Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004619.1 Hibiscus syriacus cultivar Beakdansim tig00010336_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: 49181
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:6250 original size:34 final size:34
Alignment explanation
Indices: 6137--6364 Score: 197
Period size: 34 Copynumber: 6.4 Consensus size: 34
6127 TTTCAAAAAT
* *
6137 ATATATAATATATAGTTTTGAGAAA-TTTTTTGAAT
1 ATATATAATATATA-TTTTGA-AAACATTTTTGAAA
* * *
6172 ATATATGATATATAGTTTGGAAAACATTTTTCAAAAAA
1 ATATATAATATATA-TTTTGAAAACATTTTT---GAAA
* *
6210 ATATATAATATATATTTTTAAAACGTTTTTGAAA
1 ATATATAATATATATTTTGAAAACATTTTTGAAA
* ***
6244 ATATATAATATATATTTTTAAAATGGTTTTGAAA
1 ATATATAATATATATTTTGAAAACATTTTTGAAA
* * *
6278 ATATATAATATATATTTTAAAAACATGTTGGAAA
1 ATATATAATATATATTTTGAAAACATTTTTGAAA
* * * *
6312 ACTATATAATATTTGGGTTTTGAAAACATTTTTCAAT
1 A-TATATAATATAT--ATTTTGAAAACATTTTTGAAA
6349 ATATATATATATATAT
1 ATATATA-ATATATAT
6365 ATTATAATAT
Statistics
Matches: 158, Mismatches: 27, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
34 67 0.42
35 36 0.23
36 6 0.04
37 34 0.22
38 15 0.09
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (34 bp):
ATATATAATATATATTTTGAAAACATTTTTGAAA
Found at i:7651 original size:14 final size:14
Alignment explanation
Indices: 7627--7683 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
7617 AAATTTAACA
7627 TTTTTATTTTTTATT
1 TTTTTA-TTTTTATT
7642 TTTTTATTTTAATATT
1 TTTTTATTTT--TATT
* *
7658 TTCTTAATTTTATT
1 TTTTTATTTTTATT
*
7672 TTATTTGTTTTT
1 TT-TTTATTTTT
7684 TTTAAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.29
15 12 0.35
16 12 0.35
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:7657 original size:16 final size:16
Alignment explanation
Indices: 7627--7669 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
7617 AAATTTAACA
*
7627 TTTTTATTTT-TTATT
1 TTTTTATTTTAATATT
7642 TTTTTATTTTAATATT
1 TTTTTATTTTAATATT
*
7658 TTCTTAATTTTA
1 TT-TTTATTTTA
7670 TTTTATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 6 0.25
17 8 0.33
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTAATATT
Found at i:7668 original size:32 final size:32
Alignment explanation
Indices: 7632--7726 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
7622 TAACATTTTT
7632 ATTTTTTATTT-TTTTATTTTAATATTTTCTTA
1 ATTTTTTATTTCTTTT-TTTTAATATTTTCTTA
*
7664 ATTTTATTTTATTTGTTTTTTTTAAAATATTTTCTTA
1 A--TT-TTTTATTTCTTTTTTTT--AATATTTTCTTA
7701 A--TTTTATTTCTTTTCGTTTTAATATT
1 ATTTTTTATTTCTTTT--TTTTAATATT
7727 GTTGTATTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
32 19 0.35
34 6 0.11
35 12 0.22
36 4 0.07
37 13 0.24
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (32 bp):
ATTTTTTATTTCTTTTTTTTAATATTTTCTTA
Found at i:7669 original size:37 final size:38
Alignment explanation
Indices: 7628--7709 Score: 118
Period size: 37 Copynumber: 2.2 Consensus size: 38
7618 AATTTAACAT
7628 TTTTATTTTTTATTT-TTTTATTTT-AATATTTTCTTAA
1 TTTTATTTTTTATTTGTTTT-TTTTAAATATTTTCTTAA
7665 TTTTA--TTTTATTTGTTTTTTTTAAAATATTTTCTTAA
1 TTTTATTTTTTATTTGTTTTTTTT-AAATATTTTCTTAA
7702 TTTTATTT
1 TTTTATTT
7710 CTTTTCGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
35 12 0.30
36 4 0.10
37 23 0.57
39 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.74
Consensus pattern (38 bp):
TTTTATTTTTTATTTGTTTTTTTTAAATATTTTCTTAA
Found at i:13727 original size:33 final size:33
Alignment explanation
Indices: 13674--13737 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
13664 GGAGGCAAAA
*
13674 TTAGAGACTGATGAAAAGAAATGGGAAAACAAT
1 TTAGAGACTGATGAAAAGAAAGGGGAAAACAAT
* ** *
13707 TTAGAGGCTGATGAGGAGAAAGGGGGAAACA
