Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000834.1 Hibiscus syriacus cultivar Beakdansim tig00001612_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: 64004
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3750 original size:19 final size:19
Alignment explanation
Indices: 3733--3791 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
3723 TGAAAAGATT
3733 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
** *
3753 TAATAAATAAAAGGGAAAA
1 TAATAAATAAAATAGATAA
* *
3772 TAATAAA-ATAATAAATAA
1 TAATAAATAAAATAGATAA
3790 TA
1 TA
3792 GTAGTAAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
18 8 0.26
19 19 0.61
20 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:3806 original size:27 final size:26
Alignment explanation
Indices: 3734--3807 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 26
3724 GAAAAGATTT
*
3734 AATAAAA--TAAAATAGATAATAATA
1 AATAAAAGGTAAAATAGAAAATAATA
* *
3758 AATAAAAGGGAAAATAATAAAATAATA
1 AATAAAAGGTAAAAT-AGAAAATAATA
* *
3785 AATAATAGTAGTAAAATAAAAAA
1 AATAAAAG--GTAAAATAGAAAA
3808 GGGTTTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 7 0.18
26 5 0.13
27 16 0.41
28 5 0.13
29 6 0.15
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (26 bp):
AATAAAAGGTAAAATAGAAAATAATA
Found at i:3866 original size:17 final size:18
Alignment explanation
Indices: 3830--3871 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
3820 GTTACTTTTA
3830 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
3848 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
3865 AAATAAA
1 AAATAAA
3872 TAATTGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:4376 original size:11 final size:12
Alignment explanation
Indices: 4362--4390 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4352 GAAGATATGT
4362 AGAAAA-TAGAG
1 AGAAAACTAGAG
4373 AGAAAACTAGAG
1 AGAAAACTAGAG
4385 AGAAAA
1 AGAAAA
4391 AGAAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.66, C:0.03, G:0.24, T:0.07
Consensus pattern (12 bp):
AGAAAACTAGAG
Found at i:4608 original size:44 final size:43
Alignment explanation
Indices: 4554--4686 Score: 128
Period size: 44 Copynumber: 3.3 Consensus size: 43
4544 ATATAAAAAT
4554 AATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAA
1 AATA-CCTAAAACTTAATTAAAATACTAAAA-CTATTTAAACTAA
* *
4599 AATACCTAAAAC-AAAGATAAAATA-TAAAA--A--T-AA-T--
1 AATACCTAAAACTTAA-TTAAAATACTAAAACTATTTAAACTAA
4633 -AT-CCTAAAACTTAATTAAAATACTAAAATCTATTTAAACTAA
1 AATACCTAAAACTTAATTAAAATACTAAAA-CTATTTAAACTAA
4675 AATACCTAAAAC
1 AATACCTAAAAC
4687 AAAGATAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 29
0.68 0.04 0.28
Matches are distributed among these distances:
32 15 0.21
33 9 0.13
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 9 0.13
44 23 0.33
45 4 0.06
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.28
Consensus pattern (43 bp):
AATACCTAAAACTTAATTAAAATACTAAAACTATTTAAACTAA
Found at i:4641 original size:76 final size:75
Alignment explanation
Indices: 4494--4701 Score: 348
Period size: 76 Copynumber: 2.8 Consensus size: 75
4484 ATCTTAAATC
* * *
4494 TAATTAAAACACTTAAAATTATTTAAACTAAACTACCT-AAA-AAAGATAAAATATAAAAATAAT
1 TAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
4557 ATCCTAAAACT
65 ATCCTAAAACT
4568 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
4633 ATCCTAAAACT
65 ATCCTAAAACT
4644 TAATTAAAATACTAAAATCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAATTAAAATACTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
4702 TATTTAAAAT
Statistics
Matches: 127, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
73 5 0.04
74 29 0.23
75 3 0.02
76 90 0.71
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.27
Consensus pattern (75 bp):
TAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATA
TCCTAAAACT
Found at i:6696 original size:36 final size:36
Alignment explanation
Indices: 6648--6717 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
6638 CAAAGGTTTA
*
6648 TGTTTCATGAGAAACTGTCTCAAGCGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATT
*
