Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006024.1 Hibiscus syriacus cultivar Beakdansim tig00014214_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: 91735
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:292 original size:28 final size:28
Alignment explanation
Indices: 246--305 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
236 GTACCTAAGA
* * *
246 TATTTTCTGGTCAAAATAGTTACCCAAAG
1 TATTTTATGGTCAAAATAGATA-CCAAAC
275 TATTTTAT-GTCAAAATAGATACCAAAC
1 TATTTTATGGTCAAAATAGATACCAAAC
302 TATT
1 TATT
306 CAATCTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 9 0.32
28 12 0.43
29 7 0.25
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (28 bp):
TATTTTATGGTCAAAATAGATACCAAAC
Found at i:488 original size:28 final size:26
Alignment explanation
Indices: 412--490 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 26
402 ATTTTGACCC
* *
412 AAAAAATGCTTTTAGGTACGTATTTTG
1 AAAAAATAC-TTTAGGTACTTATTTTG
439 AAAAATTATAACTTTAGGTACTTATTTTG
1 AAAAA--AT-ACTTTAGGTACTTATTTTG
468 ATTAAAAATACTTTAGGTACTTA
1 A--AAAAATACTTTAGGTACTTA
491 AACAAAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
27 5 0.11
28 14 0.31
29 21 0.47
30 1 0.02
31 4 0.09
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (26 bp):
AAAAAATACTTTAGGTACTTATTTTG
Found at i:1831 original size:16 final size:15
Alignment explanation
Indices: 1812--1860 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
1802 AAAAAATATC
1812 AAATAATAAAAATAAA
1 AAATAAT-AAAATAAA
*
1828 AAATAGTAAAATAAA
1 AAATAATAAAATAAA
1843 AACA-ACATAAAATAAA
1 AA-ATA-ATAAAATAAA
1859 AA
1 AA
1861 TAAGATAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (15 bp):
AAATAATAAAATAAA
Found at i:1868 original size:16 final size:15
Alignment explanation
Indices: 1820--1869 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
1810 TCAAATAATA
1820 AAAATAAAAAATAG-T
1 AAAATAAAAAA-AGAT
*
1835 AAAATAAAAACAACAT
1 AAAATAAAAA-AAGAT
1851 AAAATAAAAATAAGAT
1 AAAATAAAAA-AAGAT
1867 AAA
1 AAA
1870 GAGAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (15 bp):
AAAATAAAAAAAGAT
Found at i:1996 original size:24 final size:24
Alignment explanation
Indices: 1951--1996 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1941 GGGACTTAAA
* * **
1951 TAAATTAAATTAAAATTCAAAAGC
1 TAAATCAAAATAAAATGAAAAAGC
1975 TAAATCAAAATAAAATGAAAAA
1 TAAATCAAAATAAAATGAAAAA
1997 TAAAGAGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (24 bp):
TAAATCAAAATAAAATGAAAAAGC
Found at i:3580 original size:38 final size:39
Alignment explanation
Indices: 3529--3616 Score: 133
Period size: 39 Copynumber: 2.3 Consensus size: 39
3519 AAGAAAAATA
* *
3529 ATCTCAAGTGAGAT-AAATATTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATATTATGTTTCGAGTAAAACT
* *
3567 ATCTCAAGCGAGATAAAATCTTTTGTTTCGAGTAAAACT
1 ATCTCAAGCGAGATAAAATATTATGTTTCGAGTAAAACT
3606 ATCTCAAGCGA
1 ATCTCAAGCGA
3617 TAAGTTGATC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 13 0.29
39 32 0.71
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (39 bp):
ATCTCAAGCGAGATAAAATATTATGTTTCGAGTAAAACT
Found at i:3870 original size:136 final size:136
Alignment explanation
Indices: 3624--3889 Score: 399
