Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005598.1 Hibiscus syriacus cultivar Beakdansim tig00013022_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: 66613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2393 original size:20 final size:20
Alignment explanation
Indices: 2368--2424 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
2358 GAATATCATG
2368 AGGGTATCGATACCCCCAGT
1 AGGGTATCGATACCCCCAGT
2388 AGGGTATCGATACCCCCAGT
1 AGGGTATCGATACCCCCAGT
2408 AGGGTATCGATACCCCC
1 AGGGTATCGATACCCCC
2425 TAAAGGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.19
Consensus pattern (20 bp):
AGGGTATCGATACCCCCAGT
Found at i:3954 original size:23 final size:23
Alignment explanation
Indices: 3890--3967 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 23
3880 CATTATTATA
3890 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGTAATTCTACG
**
3913 TGG--C-ACGGTACAATTCTACG
1 TGGCACTACGGTGTAATTCTACG
*
3933 TGGCACTACGTTGTAATTCTACG
1 TGGCACTACGGTGTAATTCTACG
*
3956 -GGCACTTCGGTG
1 TGGCACTACGGTG
3968 CATTTATACG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 17 0.38
21 1 0.02
22 11 0.24
23 16 0.36
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGTAATTCTACG
Found at i:14669 original size:20 final size:20
Alignment explanation
Indices: 14644--14686 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14634 TCTAAAGGCC
14644 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
14664 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
14684 CAT
1 CAT
14687 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:17866 original size:57 final size:56
Alignment explanation
Indices: 17731--17896 Score: 217
Period size: 57 Copynumber: 3.0 Consensus size: 56
17721 ACCATACAAC
* * * * * *
17731 CCCGTCACGAACAGTAAGGCCCTGAGCACAAAGCCAAGGAACATGCAAGTATT-TA
1 CCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATTCAA
* * * *
17786 CCCGTCACGAACAGTACGACTCTCAGCACAAAGCCGAGGAGCCTATAAGTATTCAA
1 CCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATTCAA
*
17842 CCCTGTCACGAACAGTAAGGCTCTCAGCACAAAGCTGAGGAACCTACAAGTATTC
1 CCC-GTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATTC
17897 TTCCTCCAAC
Statistics
Matches: 94, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
55 44 0.47
56 4 0.04
57 46 0.49
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.16
Consensus pattern (56 bp):
CCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTACAAGTATTCAA
Found at i:20452 original size:24 final size:24
Alignment explanation
Indices: 20418--20468 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
20408 GGTCAACGCC
* *
20418 GGTCAATGGTCAACGCCGGTCAAT
1 GGTCAACGGTCAACGCAGGTCAAT
20442 GGTCAACGGTCAACGCAGGTCAAT
1 GGTCAACGGTCAACGCAGGTCAAT
20466 GGT
1 GGT
20469 AAATAGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (24 bp):
GGTCAACGGTCAACGCAGGTCAAT
Found at i:20464 original size:17 final size:17
Alignment explanation
Indices: 20407--20449 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
20397 TGGTCAACAG
20407 TGGTCAACGCCGGTCAA
1 TGGTCAACGCCGGTCAA
20424 TGGTCAACGCCGGTCAA
1 TGGTCAACGCCGGTCAA
20441 TGGTCAACG
1 TGGTCAACG
20450 GTCAACGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (17 bp):
TGGTCAACGCCGGTCAA
Found at i:22557 original size:57 final size:57
Alignment explanation
Indices: 22490--22652 Score: 236
Period size: 57 Copynumber: 2.9 Consensus size: 57
22480 TACAACCCTG
* *
22490 TCACAAATAGTAAGGCCCTGAGCACAAAGCCAAGGAACCTGCAAGTATTCAACCCCA
1 TCACAAATAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATTCAACCCCA
* * * **
22547 TCACAGATAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGTAAGTATTCAACCCTG
1 TCACAAATAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATTCAACCCCA
** *
22604 TCACAAACGGTAAGGCTCTCAGCACAAAGCCAAGAAACCTGCAAGTATT
1 TCACAAATAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATT
22653 ATTCCTCTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 93 1.00
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.17
Consensus pattern (57 bp):
TCACAAATAGTAAGGCTCTCAGCACAAAGCCAAGGAACCTGCAAGTATTCAACCCCA
Found at i:27734 original size:60 final size:59
Alignment explanation
Indices: 27625--27747 Score: 140
Period size: 60 Copynumber: 2.1 Consensus size: 59
27615 TCTAGTAAAT
** * * * *
27625 TAATAATTATTAAATAATAATTTAGTATTTTTGTTGTTTATTCAAAAATTAATAAATTAG
1 TAATAATTATTAAATAATAATTTAACATTTTTATTATCTACTCAAAAATTAAT-AATTAG
* * *
27685 TAATAATTATTAATTAATAATTTAACATTTTTATTATCTACT-AGTAAATTAATAATTAT
1 TAATAATTATTAAATAATAATTTAACATTTTTATTATCTACTCA-AAAATTAATAATTAG
27744 TAAT
1 TAAT
27748 TAGATTTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
59 10 0.19
60 43 0.81
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (59 bp):
TAATAATTATTAAATAATAATTTAACATTTTTATTATCTACTCAAAAATTAATAATTAG
Found at i:31207 original size:16 final size:17
Alignment explanation
Indices: 31175--31211 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
31165 TATATTACAT
*
31175 GTGTCATAGATATTAAA
1 GTGTCATAGAAATTAAA
31192 GTGTCAT-GAAATTAAA
1 GTGTCATAGAAATTAAA
31208 GTGT
1 GTGT
31212 ATATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (17 bp):
GTGTCATAGAAATTAAA
Found at i:32523 original size:21 final size:20
Alignment explanation
Indices: 32485--32538 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
32475 TATTTTAAAA
32485 ATTT-AAAAAATAAATTATTAT
1 ATTTAAAAAAAT-AATTATT-T
*
32506 ATTTAAAAAAATATTTATTT
1 ATTTAAAAAAATAATTATTT
*
32526 -TATAAAAAAATAA
1 ATTTAAAAAAATAA
32539 CAAATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.38
20 1 0.03
21 10 0.34
22 7 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTAAAAAAATAATTATTT
Found at i:32937 original size:23 final size:23
Alignment explanation
Indices: 32893--32946 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
32883 TAGATTAAGT
* *
32893 TTAATTTATTTAATATTTTAATC
1 TTAATTTATTTAAAATTATAATC
*
32916 TTAATTT-TTATAAAATTATAATA
1 TTAATTTATT-TAAAATTATAATC
*
32939 ATAATTTA
1 TTAATTTA
32947 AATAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATTTATTTAAAATTATAATC
Found at i:32971 original size:23 final size:23
Alignment explanation
Indices: 32925--32973 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
32915 CTTAATTTTT
*
32925 ATAAAATTATAATAATAATTTAA
1 ATAAAATTATAATAATAATGTAA
*
32948 ATAAATTTAT-ATAATAATAGTAA
1 ATAAAATTATAATAATAAT-GTAA
32971 ATA
1 ATA
32974 TTTCATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATAAAATTATAATAATAATGTAA
Found at i:33536 original size:35 final size:35
Alignment explanation
Indices: 33483--33560 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
33473 ACAACACATT
33483 CATCAATTACATTCTAAACCCCAAATTCCAAAATA
1 CATCAATTACATTCTAAACCCCAAATTCCAAAATA
* * *
33518 CTTCAATTACATTTTAAACCTCAAATTCCAAAATA
1 CATCAATTACATTCTAAACCCCAAATTCCAAAATA
33553 CATCAATT
1 CATCAATT
33561 GCATACCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.31
Consensus pattern (35 bp):
CATCAATTACATTCTAAACCCCAAATTCCAAAATA
Found at i:33578 original size:35 final size:34
Alignment explanation
Indices: 33483--33589 Score: 99
Period size: 35 Copynumber: 3.1 Consensus size: 34
33473 ACAACACATT
* *