6684 TGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAA
6718 CCTTTTTAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATT
Found at i:9666 original size:20 final size:20
Alignment explanation
Indices: 9638--9706 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
9628 ATCCATTTTC
*
9638 TTTCTTTCTTTCTTTTTCTCT
1 TTTC-TTCTTTCTTTCTCTCT
*
9659 TTTCTTCTTTTCTCTTCGCTCT
1 TTTCTTC-TTTCT-TTCTCTCT
*
9681 TTT-TTTTTTCTTTGCTCTCT
1 TTTCTTCTTTCTTT-CTCTCT
9701 TTTCTT
1 TTTCTT
9707 TTCATTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.05
20 16 0.40
21 13 0.32
22 9 0.22
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTCTTCTTTCTTTCTCTCT
Found at i:9692 original size:18 final size:19
Alignment explanation
Indices: 9661--9709 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
9651 TTTTCTCTTT
* *
9661 TCTTCTTTTCTCTTCGCTC
1 TCTTTTTTTTTCTTCGCTC
*
9680 T-TTTTTTTTTCTTTGCTC
1 TCTTTTTTTTTCTTCGCTC
*
9698 TCTTTTCTTTTC
1 TCTTTTTTTTTC
9710 ATTTTTCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.00, C:0.27, G:0.04, T:0.69
Consensus pattern (19 bp):
TCTTTTTTTTTCTTCGCTC
Found at i:12657 original size:27 final size:28
Alignment explanation
Indices: 12627--12681 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
12617 GTTTAAAAAT
* *
12627 AATTATGATTTATTTTGAA-AAATTGAC
1 AATTATGAATTAATTTGAATAAATTGAC
*
12654 AATTTTGAATTAATTTGAATTAAATTGA
1 AATTATGAATTAATTTGAA-TAAATTGA
12682 ATGAGATTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.70
29 7 0.30
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (28 bp):
AATTATGAATTAATTTGAATAAATTGAC
Found at i:13525 original size:15 final size:15
Alignment explanation
Indices: 13486--13529 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
13476 AATCAATAAC
13486 AATGAGT-TAAACAAT
1 AATGAGTCT-AACAAT
13501 AAT-A--CTAACAAT
1 AATGAGTCTAACAAT
13513 AATGAGTCTAACAAT
1 AATGAGTCTAACAAT
13528 AA
1 AA
13530 AAAATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 9 0.36
13 2 0.08
14 1 0.04
15 13 0.52
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (15 bp):
AATGAGTCTAACAAT
Found at i:14529 original size:23 final size:23
Alignment explanation
Indices: 14489--14534 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
14479 ACGAGCTAAG
14489 TCTTTTCTATTTTCATTTTTTTC
1 TCTTTTCTATTTTCATTTTTTTC
*
14512 TCTTTTCGTCTTTT-ATTTTTTTC
1 TCTTTTC-TATTTTCATTTTTTTC
14535 CTTCTCTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (23 bp):
TCTTTTCTATTTTCATTTTTTTC
Found at i:17199 original size:12 final size:11
Alignment explanation
Indices: 17152--17211 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
17142 GGTCTAAAAA
17152 TTATAATT-AT
1 TTATAATTAAT
17162 TTA-AATTAAATT
1 TTATAATT-AA-T
* *
17174 TTTTATTTAAT
1 TTATAATTAAT
17185 TTATAATTAAT
1 TTATAATTAAT
17196 TT-TAATT-AT
1 TTATAATTAAT
17205 TTATAAT
1 TTATAAT
17212 AAAAATAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 8 0.20
10 12 0.29
11 13 0.32
12 5 0.12
13 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTATAATTAAT
Found at i:17348 original size:17 final size:18
Alignment explanation
Indices: 17321--17355 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17311 TTATAAACAA
*
17321 ATTTGAAAATTTATAAAT
1 ATTTGAAAATTCATAAAT
17339 ATTT-AAAATTCATAAAT
1 ATTTGAAAATTCATAAAT
17356 TAAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTTGAAAATTCATAAAT
Found at i:17875 original size:15 final size:17
Alignment explanation
Indices: 17855--17887 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
17845 TGATTTTTTT
17855 TTAAATT-CAAG-TAGA
1 TTAAATTACAAGATAGA
17870 TTAAATTACAAGATAGA
1 TTAAATTACAAGATAGA
17887 T
1 T
17888 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
TTAAATTACAAGATAGA
Found at i:19346 original size:15 final size:17
Alignment explanation
Indices: 19326--19357 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
19316 CATAATATAA
19326 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
19341 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
19358 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:22271 original size:42 final size:41