Period size: 136 Copynumber: 2.0 Consensus size: 136
3614 CGATAAGTTG
** * * ** *
3624 ATCCCTCAAGTGAGGCATTGCTGATTCTAAATGTTCTGAATCGAGCGATAGGTTGAACAAGCTCT
1 ATCCCTCAAGCAAGGCATAGCTGATTCAAAATGACCTGAATCGAGCGATAGGTCGAACAAGCTCT
*
3689 TCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTATCCTCATTATGAACTCTCCATTTGAA
66 TCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAATTATCCTCATTATGAACTCTCCATTTGAA
3754 GTGTTA
131 GTGTTA
*
3760 ATCCCTCAAGCAAGGCATAGCTGATTCAAAAT-ACCGTGAATCGAGTGATAGGTCGAACAAGCTC
1 ATCCCTCAAGCAAGGCATAGCTGATTCAAAATGACC-TGAATCGAGCGATAGGTCGAACAAGCTC
* ** *
3824 TTCTCATTATGAACTTCTTCTCCCTCTTTCAGATGTGTTATTCTCATTATGAACTCTCCATTTGA
65 TTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAATTATCCTCATTATGAACTCTCCATTTGA
3889 A
130 A
3890 AATGTTGAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
135 1 0.01
136 115 0.99
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (136 bp):
ATCCCTCAAGCAAGGCATAGCTGATTCAAAATGACCTGAATCGAGCGATAGGTCGAACAAGCTCT
TCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAATTATCCTCATTATGAACTCTCCATTTGAA
GTGTTA
Found at i:4217 original size:110 final size:108
Alignment explanation
Indices: 4072--4495 Score: 519
Period size: 110 Copynumber: 3.8 Consensus size: 108
4062 TTTCAGTTAT
* * *
4072 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTTGAAATAATCATCAAG
1 CATCAAGAAA-CCCTAAAAATTAGGCTTAGCTTCTTTAAAAAATTC-ATTGAAATCATCATCAAG
* * *
4137 AAACCCCTCAAAATCAAGCTTTGTTTCTAAAAACCCATTTGAAAA
64 AAACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAAAA
* *
4182 CATCAAGAAACCCATAAAAATTAGGCTTAGTTTCTTTTAAAAATTCATTGAAATCATCATCAAGA
1 CATCAAGAAACCC-TAAAAATTAGGCTTAGCTTCTTTAAAAAATTCATTGAAATCATCATCAAGA
* * *
4247 AACCCCTGAATATCAAGCTTAGTTTCTTAAAAAATTCTTTTGAAAA
65 AACCCCTGAAAATCAAGCTTAGTTTC-T-AAAAACTCATTTGAAAA
* * * * * *
4293 CATAAAAAAACACCT-AAAATTAGGCTTAGCTTCTCTGAAAAAATTCTTTAGAAATGATCTTCAA
1 CATCAAGAAAC-CCTAAAAATTAGGCTTAGCTTCT-TTAAAAAATTCATT-GAAATCATCATCAA
* * *
4357 GAAAGCCCTGAAAATTAAGCTTAATTTCTAAAAACTCATTTGAAAA
63 GAAACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAAAA
* * *
4403 CATCAAGAAAACTCTAAAAAATAGGCTTAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAA
1 CATCAAG-AAACCCTAAAAATTAGGCTTAGCTTC-TTTAAAAAATTCATTG-AAATCATCATCAA
*
4468 G-AACCTCTGAAAATCAAGCTTAGTTTCT
63 GAAACCCCTGAAAATCAAGCTTAGTTTCT
4496 TTAAAAAATT
Statistics
Matches: 266, Mismatches: 38, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
109 43 0.16
110 104 0.39
111 80 0.30
112 39 0.15
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (108 bp):
CATCAAGAAACCCTAAAAATTAGGCTTAGCTTCTTTAAAAAATTCATTGAAATCATCATCAAGAA
ACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAAAA
Found at i:4400 original size:221 final size:224
Alignment explanation
Indices: 4079--4516 Score: 663
Period size: 221 Copynumber: 2.0 Consensus size: 224
4069 TATCATCAAG
* *
4079 AAACCCCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTTGAAATAATCATCAAGAAACCCC
1 AAACACCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTAGAAATAATCATCAAGAAACCCC
** *
4144 TCAAAATCAAGCTTTGTTTCTAAAAACCCATTTGAAAACATCAAG-AAACCCATAAAAATTAGGC
66 TCAAAATCAAGCTTAATTTCTAAAAACCCATTTGAAAACATCAAGAAAACCC-TAAAAAATAGGC
* *