33483 CATCAATTACATTCTAAACCCCAAATTCCAAAATA
1 CATCAATTACATACCAAA-CCCAAATTCCAAAATA
* ***
33518 CTTCAATTACATTTTAAACCTCAAATTCCAAAATA
1 CATCAATTACATACCAAACC-CAAATTCCAAAATA
* * *
33553 CATCAATTGCATACCCAACTCCAAATT-CATAATA
1 CATCAATTACATACCAAAC-CCAAATTCCAAAATA
33587 CAT
1 CAT
33590 TCTCAAAATC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
34 11 0.18
35 49 0.80
36 1 0.02
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.29
Consensus pattern (34 bp):
CATCAATTACATACCAAACCCAAATTCCAAAATA
Found at i:34585 original size:35 final size:35
Alignment explanation
Indices: 34539--34618 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
34529 GGGGTTAGGC
*
34539 ATGTAATTGAAGTATTTTAGAATCTAAGGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATCTAAGGTTTAGA
* * * **
34574 ATGTAATTGAAGCATTTTGGATTTTGGGGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATCTAAGGTTTAGA
*
34609 ATATAATTGA
1 ATGTAATTGA
34619 TGAATGTGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.41
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTAGAATCTAAGGTTTAGA
Found at i:36146 original size:44 final size:44
Alignment explanation
Indices: 36056--36337 Score: 236
Period size: 44 Copynumber: 6.5 Consensus size: 44
36046 AGATCTACGC
* * * *
36056 CGCAAAATGTCGATATTTATAGCG--GTATTTTGGAACAAACGC
1 CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGAACAAACGT
*
36098 CGCAAAAGGTCGATATCTATATCGACGTTTTTTGGAACAAACGT
1 CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGAACAAACGT
** * *
36142 CGCAAAAGGTCGAGCTCTTTAGCGACGTTTTTTGGATACAAATGT
1 CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGA-ACAAACGT
* * * *
36187 CGCAAAAGGTTAGATA--TATAGCGGC-ATTTTTGGAATAAACGT
1 CGCAAAAGG-TCGATATCTATAGCGACGTTTTTTGGAACAAACGT
* * * **
36229 AGCAAAAGGTCGAAATCTATAGCGACGTTTTTTAGATACAAACAC
1 CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGA-ACAAACGT
** * * * *
36274 CGCAAAAGG-AAAGATCTATAGCGGCG-TTTTTGGAATAAACGC
1 CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGAACAAACGT
* * * *
36316 CACAAAATGTTGAGATCTATAG
1 CGCAAAAGGTCGATATCTATAG
36338 AGGCATTTTC
Statistics
Matches: 192, Mismatches: 39, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
41 4 0.02
42 48 0.25
43 33 0.17
44 75 0.39
45 29 0.15
46 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (44 bp):
CGCAAAAGGTCGATATCTATAGCGACGTTTTTTGGAACAAACGT
Found at i:36296 original size:131 final size:130
Alignment explanation
Indices: 36073--36355 Score: 320
Period size: 131 Copynumber: 2.2 Consensus size: 130
36063 TGTCGATATT
* * * * * *
36073 TATAGCGGTA-TTTTGGAACAAACGCCGCAAAAGGTCGATATCTATATCGACGTTTTTTGGAACA
1 TATAGCGGCATTTTTGGAATAAACGCAGCAAAAGGTCGAAATCTATAGCGACGTTTTTTAGAACA
** ** * * * * *
36137 AACGTCGCAAAAGGTCGAGCTCTTTAGCGACGTTTTTTGGATACAAATGTCGCAAAAGGTT-AGA
66 AACACCGCAAAAGGTAAAGATCTATAGCGACG-TTTTTGGA-ACAAACGCCACAAAAGGTTGAGA
36201 TA
129 TA
*
36203 TATAGCGGCATTTTTGGAATAAACGTAGCAAAAGGTCGAAATCTATAGCGACGTTTTTTAGATAC
1 TATAGCGGCATTTTTGGAATAAACGCAGCAAAAGGTCGAAATCTATAGCGACGTTTTTTAGA-AC
* * *
36268 AAACACCGCAAAAGG-AAAGATCTATAGCGGCGTTTTTGGAATAAACGCCACAAAATGTTGAGAT
65 AAACACCGCAAAAGGTAAAGATCTATAGCGACGTTTTTGGAACAAACGCCACAAAAGGTTGAGAT
*
36332 C
130 A
* *
36333 TATAGAGGCATTTTCGGAATAAA
1 TATAGCGGCATTTTTGGAATAAA
36356 TGCCACAAAT
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
129 14 0.11
130 42 0.33
131 57 0.45
132 15 0.12
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (130 bp):
TATAGCGGCATTTTTGGAATAAACGCAGCAAAAGGTCGAAATCTATAGCGACGTTTTTTAGAACA
AACACCGCAAAAGGTAAAGATCTATAGCGACGTTTTTGGAACAAACGCCACAAAAGGTTGAGATA