Alignment explanation
Indices: 22212--22291 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 41
22202 ATATGTTATG
*
22212 CTATTATACCTTTGCTTACTTGTTTTCTCTTTAAACACAGTA
1 CTATTATACCTTTGCTTACTT-TTATCTCTTTAAACACAGTA
22254 CTATTATACCTTTGCTTACTTTTATCTCTTTAAACACA
1 CTATTATACCTTTGCTTACTTTTATCTCTTTAAACACA
22292 TAATAACTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 16 0.43
42 21 0.57
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.47
Consensus pattern (41 bp):
CTATTATACCTTTGCTTACTTTTATCTCTTTAAACACAGTA
Found at i:24739 original size:20 final size:20
Alignment explanation
Indices: 24714--24752 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
24704 ACATCTAAAA
24714 TTAATAACA-ATCTTTAATTT
1 TTAATAACACAT-TTTAATTT
*
24734 TTAATATCACATTTTAATT
1 TTAATAACACATTTTAATT
24753 AAATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATAACACATTTTAATTT
Found at i:25295 original size:2 final size:2
Alignment explanation
Indices: 25288--25312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25278 TTGCAGGTCA
25288 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
25313 GCGCTATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28765 original size:28 final size:26
Alignment explanation
Indices: 28712--28765 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
28702 GATACCAGAG
*
28712 ATAAAAAAACAAAGATCAGAATCCAT
1 ATAAAAAAACAAAGATCAGAAACCAT
* *
28738 ATAACAAAAACCAGAGATCATAAACCAT
1 ATAA-AAAAA-CAAAGATCAGAAACCAT
28766 GTTTTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.17
27 5 0.22
28 14 0.61
ACGTcount: A:0.59, C:0.19, G:0.07, T:0.15
Consensus pattern (26 bp):
ATAAAAAAACAAAGATCAGAAACCAT
Found at i:37806 original size:29 final size:29
Alignment explanation
Indices: 37774--37848 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
37764 TTTAAAATAA
*
37774 TTACCGGAATAGCACCAAAACCGAATTAT
1 TTACCAGAATAGCACCAAAACCGAATTAT
*
37803 TTACCAGAATATCACCAAAACCGAATTAT
1 TTACCAGAATAGCACCAAAACCGAATTAT
37832 TTACCAGAATAGCACCA
1 TTACCAGAATAGCACCA
37849 GTCAACGGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAACCGAATTAT
Found at i:45154 original size:29 final size:29
Alignment explanation
Indices: 45117--45190 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
45107 TTTAAAATAA
45117 TTACCAGAATAGCACCAAAACCGAATTAT
1 TTACCAGAATAGCACCAAAACCGAATTAT
45146 TTACCAGAATAGCACCAAAACCGAATTAT
1 TTACCAGAATAGCACCAAAACCGAATTAT
45175 TTACCAGAATAGCACC
1 TTACCAGAATAGCACC
45191 GGTCAACGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAACCGAATTAT
Found at i:45209 original size:13 final size:13
Alignment explanation
Indices: 45191--45220 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
45181 GAATAGCACC
45191 GGTCAACGGGTCG
1 GGTCAACGGGTCG
45204 GGTCAACGGGTCG
1 GGTCAACGGGTCG
45217 GGTC
1 GGTC
45221 GTGACCGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:50867 original size:14 final size:14
Alignment explanation
Indices: 50810--50869 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
50800 AGTATTAGAT
50810 ACCAGAGATA-AAAA
1 ACCAGAGA-ACAAAA
* *
50824 ACCATAGAACATAA
1 ACCAGAGAACAAAA
* * *
50838 TCCAGATAACAGAA
1 ACCAGAGAACAAAA
*
50852 ACCAGAGATCAAAA
1 ACCAGAGAACAAAA
50866 ACCA
1 ACCA
50870 TGTTTTTATT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
13 1 0.03
14 34 0.97
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.10
Consensus pattern (14 bp):
ACCAGAGAACAAAA
Found at i:52207 original size:14 final size:14
Alignment explanation
Indices: 52188--52221 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
52178 TTGACCCAGT
52188 TTTGACCCGAACCG
1 TTTGACCCGAACCG
*
52202 TTTGACCCGACCCG
1 TTTGACCCGAACCG
52216 -TTGACC
1 TTTGACC
52222 TGACTCGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.18, C:0.38, G:0.21, T:0.24
Consensus pattern (14 bp):
TTTGACCCGAACCG
Found at i:52221 original size:13 final size:13
Alignment explanation
Indices: 52189--52232 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
52179 TGACCCAGTT
*
52189 TTGACCCGAACCG
1 TTGACCCGACCCG
52202 TTTGACCCGACCCG
1 -TTGACCCGACCCG
* *
52216 TTGACCTGACTCG