4208 TTAGTTTCTTTTAA-AAATTCATTG-AAATCATCATCAAGAAACCCCTGAATATCAAGCTTAGTT
130 TTAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAAG-AACCCCTGAAAATCAAGCTTAGTT
4271 TC-TTAAAAAA-TTCTTTTGAAAACATAAAA
194 TCTTTAAAAAATTTCTTTTGAAAACATAAAA
* * * *
4300 AAACACCT-AAAATTAGGCTTAGCTTCTCTGAAAAAATTCTTTAGAAATGATCTTCAAGAAAGCC
1 AAACACCTAAAAATTAGGCTTAGCTTCT-TAAAAAAATTCTTTAGAAATAATCATCAAGAAACCC
* * * *
4364 CTGAAAATTAAGCTTAATTTCTAAAAACTCATTTGAAAACATCAAGAAAACTCTAAAAAATAGGC
65 CTCAAAATCAAGCTTAATTTCTAAAAACCCATTTGAAAACATCAAGAAAACCCTAAAAAATAGGC
*
4429 TTAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAAGAACCTCTGAAAATCAAGCTTAGTTT
130 TTAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAAGAACCCCTGAAAATCAAGCTTAGTTT
4494 CTTTAAAAAATTTCTTTTGAAAA
195 CTTTAAAAAATTTCTTTTGAAAA
4517 TATCTTGTAA
Statistics
Matches: 195, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
220 19 0.10
221 103 0.53
222 39 0.20
223 22 0.11
224 12 0.06
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (224 bp):
AAACACCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTAGAAATAATCATCAAGAAACCCC
TCAAAATCAAGCTTAATTTCTAAAAACCCATTTGAAAACATCAAGAAAACCCTAAAAAATAGGCT
TAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAAGAACCCCTGAAAATCAAGCTTAGTTTC
TTTAAAAAATTTCTTTTGAAAACATAAAA
Found at i:9157 original size:15 final size:15
Alignment explanation
Indices: 9139--9209 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 15
9129 ATTTAATTTT
*
9139 AAAAAATAAAATATC
1 AAAAAATAAAATATA
9154 AAAAAATAAAA-ATA
1 AAAAAATAAAATATA
9168 AAAAACAGTAAAATA-A
1 AAAAA-A-TAAAATATA
*
9184 AAACAATATAAAATAAA
1 AAA-AA-ATAAAATATA
9201 CAAAAAATA
1 -AAAAAATA
9210 TGAGGACCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.15
15 12 0.25
16 19 0.40
17 7 0.15
18 3 0.06
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.15
Consensus pattern (15 bp):
AAAAAATAAAATATA
Found at i:9179 original size:16 final size:16
Alignment explanation
Indices: 9154--9200 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
9144 ATAAAATATC
9154 AAAA-AATAAAAATAA
1 AAAACAATAAAAATAA
*
9169 AAAACAGT-AAAAT-A
1 AAAACAATAAAAATAA
9183 AAAACAATATAAAATAA
1 AAAACAATA-AAAATAA
9200 A
1 A
9201 CAAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 8 0.31
15 9 0.35
16 7 0.27
17 2 0.08
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (16 bp):
AAAACAATAAAAATAA
Found at i:9655 original size:28 final size:28
Alignment explanation
Indices: 9597--9662 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
9587 CAGCCCATTA
* **
9597 CCGACCGACCCCAAACCAGTTACGATTG
1 CCGATCGACCCCAAACCAGTTACGACCG
9625 CCGATCGACCCCAAACCAGTTACGACCG
1 CCGATCGACCCCAAACCAGTTACGACCG
*
9653 CCGGTCGACC
1 CCGATCGACC
9663 ACTATATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.26, C:0.42, G:0.20, T:0.12
Consensus pattern (28 bp):
CCGATCGACCCCAAACCAGTTACGACCG
Found at i:10460 original size:9 final size:9
Alignment explanation
Indices: 10446--10470 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
10436 TGGGTGTGCT
10446 TGAGATGCA
1 TGAGATGCA
10455 TGAGATGCA
1 TGAGATGCA
10464 TGAGATG
1 TGAGATG
10471 TTTGATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (9 bp):
TGAGATGCA
Found at i:12117 original size:22 final size:22