Found at i:36322 original size:87 final size:87
Alignment explanation
Indices: 36052--36337 Score: 274
Period size: 87 Copynumber: 3.3 Consensus size: 87
36042 GTCTAGATCT
* * * * * ** *
36052 ACGCCGCAAAATGTCGATATTTATAGCG--GTATTTTGGA-ACAAACGCCGCAAAAGGTCGATAT
1 ACGCCACAAAAGGTCGAGATCTATAGCGACGTTTTTTGGATACAAACGCCGCAAAAGG-AAAGAT
* * *
36114 CTATATCGACGTTTTTTGGAACAA
65 CTATAGCGGCG-TTTTTGGAATAA
* * * * * * ** *
36138 ACGTCGCAAAAGGTCGAGCTCTTTAGCGACGTTTTTTGGATACAAATGTCGCAAAAGGTTAGATA
1 ACGCCACAAAAGGTCGAGATCTATAGCGACGTTTTTTGGATACAAACGCCGCAAAAGGAAAGATC
*
36203 TATAGCGGCATTTTTGGAATAA
66 TATAGCGGCGTTTTTGGAATAA
* * * *
36225 ACG-TAGCAAAAGGTCGAAATCTATAGCGACGTTTTTTAGATACAAACACCGCAAAAGGAAAGAT
1 ACGCCA-CAAAAGGTCGAGATCTATAGCGACGTTTTTTGGATACAAACGCCGCAAAAGGAAAGAT
36289 CTATAGCGGCGTTTTTGGAATAA
65 CTATAGCGGCGTTTTTGGAATAA
* *
36312 ACGCCACAAAATGTTGAGATCTATAG
1 ACGCCACAAAAGGTCGAGATCTATAG
36338 AGGCATTTTC
Statistics
Matches: 161, Mismatches: 34, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
86 22 0.14
87 104 0.65
88 20 0.12
89 15 0.09
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (87 bp):
ACGCCACAAAAGGTCGAGATCTATAGCGACGTTTTTTGGATACAAACGCCGCAAAAGGAAAGATC
TATAGCGGCGTTTTTGGAATAA
Found at i:36582 original size:21 final size:21
Alignment explanation
Indices: 36542--36583 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36532 ATGACATGAC
* *
36542 AACAACAAACTTTAATTCCAT
1 AACAACAAACTTCAAATCCAT
*
36563 AACAACAATCTTCAAATCCAT
1 AACAACAAACTTCAAATCCAT
36584 TATATTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (21 bp):
AACAACAAACTTCAAATCCAT
Found at i:37555 original size:3 final size:3
Alignment explanation
Indices: 37547--37640 Score: 172
Period size: 3 Copynumber: 31.7 Consensus size: 3
37537 TTTTTACCCA
37547 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
37594 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
37641 AATATATATT
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:39053 original size:13 final size:13
Alignment explanation
Indices: 39037--39082 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
39027 ATATAATAAA
39037 TAAATATTTATTT
1 TAAATATTTATTT
*
39050 TAAATAAATTATTT
1 TAAAT-ATTTATTT
39064 T-AATATTTATTT
1 TAAATATTTATTT
*
39076 TTAATAT
1 TAAATAT
39083 CGAAGGAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:41978 original size:42 final size:42
Alignment explanation
Indices: 41926--42011 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
41916 CATGTCACTT
41926 GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
1 GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
41968 GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
1 GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
42010 GA
1 GA
42012 ACTTAACACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (42 bp):
GATTAAAGAAGTCAGCTTGTACCAAGAGAAGAGAAACTTGAC
Found at i:49586 original size:2 final size:2
Alignment explanation
Indices: 49579--49604 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49569 GAAAAACATG
49579 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
49605 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54203 original size:18 final size:18
Alignment explanation
Indices: 54180--54232 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
54170 ACTATATATT
54180 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
54198 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
54216 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
54233 CCTTAAGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:55099 original size:21 final size:21