1 TTAGAGACTGATGAAAAGAAAGGGGAAAACA
13738 TGGGGAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.45, C:0.06, G:0.33, T:0.16
Consensus pattern (33 bp):
TTAGAGACTGATGAAAAGAAAGGGGAAAACAAT
Found at i:17346 original size:89 final size:88
Alignment explanation
Indices: 17243--17515 Score: 252
Period size: 89 Copynumber: 3.1 Consensus size: 88
17233 TACAAGAACC
* *
17243 AAAATAGCAAAAACATAAACTTAAAGGACCAAAATAGTACAAACATG-AATTTAAAGGACTAAAA
1 AAAATAG-AAAAACATAAACTTAAAGGACTAAAATAGTA-AAACA-GAAACTTAAAGGACTAAAA
*
17307 TAATAAAAACAAAAACTTAAAGGGCT
63 TAACAAAAACAAAAACTTAAAGGGCT
* * *
17333 AAAA-AGAATAAACAGAAACTTAAAAGG-CTAAAACAGCAAAAACAGAAACTTAAAGGACT-AAA
1 AAAATAGAA-AAACATAAACTT-AAAGGACTAAAATAG-TAAAACAGAAACTTAAAGGACTAAAA
* * * **
17395 CAACAAAAACATAAACCTAAAGGATT
63 TAACAAAAACAAAAACTTAAAGGGCT
* * * *
17421 AAAATAGCAAAA-ATAGATACTTAAAAGACTAAAATAGCTAAAACAGAAAGTTAAAAGACTAAAA
1 AAAATAGAAAAACATA-A-ACTTAAAGGACTAAAATAG-TAAAACAGAAACTTAAAGGACTAAAA
* * *
17485 TAGCAAAAATAGAAACTT-AAGGGACT
63 TAACAAAAACAAAAACTTAAAGGG-CT
17511 AAAAT
1 AAAAT
17516 GGTATTAACA
Statistics
Matches: 148, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
87 2 0.01
88 38 0.26
89 76 0.51
90 32 0.22
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (88 bp):
AAAATAGAAAAACATAAACTTAAAGGACTAAAATAGTAAAACAGAAACTTAAAGGACTAAAATAA
CAAAAACAAAAACTTAAAGGGCT
Found at i:17355 original size:29 final size:30
Alignment explanation
Indices: 17243--17515 Score: 279
Period size: 30 Copynumber: 9.2 Consensus size: 30
17233 TACAAGAACC
* *
17243 AAAATAGCAAAAACATAAACTTAAAGGACC
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
17273 AAAATAGTACAAACATG-AATTTAAAGGACT
1 AAAATAGCAAAAACA-GAAACTTAAAGGACT
** * *
17303 AAAATAATAAAAACAAAAACTTAAAGGGCT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
17333 AAAA-AG-AATAAACAGAAACTTAAAAGG-CT
1 AAAATAGCAA-AAACAGAAACTT-AAAGGACT
*
17362 AAAACAGCAAAAACAGAAACTTAAAGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
17392 AAACA-A-CAAAAACATAAACCTAAAGGATT
1 AAA-ATAGCAAAAACAGAAACTTAAAGGACT
* * *
17421 AAAATAGCAAAAATAGATACTTAAAAGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
17451 AAAATAGCTAAAACAGAAAGTTAAAAGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* *
17481 AAAATAGCAAAAATAGAAACTTAAGGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
17511 AAAAT
1 AAAAT
17516 GGTATTAACA
Statistics
Matches: 203, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.01
29 47 0.23
30 150 0.74
31 3 0.01
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (30 bp):
AAAATAGCAAAAACAGAAACTTAAAGGACT
Found at i:17543 original size:60 final size:60
Alignment explanation
Indices: 17243--17536 Score: 183
Period size: 59 Copynumber: 5.0 Consensus size: 60
17233 TACAAGAACC
* * * * * * *
17243 AAAATAGCAAAAACATAAACTTAAAGGACCAAAATAG-TACAAACATG-AATTTAAAGGACT
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTA-AAACA-GAAAATCAAAAGACT
** * * * * * * * *
17303 AAAATAATAAAAACAAAAACTTAAAGGGCTAAAA-AG-AATAAACAGAAACTTAAAAGGCT
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTA-AAACAGAAAATCAAAAGACT
* * * * * * * *
17362 AAAACAGCAAAAACAGAAACTTAAAGGACTAAACA-A-CAAAAACA-TAAACCTAAAGGATT
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAA-ATAGCTAAAACAGAAAATC-AAAAGACT
* * *
17421 AAAATAGCAAAAATAGATACTTAAAAGACTAAAATAGCTAAAACAGAAAGTTAAAAGACT
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTAAAACAGAAAATCAAAAGACT
** * *
17481 AAAATAGCAAAAATAGAAACTTAAGGGACTAAAAT-GGTATTAACA-AAAATCAAAAG
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTA-AAACAGAAAATCAAAAG
17537 GGCTAAACAT
Statistics