Alignment explanation
Indices: 12087--12136 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
12077 GATGTACTGA
12087 ATCGCGATTTTGAAACGATCCG
1 ATCGCGATTTTGAAACGATCCG
*
12109 ATCGTGATTTTGAAACGATCCG
1 ATCGCGATTTTGAAACGATCCG
*
12131 AACGCG
1 ATCGCG
12137 TTCGTACCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (22 bp):
ATCGCGATTTTGAAACGATCCG
Found at i:18445 original size:12 final size:12
Alignment explanation
Indices: 18428--18452 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18418 TTGGGGGTGG
18428 TCCTCCTATACT
1 TCCTCCTATACT
18440 TCCTCCTATACT
1 TCCTCCTATACT
18452 T
1 T
18453 GCAGAGCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.40, G:0.00, T:0.44
Consensus pattern (12 bp):
TCCTCCTATACT
Found at i:20439 original size:144 final size:144
Alignment explanation
Indices: 20246--20529 Score: 532
Period size: 144 Copynumber: 2.0 Consensus size: 144
20236 ACATGAGGTC
* *
20246 ATTCATGAAATGTTTAAGAAATTCAGTAAAAGCATATAATTGAACATCAAAGCTAAAAAGTTAAG
1 ATTCATGAAATGTTTAAGAAATTCAGGAAAAGCATATAATTGAACATCAAAGCTAAAAACTTAAG
*
20311 AATCTAACATACAATATTTTGTAATGATTGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
66 AATCTAACATACAATATTTTGTAATGATCGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
20376 TTGGAAGTTCATTT
131 TTGGAAGTTCATTT
*
20390 ATTCATGAAATGTTTAAGAAATTCAGGAAAAGCATATAATTGAACATCAAAGCTAAAAACTTAGG
1 ATTCATGAAATGTTTAAGAAATTCAGGAAAAGCATATAATTGAACATCAAAGCTAAAAACTTAAG
20455 AATCTAACATACAATATTTTGTAATGATCGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
66 AATCTAACATACAATATTTTGTAATGATCGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
20520 TTGGAAGTTC
131 TTGGAAGTTC
20530 CTTTCTTATT
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 136 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (144 bp):
ATTCATGAAATGTTTAAGAAATTCAGGAAAAGCATATAATTGAACATCAAAGCTAAAAACTTAAG
AATCTAACATACAATATTTTGTAATGATCGATGGCTAGACAATCCAGAAAACAAAGCAAGAAGTT
TTGGAAGTTCATTT
Found at i:28791 original size:25 final size:24
Alignment explanation
Indices: 28762--28822 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
28752 ATTGGAGTGC
*
28762 AAAAATAAAGAAAAGAAAAAAAGA
1 AAAAAAAAAGAAAAGAAAAAAAGA
* * *
28786 AAAAAAATCAGAATAGAAGAAAAGA
1 AAAAAAA-AAGAAAAGAAAAAAAGA
28811 AAAAAAAAAGAA
1 AAAAAAAAAGAA
28823 TTTCAAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.05
Consensus pattern (24 bp):
AAAAAAAAAGAAAAGAAAAAAAGA
Found at i:32870 original size:26 final size:26
Alignment explanation
Indices: 32848--32898 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
32838 TGCAAAAAGA
*
32848 AAGAAAAGAATAAAAGAAAAAAAAAT
1 AAGAAAAGAAGAAAAGAAAAAAAAAT
* *
32874 CAGAATAGAAGAAAAGAAAAAAAAA
1 AAGAAAAGAAGAAAAGAAAAAAAAA
32899 AGAATTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (26 bp):
AAGAAAAGAAGAAAAGAAAAAAAAAT
Found at i:32880 original size:21 final size:22
Alignment explanation
Indices: 32854--32894 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
32844 AAGAAAGAAA
32854 AGAATAAAAGAAAA-AAAAATC
1 AGAATAAAAGAAAAGAAAAATC
*
32875 AGAATAGAAGAAAAGAAAAA
1 AGAATAAAAGAAAAGAAAAA
32895 AAAAAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (22 bp):
AGAATAAAAGAAAAGAAAAATC
