG
1 ACCGGTTTG
*
60259 AACCGATTTG
1 -ACCGGTTTG
*
60269 ACCGGTCTG
1 ACCGGTTTG
*
60278 AACCGGGTTG
1 -ACCGGTTTG
60288 ACC
1 ACC
60291 CGACCCGACT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 25 0.52
10 16 0.33
11 7 0.15
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:60263 original size:19 final size:19
Alignment explanation
Indices: 60220--60290 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
60210 GCTGCTGGAA
* *
60220 AACCGGTTTGACCAGTTTCG
1 AACCGGTTTGACCGGTCT-G
60240 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
60259 AACCGATTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
60278 AACCGGGTTGACC
1 AACCGGTTTGACC
60291 CGACCCGACT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 30 0.65
20 16 0.35
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:60309 original size:17 final size:17
Alignment explanation
Indices: 60287--60341 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
60277 GAACCGGGTT
*
60287 GACCCGACCCGACTGTG
1 GACCCGACCCGACCGTG
*
60304 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTG
*
60321 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTG
60338 GACC
1 GACC
60342 GTTGACCGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.18, C:0.45, G:0.25, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTG
Found at i:60341 original size:7 final size:7
Alignment explanation
Indices: 60331--60380 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
60321 GACCCGACCC
60331 GACCGTT
1 GACCGTT
60338 GACCGTT
1 GACCGTT
60345 GACCG-T
1 GACCGTT
60351 GACCGTT
1 GACCGTT
60358 GACCG-T
1 GACCGTT
60364 GACCGTT
1 GACCGTT
60371 GACCGTT
1 GACCGTT
60378 GAC
1 GAC
60381 TTTCTTTGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:60355 original size:13 final size:13
Alignment explanation
Indices: 60331--60376 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
60321 GACCCGACCC
60331 GACCGTTGACCGTT
1 GACCG-TGACCGTT
60345 GACCGTGACCGTT
1 GACCGTGACCGTT
60358 GACCGTGACCGTT
1 GACCGTGACCGTT
60371 GACCGT
1 GACCGT
60377 TGACTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 27 0.84
14 5 0.16
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:60356 original size:20 final size:20
Alignment explanation
Indices: 60331--60380 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
60321 GACCCGACCC
60331 GACCGTTGACCGTTGACCG-T
1 GACCGTTGACCG-TGACCGTT
60351 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
60371 GACCGTTGAC
1 GACCGTTGAC
60381 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:63178 original size:15 final size:15
Alignment explanation
Indices: 63155--63189 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
63145 CATGATCGAG
* *
63155 GAAGGTGAAAATTCT
1 GAAGATGAAAATCCT
63170 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
63185 GAAGA
1 GAAGA
63190 AGATCAAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.20
Consensus pattern (15 bp):
GAAGATGAAAATCCT
Found at i:66821 original size:2 final size:2
Alignment explanation
Indices: 66814--66843 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
66804 AAAATTGTTA
*
66814 AT AT AT AT AT AA 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
66844 GAACAGAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:79397 original size:2 final size:2
Alignment explanation
Indices: 79390--79428 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
79380 TCAACGTCGT
79390 TA TA TA 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 TA TA TA T
79429 CAAACACCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:80410 original size:2 final size:2
Alignment explanation
Indices: 80403--80436 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
80393 TAATATTGAA
80403 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
80437 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81351 original size:83 final size:84
Alignment explanation
Indices: 81195--81351 Score: 264
Period size: 83 Copynumber: 1.9 Consensus size: 84
81185 TCTGCCTTTG
* * *
81195 AATTATTGCCCTCCTTCCCAGGGTAGTTGAGATTTTTTTCTATTTTGCCCCGCCTTATTATGTGG
1 AATTATTGCCCTCCTTCCCAGGGCAGTTGAGATTTTTTACTATTTTCCCCCGCCTTATTATGTGG
81260 TATTGGTGCTAGTAGTTAT
66 TATTGGTGCTAGTAGTTAT
81279 AATTATTGCCCTCCTTCCCAGGGCAGTTGAGA-TTTTTACTATTTTCCCCCGCCATT-TTATGTG