Matches: 186, Mismatches: 40, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
58 4 0.02
59 98 0.53
60 82 0.44
61 2 0.01
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (60 bp):
AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTAAAACAGAAAATCAAAAGACT
Found at i:17832 original size:16 final size:16
Alignment explanation
Indices: 17813--17850 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
17803 CTTAACTATA
17813 AATAACATTAAAGTAC
1 AATAACATTAAAGTAC
*
17829 AATAACATTAAATTAC
1 AATAACATTAAAGTAC
17845 AATAAC
1 AATAAC
17851 CTCATCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (16 bp):
AATAACATTAAAGTAC
Found at i:18731 original size:3 final size:3
Alignment explanation
Indices: 18723--18784 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
18713 AAACAAAATA
*
18723 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18771 AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT
18785 TAAATAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:18791 original size:8 final size:7
Alignment explanation
Indices: 18719--18791 Score: 63
Period size: 6 Copynumber: 11.3 Consensus size: 7
18709 ATGTAAACAA
18719 AATAAAT
1 AATAAAT
18726 AAT-AAT
1 AATAAAT
18732 AAT-AAT
1 AATAAAT
18738 AAT-AAT
1 AATAAAT
*
18744 AGT-AAT
1 AATAAAT
18750 AAT-AAT
1 AATAAAT
18756 AAT-AAT
1 AATAAAT
18762 AAT-AAT
1 AATAAAT
18768 AAT-AAT
1 AATAAAT
18774 AATAATAT
1 AATAA-AT
18782 AATTAAAT
1 AA-TAAAT
18790 AA
1 AA
18792 AAAAAGACCC
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
6 46 0.75
7 4 0.07
8 8 0.13
9 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (7 bp):
AATAAAT
Found at i:19391 original size:133 final size:134
Alignment explanation
Indices: 18964--19455 Score: 423
Period size: 130 Copynumber: 3.7 Consensus size: 134
18954 ATGAAGAGGT
* * * * * **
18964 CTGGTTGTCTAAGAGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTAGATGACACAACT
1 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAACT
* * * * * * * *
19029 CATA---G-TGAAGA-GTTCTGGTCATCTTTAGAAAGGGTGATAACACAGTCCCTACACGATAAG
66 CATACGCGATGAAGACGTTAT-GCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCTATGAG
19089 GACGA
130 GACGA
* * * * ***
19094 CAGGTTATCTAGGGGTGATACGACTCCTACGTGATGATGAGGTTTGGTCGGGGGATGACACGGTT
1 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAACT
* * * ** * * *
19159 CCTATGCGATGAGGACGGCATTCCATCTTTAAGAA---TGATAATACGGTTCCTACG-TGATGAG
66 CATACGCGATGAAGACGTTATGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCT-ATGAG
19220 GACGA
130 GACGA
* * * * * *
19225 CTGGTTATC-AGGGGCGAAACGGCTCCTATGTGATGAGGAGGTGTGGTCGGGGGATGGCACAACT
1 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAACT
* * ** *
19289 CATACGCGATGAAGA-GTTATGGCCATCTTTAGGAAGGGCGATAACATGGTTCAAATGCTATGAG
66 CATACGCGATGAAGACGTTAT-GCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCTATGAG
*
19353 GACAA
130 GACGA
* **
19358 CTGGTTATCTA-GGGTGACACGACTCCTACGTGATGAAGAGGTCTGGTCGGGGGGATGACACAGT
1 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTC-GGGGGATGACACAAC
* * * *
19422 TCCTACGTGATGAGGACGATATGCCATCTTTAGG
65 TCATACGCGATGAAGACGTTATGCCATCTTTAGG
19456 GATAATCGTT
Statistics
Matches: 281, Mismatches: 67, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
129 3 0.01
130 123 0.44
131 32 0.11
133 63 0.22
134 54 0.19
135 6 0.02
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (134 bp):
CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAACT
CATACGCGATGAAGACGTTATGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCTATGAGG
ACGA
Found at i:19568 original size:34 final size:35
Alignment explanation
Indices: 19529--19596 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