Found at i:36977 original size:23 final size:22
Alignment explanation
Indices: 36936--36978 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
36926 AAAGAAAAAA
**
36936 AAGAAAAAAAAAATCAGAATAG
1 AAGAAAAAAAAAAAAAGAATAG
36958 AAGAAAAGAAAAAAAAAGAAT
1 AAGAAAA-AAAAAAAAAGAAT
36979 TTCAAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (22 bp):
AAGAAAAAAAAAAAAAGAATAG
Found at i:53243 original size:32 final size:32
Alignment explanation
Indices: 53179--53244 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
53169 AACGATACAT
* * **
53179 AACAATGTCGGTGTTGCATTCAGATATTGCAC
1 AACAATGTCAGTGTTACATTCAGATAACGCAC
* *
53211 AACAATGTTAGTGTTACATTTAGATAACGCAC
1 AACAATGTCAGTGTTACATTCAGATAACGCAC
53243 AA
1 AA
53245 TAGTGTGAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (32 bp):
AACAATGTCAGTGTTACATTCAGATAACGCAC
Found at i:55938 original size:24 final size:24
Alignment explanation
Indices: 55911--55957 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
55901 AACTGCCGCA
*
55911 TAGAATTTGCACCGAAGTGCCACG
1 TAGAATATGCACCGAAGTGCCACG
55935 TAGAATATGCACCGAAGTGCCAC
1 TAGAATATGCACCGAAGTGCCAC
55958 ATTGATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (24 bp):
TAGAATATGCACCGAAGTGCCACG
Found at i:55993 original size:23 final size:23
Alignment explanation
Indices: 55964--56032 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
55954 CCACATTGAT
* *
55964 TTATCCCGAAGGACCGCTTATAA
1 TTATCCCGAAGGACCGCATAGAA
* * *
55987 TTGTCCCAAAGGACCACATAGAA
1 TTATCCCGAAGGACCGCATAGAA
*
56010 TTATCCCGAAGGACCGCGTAGAA
1 TTATCCCGAAGGACCGCATAGAA
56033 CCCTCAACTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (23 bp):
TTATCCCGAAGGACCGCATAGAA
Found at i:56173 original size:12 final size:12
Alignment explanation
Indices: 56156--56184 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
56146 AACAATTACT
56156 CATAGCATTTCA
1 CATAGCATTTCA
56168 CATAGCATTTCA
1 CATAGCATTTCA
56180 CATAG
1 CATAG
56185 ATAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (12 bp):
CATAGCATTTCA
Found at i:61895 original size:24 final size:24
Alignment explanation
Indices: 61837--61895 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
61827 CAGTCAAAAT
* *
61837 TGCCACGTAGAATTTGCACCAAAG
1 TGCCACATAGAATATGCACCAAAG
* **
61861 TGCCACGTAGAATATGCACTGAAG
1 TGCCACATAGAATATGCACCAAAG
*
61885 TGCTACATAGA
1 TGCCACATAGA
61896 TTTGTCCCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (24 bp):
TGCCACATAGAATATGCACCAAAG
Found at i:61926 original size:23 final size:24
Alignment explanation
Indices: 61895--61939 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
61885 TGCTACATAG
* *
61895 ATTTGTCCCGAAGGACCTCGTAAA
1 ATTTGTCCCAAAGGACCGCGTAAA
61919 ATTT-TCCCAAAGGACCGCGTA
1 ATTTGTCCCAAAGGACCGCGTA
61940 GAACCTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (24 bp):
ATTTGTCCCAAAGGACCGCGTAAA
Found at i:63089 original size:24 final size:24
Alignment explanation
Indices: 63055--63163 Score: 128
Period size: 24 Copynumber: 4.5 Consensus size: 24
63045 AAATGGAGAT
* *
63055 ATCATAAATCAAAACATAATTCAG
1 ATCAGAAATCATAACATAATTCAG
* * * *
63079 ATCATATATCATAACAAAATCCAG
1 ATCAGAAATCATAACATAATTCAG
* *
63103 ATCAGAAATTAGAACATAATTCAG
1 ATCAGAAATCATAACATAATTCAG