Alignment explanation
Indices: 55075--55128 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
55065 TTTGAGAGTG
*
55075 CATCGATATACATTGAAGATA
1 CATCGATACACATTGAAGATA
* *
55096 CATCGATGCACATTGAAGATG
1 CATCGATACACATTGAAGATA
*
55117 CATCGATGCACA
1 CATCGATACACA
55129 CAACCCATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (21 bp):
CATCGATACACATTGAAGATA
Found at i:60362 original size:12 final size:12
Alignment explanation
Indices: 60342--60388 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
60332 TTTACAAACA
60342 AACTCGTTTATG
1 AACTCGTTTATG
** *
60354 AGTTCGTTTATA
1 AACTCGTTTATG
60366 AACTCGTTTATG
1 AACTCGTTTATG
60378 AACTCGTTTAT
1 AACTCGTTTAT
60389 AAGCGTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (12 bp):
AACTCGTTTATG
Found at i:60371 original size:24 final size:24
Alignment explanation
Indices: 60341--60390 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
60331 GTTTACAAAC
**
60341 AAACTCGTTTATGAGTTCGTTTAT
1 AAACTCGTTTATGAACTCGTTTAT
60365 AAACTCGTTTATGAACTCGTTTAT
1 AAACTCGTTTATGAACTCGTTTAT
60389 AA
1 AA
60391 GCGTTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (24 bp):
AAACTCGTTTATGAACTCGTTTAT
Found at i:60907 original size:2 final size:2
Alignment explanation
Indices: 60900--60951 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
60890 ATTATGGCAG
60900 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
60942 AT AT AT AT AT
1 AT AT AT AT AT
60952 TGGTGCCTGT
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:62993 original size:207 final size:207
Alignment explanation
Indices: 62628--63045 Score: 786
Period size: 207 Copynumber: 2.0 Consensus size: 207
62618 ATGTTGTTTA
62628 TTCTTGTTAATTTATCAAGTCTCTCATCCTAGACAAACTGTATTGTTGCTTGTTTCATGCTTGGA
1 TTCTTGTTAATTTATCAAGTCTCTCATCCTAGACAAACTGTATTGTTGCTTGTTTCATGCTTGGA
62693 CCTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGTCCCTCG
66 CCTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGTCCCTCG
*
62758 ACGAGGTGGTCTACTGAGGTTGTCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATTCC
131 ACGAGGTGGTCTACTGAGGTTATCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATTCC
62823 TCTCACTTCATG
196 TCTCACTTCATG
*
62835 TTCTTGTTAA-TTATCAAGTCTCTCATCCTAGACAAACTTTATTGTCTGCTTGTTTCATGCTTGG
1 TTCTTGTTAATTTATCAAGTCTCTCATCCTAGACAAACTGTATTGT-TGCTTGTTTCATGCTTGG
62899 A-CTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGTCCCCT
65 ACCTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGT-CCCT
62963 CGACGAGGTGGTCTACTGAGGTTATCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATT
129 CGACGAGGTGGTCTACTGAGGTTATCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATT
63028 CCTCTCACTTCATG
194 CCTCTCACTTCATG
63042 TTCT
1 TTCT
63046 AAGCCTAAGA
Statistics
Matches: 207, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
206 92 0.44
207 115 0.56
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (207 bp):
TTCTTGTTAATTTATCAAGTCTCTCATCCTAGACAAACTGTATTGTTGCTTGTTTCATGCTTGGA
CCTCATGGTTGATAGTTTTGAGCCATAGAAAGACTTTGGCCTTTAGCTAATTGATGCGTCCCTCG
ACGAGGTGGTCTACTGAGGTTATCTTTCTGCAGACCGATATTCTGTAACTGGTCTAGCCAATTCC
TCTCACTTCATG
Found at i:64430 original size:23 final size:23
Alignment explanation
Indices: 64404--64457 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
64394 GTTAGTGTTC
64404 GTTCATTT-AGGATTC-TCGAACAT
1 GTTCATTTAAGG-TTCGT-GAACAT
64427 GTTCATTTAAGGTTCGTGAACAT
1 GTTCATTTAAGGTTCGTGAACAT
*
64450 GTTTATTT
1 GTTCATTT
64458 GCAAGCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (23 bp):
GTTCATTTAAGGTTCGTGAACAT
Done.