19519 ACAAAATTCA
*
19529 TTTCAAGGGAAAC-GACTCAAAGATAGGTATTTTG
1 TTTCAAGGGAAACAAACTCAAAGATAGGTATTTTG
* *
19563 TTTCAATGGAAACAAACTCAAAGATAGGTGTTTT
1 TTTCAAGGGAAACAAACTCAAAGATAGGTATTTT
19597 CAAAAGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (35 bp):
TTTCAAGGGAAACAAACTCAAAGATAGGTATTTTG
Found at i:19696 original size:65 final size:64
Alignment explanation
Indices: 19559--19736 Score: 230
Period size: 65 Copynumber: 2.7 Consensus size: 64
19549 AGATAGGTAT
* * * * *
19559 TTTGTTTCAATGGAAACAAACTCAAAGATAGGTGTTTTCAAAAGAAACTGTCTCGAGAGACAAAA
1 TTTGTTTCAAAGGAAACAAACTCAAAGAT--TTTTTTTCAAAAGAAACTGACTCAAGAGACAAAA
*
19624 T
64 C
* *
19625 TTTGTTTTAAAGGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGACTCAAGAGACAAAAC
1 TTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTT-TCAAAAGAAACTGACTCAAGAGACAAAAC
* *
19690 TTTGTTTCCAATGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAAC
1 TTTGTTTCAAAGGAAACAAACTCAAAGATTTTT-TTTCAAAAGAAAC
19737 AACTCAAAGA
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
64 4 0.04
65 65 0.66
66 29 0.30
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (64 bp):
TTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTTCAAAAGAAACTGACTCAAGAGACAAAAC
Found at i:19750 original size:29 final size:29
Alignment explanation
Indices: 19690--19787 Score: 115
Period size: 32 Copynumber: 3.2 Consensus size: 29
19680 GAGACAAAAC
* *
19690 TTTGTTTCCAATGAAACAAACTCAAAGATT
1 TTTGTTTCAAAAGAAAC-AACTCAAAGATT
19720 TTTGTTTCAAAAGAAACAACTCAAAGATTTTT
1 TTTGTTTCAAAAGAAACAACTCAAAGA---TT
* *
19752 TTTATTTCAAAAGAAACGACTCAAAGATT
1 TTTGTTTCAAAAGAAACAACTCAAAGATT
*
19781 TTGGTTT
1 TTTGTTT
19788 GTTTCCAGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
29 17 0.29
30 15 0.25
32 27 0.46
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAACTCAAAGATT
Found at i:19907 original size:34 final size:36
Alignment explanation
Indices: 19812--19911 Score: 107
Period size: 34 Copynumber: 2.8 Consensus size: 36
19802 AAATTCATAA
* * *
19812 TTTG-GAAAATTGTCTTGAGTGAGACAACATTTTGT
1 TTTGAGAAAATTGTCTTAAGCGAGACAACAATTTGT
* *
19847 TTTGAGAGAAATTATCTCAAGCGAGACAA-AATTTGT
1 TTTGAGA-AAATTGTCTTAAGCGAGACAACAATTTGT
* *
19883 TTT-AGAAAAATGTCTTTAGCGAGACAACA
1 TTTGAGAAAATTGTCTTAAGCGAGACAACA
19912 TCAAAGGATA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
34 17 0.32
35 8 0.15
36 11 0.21
37 17 0.32
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (36 bp):
TTTGAGAAAATTGTCTTAAGCGAGACAACAATTTGT
Found at i:21535 original size:2 final size:2
Alignment explanation
Indices: 21528--21593 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
21518 GTATACATAC
21528 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
21570 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
21594 TGAGTAAATG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22034 original size:21 final size:22
Alignment explanation
Indices: 21984--22036 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
21974 AATTTCCAGA
* *
21984 ATGCTACAGGGGTATCGATACCC
1 ATGCTACA-GTGTACCGATACCC
*
22007 A-GTTACAGTGTACCGATA-CC
1 ATGCTACAGTGTACCGATACCC
22027 ATGCTACAGT
1 ATGCTACAGT
22037 AATTTTGGCC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 16 0.64
22 5 0.20
23 1 0.04
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
ATGCTACAGTGTACCGATACCC
Found at i:27999 original size:30 final size:30
Alignment explanation
Indices: 27968--28238 Score: 221
Period size: 30 Copynumber: 9.2 Consensus size: 30
27958 TATAATAACC
* * *
27968 AAAATAGCAAAAACATAAACTCAAAGGACC
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * * *
27998 AAAATAGTATAAACAGGAATTTAAAGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
** *
28028 AAAATAATAAAAATAGAAACTTAAAGGGA-T
1 AAAATAGCAAAAACAGAAACTTAAA-GGACT
* * *
28058 AAAACA-CATAAACAAAAACTTAAAAGG-CT
1 AAAATAGCAAAAACAGAAACTT-AAAGGACT
* * *
28087 AAAACAAC-AAAACAGAAACTTAAA--AAT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * * *
28114 TAAATAGCAAAAACAAAAACCTAAAGGATT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
28144 AAAATAGCAAAAACATATACTTAAAAGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
28174 AAAATAGCTAAAACAGAAAGTTAAAAGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
28204 AAAATAGCAAAAAAATAAACTTAAGGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
28234 AAAAT
1 AAAAT
28239 GATATTAACA
Statistics
Matches: 191, Mismatches: 42, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
27 6 0.03
28 17 0.09
29 31 0.16
30 134 0.70
31 3 0.02
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (30 bp):
AAAATAGCAAAAACAGAAACTTAAAGGACT
Found at i:28089 original size:29 final size:29
Alignment explanation
Indices: 28044--28111 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
28034 ATAAAAATAG
*
28044 AAACTTAAAGGGATAAAAC-ACATAAACAA
1 AAACTTAAAAGGATAAAACAACA-AAACAA
* *
28073 AAACTTAAAAGGCTAAAACAACAAAACAG
1 AAACTTAAAAGGATAAAACAACAAAACAA
28102 AAACTTAAAA
1 AAACTTAAAA
28112 ATTAAATAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 32 0.91
30 3 0.09
ACGTcount: A:0.63, C:0.15, G:0.09, T:0.13
Consensus pattern (29 bp):
AAACTTAAAAGGATAAAACAACAAAACAA
Found at i:29219 original size:7 final size:7
Alignment explanation
Indices: 29157--29215 Score: 100
Period size: 7 Copynumber: 8.4 Consensus size: 7
29147 TACTCCCTAT
29157 TTCCCTC
1 TTCCCTC
29164 TTCCCTC
1 TTCCCTC
29171 TTCCCTC
1 TTCCCTC
29178 TTCCCTC
1 TTCCCTC
29185 TTCCCTC
1 TTCCCTC
29192 TTCCCTC
1 TTCCCTC
*
29199 TTCTCTC
1 TTCCCTC
*
29206 TTCTCTC
1 TTCCCTC
29213 TTC
1 TTC
29216 TCTCATCTGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (7 bp):
TTCCCTC
Found at i:37044 original size:20 final size:20
Alignment explanation
Indices: 37008--37045 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36998 CTTGAACATC
*
37008 GACGAAACCAATATTTCGCA
1 GACGAAACAAATATTTCGCA
37028 GACGAAATCAAAT-TTTCG
1 GACGAAA-CAAATATTTCG
37046 GACCGTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (20 bp):
GACGAAACAAATATTTCGCA
Found at i:45686 original size:3 final size:3
Alignment explanation
Indices: 45678--45771 Score: 188
Period size: 3 Copynumber: 31.3 Consensus size: 3
45668 GGCTTAATAC
45678 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
45726 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45772 TGTTTCAAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47344 original size:24 final size:26
Alignment explanation
Indices: 47294--47346 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
47284 TGTCCGGGTT
* *
47294 TTTTATATATATTATTATTATCGTTA
1 TTTTATATATATTATTATTAGCATTA
*
47320 TTTTA-ATA-ATTATTTTTAGCATTA
1 TTTTATATATATTATTATTAGCATTA
47344 TTT
1 TTT
47347 ATTATTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.67
25 3 0.12
26 5 0.21
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTTATATATATTATTATTAGCATTA
Found at i:47984 original size:18 final size:18
Alignment explanation
Indices: 47944--47987 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 18
47934 CAAGAAAAGA
47944 GGTATTGATTCCTTAGCTT
1 GGTA-TGATTCCTTAGCTT
47963 -GTATGATTCCTTAGCTT
1 GGTATGATTCCTTAGCTT
47980 GGTATGAT
1 GGTATGAT
47988 ATATGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (18 bp):
GGTATGATTCCTTAGCTT
Done.