1 AATTATTGCCCTCCTTCCCAGGGCAGTTGAGATTTTTTACTATTTTCCCCCGCC-TTATTATGTG
81342 GTATTGGTGC
65 GTATTGGTGC
81352 CGGTAGATAC
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
83 36 0.52
84 33 0.48
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (84 bp):
AATTATTGCCCTCCTTCCCAGGGCAGTTGAGATTTTTTACTATTTTCCCCCGCCTTATTATGTGG
TATTGGTGCTAGTAGTTAT
Found at i:89733 original size:42 final size:42
Alignment explanation
Indices: 89675--89769 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
89665 GAGGTGAATA
* ** *
89675 AGAAGATCTCCGAGCTGGATTCAACGCAGACAGAGGCCAATG
1 AGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCCAATG
*
89717 AGAAGACCTCCAAGCTGGAAGCAACGCAGACAAAGGCCAATG
1 AGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCCAATG
89759 AGAAGATCTCC
1 AGAAGATCTCC
89770 GAGGATGCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.37, C:0.25, G:0.26, T:0.12
Consensus pattern (42 bp):
AGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCCAATG
Found at i:93051 original size:31 final size:31
Alignment explanation
Indices: 93016--93110 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
93006 GAAAGAAGTT
93016 TTTTCTTAACTTCAATTCTTTTGGTTTTATG
1 TTTTCTTAACTTCAATTCTTTTGGTTTTATG
*** *
93047 TTTTCTT---TT--ATT-TTCTAT-GAAATATT
1 TTTTCTTAACTTCAATTCTT-T-TGGTTTTATG
93073 TTTTCTTAACTTCAATTCTTTTGGTTTTATG
1 TTTTCTTAACTTCAATTCTTTTGGTTTTATG
93104 TTTTCTT
1 TTTTCTT
93111 TTATTTTCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 18
0.64 0.11 0.25
Matches are distributed among these distances:
25 2 0.04
26 15 0.32
27 1 0.02
28 2 0.04
29 2 0.04
30 1 0.02
31 22 0.47
32 2 0.04
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.64
Consensus pattern (31 bp):
TTTTCTTAACTTCAATTCTTTTGGTTTTATG
Found at i:93087 original size:57 final size:57
Alignment explanation
Indices: 93014--93133 Score: 240
Period size: 57 Copynumber: 2.1 Consensus size: 57
93004 TTGAAAGAAG
93014 TTTTTTCTTAACTTCAATTCTTTTGGTTTTATGTTTTCTTTTATTTTCTATGAAATA
1 TTTTTTCTTAACTTCAATTCTTTTGGTTTTATGTTTTCTTTTATTTTCTATGAAATA
93071 TTTTTTCTTAACTTCAATTCTTTTGGTTTTATGTTTTCTTTTATTTTCTATGAAATA
1 TTTTTTCTTAACTTCAATTCTTTTGGTTTTATGTTTTCTTTTATTTTCTATGAAATA
93128 TTTTTT
1 TTTTTT
93134 TCCAGTATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.18, C:0.10, G:0.07, T:0.65
Consensus pattern (57 bp):
TTTTTTCTTAACTTCAATTCTTTTGGTTTTATGTTTTCTTTTATTTTCTATGAAATA
Found at i:94318 original size:15 final size:15
Alignment explanation
Indices: 94295--94508 Score: 313
Period size: 15 Copynumber: 14.3 Consensus size: 15
94285 AATGATCGAG
* *
94295 GAAGGTGAAAATTCT
1 GAAGATGAAAATCCT
*
94310 GAAGATGAAAATTCT
1 GAAGATGAAAATCCT
*
94325 GAAGATGAAAATACT
1 GAAGATGAAAATCCT
* *
94340 GAAGGTGAAAATTCT
1 GAAGATGAAAATCCT
*
94355 GAAGATGAAAATTCT
1 GAAGATGAAAATCCT
94370 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
*
94385 GAAGATGGAAATCCT
1 GAAGATGAAAATCCT
94400 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
94415 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
94430 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
94445 GAAGATGAAAATCCT
1 GAAGATGAAAATCCT
*
94460 GAAGGTGAAAATCCT
1 GAAGATGAAAATCCT
*
94475 AAAGATGAAAATCCT
1 GAAGATGAAAATCCT
* *
94490 GTAGATG-AAATTCT
1 GAAGATGAAAATCCT
94504 GAAGA
1 GAAGA
94509 AGATCAAAGC
Statistics
Matches: 184, Mismatches: 15, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
14 10 0.05
15 174 0.95
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.22
Consensus pattern (15 bp):
GAAGATGAAAATCCT
Found at i:95210 original size:12 final size:13
Alignment explanation
Indices: 95191--95229 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 13
95181 TTCGTGATCT
95191 ATATATATTTGTAA
1 ATATATATTTGT-A
95205 ATATATATTTGTA
1 ATATATATTTGTA
95218 A-ATATATTTGTA
1 ATATATATTTGTA
95230 GTGGAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 12 0.48
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (13 bp):
ATATATATTTGTA
Found at i:95210 original size:14 final size:14
Alignment explanation
Indices: 95191--95224 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
95181 TTCGTGATCT
95191 ATATATATTTGTAA
1 ATATATATTTGTAA
95205 ATATATATTTGTAA
1 ATATATATTTGTAA
95219 ATATAT
1 ATATAT
95225 TTGTAGTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
ATATATATTTGTAA
Done.