*
63127 ATCAGAAATCATAACATAATTCAA
1 ATCAGAAATCATAACATAATTCAG
*
63151 ATCGGAAATCATA
1 ATCAGAAATCATA
63164 TAAAACATTC
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (24 bp):
ATCAGAAATCATAACATAATTCAG
Found at i:67487 original size:23 final size:22
Alignment explanation
Indices: 67461--67503 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
67451 TAACTATTCT
* *
67461 ATAAATGATTTATATTAAAAGGA
1 ATAAAAGATTTA-AATAAAAGGA
67484 ATAAAAGATTTAAATAAAAG
1 ATAAAAGATTTAAATAAAAG
67504 CCCGATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (22 bp):
ATAAAAGATTTAAATAAAAGGA
Found at i:67659 original size:67 final size:67
Alignment explanation
Indices: 67528--67683 Score: 163
Period size: 67 Copynumber: 2.3 Consensus size: 67
67518 CATGAGAGTC
* * * * ** * * *
67528 AGTGATGCACGAGGTTGAGTGATTACTGAATATTGTATTGATCACTCGTTACTGAATTATGTACC
1 AGTGGTGCACGAGGTAGAGTGATAAATGAATATCATATTGATCACTCATTACTGAATCACGTACC
67593 TCT
66 T-T
* * *
67596 -GTGGTGTATGAGGTAGAGTGATAAATGAATATCATATTGATCACTCATTACT-AACTCGCGTAC
1 AGTGGTGCACGAGGTAGAGTGATAAATGAATATCATATTGATCACTCATTACTGAA-TCACGTAC
67659 CTT
65 CTT
*
67662 AGTGGTGCACGAGGTGGAGTGA
1 AGTGGTGCACGAGGTAGAGTGA
67684 GTTCTGAACA
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
66 3 0.04
67 68 0.96
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (67 bp):
AGTGGTGCACGAGGTAGAGTGATAAATGAATATCATATTGATCACTCATTACTGAATCACGTACC
TT
Found at i:70346 original size:23 final size:22
Alignment explanation
Indices: 70269--70346 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
70259 CACCAAAGTT
70269 CCACATAGAATGTCCCAAAGGA
1 CCACATAGAATGTCCCAAAGGA
* ***
70291 CCACGTAGAAATGTCTTGAAGGA
1 CCACATAG-AATGTCCCAAAGGA
*
70314 CCA-AGAAGAATTGTCCCAAAGGA
1 CCACA-TAGAA-TGTCCCAAAGGA
70337 CCACATAGAA
1 CCACATAGAA
70347 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
22 9 0.21
23 32 0.76
24 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (22 bp):
CCACATAGAATGTCCCAAAGGA
Found at i:75630 original size:13 final size:12
Alignment explanation
Indices: 75601--75630 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
75591 GATGCAAATG
75601 ATAAAAAATGAA
1 ATAAAAAATGAA
75613 ATAAAAAATGAA
1 ATAAAAAATGAA
75625 AGTAAA
1 A-TAAA
75631 CAAGTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (12 bp):
ATAAAAAATGAA
Found at i:77292 original size:14 final size:14
Alignment explanation
Indices: 77274--77307 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
77264 ATAATAATAT
77274 ATAATAAATAGATA
1 ATAATAAATAGATA
* *
77288 CTAATATATAGATA
1 ATAATAAATAGATA
77302 ATAATA
1 ATAATA
77308 TATATATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (14 bp):
ATAATAAATAGATA
Found at i:77292 original size:21 final size:21
Alignment explanation
Indices: 77268--77417 Score: 104
Period size: 21 Copynumber: 7.1 Consensus size: 21
77258 CAAAAAATAA
*
77268 TAATATATAATAAATAGATAC
1 TAATATATAATAAATATATAC
77289 TAATATATAGAT-AATAATATA-
1 TAATATATA-ATAAAT-ATATAC
*
77310 TATATATATATATTAATATAATA-
1 TA-ATATATA-ATAAATAT-ATAC
77333 TAATACTATAAT-AATAATATA-
1 TAATA-TATAATAAAT-ATATAC
77354 TAATATA-ATATATAATATATAC
1 TAATATATA-ATA-AATATATAC
77376 TATAATATATAA-AAA-ATATAC
1 --TAATATATAATAAATATATAC
*