1 TTGACCCGACCCG
52229 TTGA
1 TTGA
52233 TTGTTGACCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.18, C:0.34, G:0.23, T:0.25
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:54497 original size:12 final size:12
Alignment explanation
Indices: 54482--54551 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
54472 GATACATAAC
54482 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
54494 CTGATTTCTGAT
1 CTGAATTCTGTT
54506 CTTG-ATTCTGTT
1 C-TGAATTCTGTT
* *
54518 ATG-ATATCTGAT
1 CTGAAT-TCTGTT
54530 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
54542 TTGATTTCTG
1 CTGAATTCTG
54552 ATATCTCCGT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
11 4 0.09
12 37 0.82
13 4 0.09
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:54513 original size:24 final size:24
Alignment explanation
Indices: 54482--54553 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
54472 GATACATAAC
*
54482 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
*
54506 CTTG-ATTCTGTTATGATATCTGAT
1 C-TGAATTCTGTTATGATTTCTGAT
*
54530 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
54554 ATCTCCGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.05
24 38 0.90
25 2 0.05
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:54550 original size:48 final size:49
Alignment explanation
Indices: 54445--54553 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 49
54435 AAATATTTTA
* *
54445 TCTGATTTCCGA-CTTGAATTCTGTTCTGATACATAACCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATACATAACCTGAATTCTGT
* *
54493 TCTGATTTCTGATCTTG-ATTCTGTTATGATATC-TGATCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATA-CATAACCTGAATTCTGT
*
54541 TTTGATTTCTGAT
1 TCTGATTTCTGAT
54554 ATCTCCGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 49 0.91
49 5 0.09
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.48
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTGTTATGATACATAACCTGAATTCTGT
Found at i:54868 original size:20 final size:20
Alignment explanation
Indices: 54843--54882 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
54833 TCCTCTTCTC
54843 TTCCCGTAAGCTCCATGGCA
1 TTCCCGTAAGCTCCATGGCA
*
54863 TTCCCGTAAGCTCTATGGCA
1 TTCCCGTAAGCTCCATGGCA
54883 AAGGTAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.28
Consensus pattern (20 bp):
TTCCCGTAAGCTCCATGGCA
Found at i:55509 original size:65 final size:64
Alignment explanation
Indices: 55369--55531 Score: 188
Period size: 65 Copynumber: 2.5 Consensus size: 64
55359 AATTGTTCAG
* * * * *
55369 AGTGTATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAGTT
1 AGTGTATCGATGCATAGGAAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGAAATT
* *
55433 AGTGCATCGATGCATTAGG-AGTGCATCGATGCATCCCCCTT-AAAATGAAAACATCGAAGGTAA
1 AGTGTATCGATGCA-TAGGAAGTGCATCGATGCA--CCCATTAAAAATGAAAACATCGAAGG-AA
55496 ATT
62 ATT
* *
55499 -GTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 AGTGTATCGATGCATAGGAAGTGCATCGATGCAC
55532 ATGTTAAAGA
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 46 0.54
66 8 0.09
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (64 bp):
AGTGTATCGATGCATAGGAAGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGAAATT
Found at i:55564 original size:20 final size:22
Alignment explanation
Indices: 55519--55576 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
55509 GCATGGGTAG
55519 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
55543 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
55563 TGCATCGATGCACT
1 TGCATCGATGCACT
55577 TCAAGGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:56296 original size:25 final size:27
Alignment explanation
Indices: 56255--56306 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
56245 GCTATGAGCT
*
56255 TATATGAACATGTGAT-A-TGAAAATG
1 TATATGAACATGAGATAAGTGAAAATG
56280 TATAGTGAA-ATGAGATAAGTGAAAATG
1 TATA-TGAACATGAGATAAGTGAAAATG
56307 CCCATGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.43
26 5 0.22
27 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.29
Consensus pattern (27 bp):
TATATGAACATGAGATAAGTGAAAATG
Done.