77397 T-ATATATTAT-AATATATAC
1 TAATATATAATAAATATATAC
77416 TA
1 TA
77418 TCCCGGACAA
Statistics
Matches: 109, Mismatches: 3, Indels: 35
0.74 0.02 0.24
Matches are distributed among these distances:
18 9 0.08
19 9 0.08
20 4 0.04
21 36 0.33
22 29 0.27
23 13 0.12
24 8 0.07
25 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (21 bp):
TAATATATAATAAATATATAC
Found at i:77308 original size:14 final size:13
Alignment explanation
Indices: 77263--77414 Score: 103
Period size: 12 Copynumber: 12.1 Consensus size: 13
77253 TAAACCAAAA
77263 AATAATAATATAT
1 AATAATAATATAT
*
77276 AAT-A-AATAGAT
1 AATAATAATATAT
* *
77287 ACTAATATATAGAT
1 AATAATA-ATATAT
77301 AATAAT-ATATAT
1 AATAATAATATAT
*
77313 ATATATATATTAATAT
1 A-ATA-ATAAT-ATAT
77329 AAT-ATAATACTAT
1 AATAATAATA-TAT
77342 AATAATAATATAT
1 AATAATAATATAT
77355 AAT-ATAATATAT
1 AATAATAATATAT
77367 AAT-AT-ATACTAT
1 AATAATAATA-TAT
77379 AATATATAA-A-A-
1 AATA-ATAATATAT
*
77390 AAT-ATACTATAT
1 AATAATAATATAT
*
77402 -ATTATAATATAT
1 AATAATAATATAT
77414 A
1 A
77415 CTATCCCGGA
Statistics
Matches: 113, Mismatches: 8, Indels: 36
0.72 0.05 0.23
Matches are distributed among these distances:
9 3 0.03
10 1 0.01
11 17 0.15
12 38 0.34
13 23 0.20
14 22 0.19
15 4 0.04
16 5 0.04
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (13 bp):
AATAATAATATAT
Found at i:77322 original size:28 final size:25
Alignment explanation
Indices: 77264--77414 Score: 116
Period size: 28 Copynumber: 5.9 Consensus size: 25
77254 AAACCAAAAA
* *
77264 ATAATA-AT-ATATAATAAATAGAT
1 ATAATATATAATATAATATATATAT
77287 ACTAATATATAGATAATAATATATATAT
1 A-TAATATATA-AT-ATAATATATATAT
77315 AT-ATATATTAATATAATATA-ATACT
1 ATAATATA-TAATATAATATATATA-T
77340 ATAATA-ATAATAT-ATAATATAATAT
1 ATAATATATAATATAAT-ATAT-ATAT
* *
77365 ATAATATATACTATAATATATAAAAAAT
1 ATAATATATAATATAATATAT---ATAT
* *
77393 ATACTATATATTATAATATATA
1 ATAATATATAATATAATATATA
77415 CTATCCCGGA
Statistics
Matches: 107, Mismatches: 6, Indels: 28
0.76 0.04 0.20
Matches are distributed among these distances:
23 3 0.03
24 17 0.16
25 22 0.21
26 23 0.21
27 7 0.07
28 35 0.33
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (25 bp):
ATAATATATAATATAATATATATAT
Found at i:78900 original size:49 final size:49
Alignment explanation
Indices: 78823--78921 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
78813 AGTTAGTTAG
*
78823 TTAGAATTGTGTTATTCAGATGATATAGAATTCATCACAATTCTTCATT
1 TTAGAATTGTGTTATTCAGATGACATAGAATTCATCACAATTCTTCATT
* *
78872 TTAGAATTGTGTTTTTCAGATGACATAGAATTCATCACATTTCTTCATT
1 TTAGAATTGTGTTATTCAGATGACATAGAATTCATCACAATTCTTCATT
78921 T
1 T
78922 CCTCTCTATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (49 bp):
TTAGAATTGTGTTATTCAGATGACATAGAATTCATCACAATTCTTCATT
Found at i:89692 original size:22 final size:23
Alignment explanation
Indices: 89667--89719 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
89657 AGGCTCCGGG
*
89667 TCGGGTTTGGTTT-GGGCCTAGT
1 TCGGGTTTAGTTTGGGGCCTAGT
* * *
89689 TCGGGTCTAGTTTGGGGCTTGGT
1 TCGGGTTTAGTTTGGGGCCTAGT
89712 TCGGGTTT
1 TCGGGTTT
89720 TGATTTCAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.04, C:0.13, G:0.42, T:0.42
Consensus pattern (23 bp):
TCGGGTTTAGTTTGGGGCCTAGT
Done.