Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009253.1 Hibiscus syriacus cultivar Beakdansim tig00112901_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: 94475
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5298 original size:3 final size:3
Alignment explanation
Indices: 5290--5334 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
5280 TATATATACG
*
5290 TTA TTA TTA TATA TAA TATA TTA TTA TTA TTA TTA TATA TTA TTA
1 TTA TTA TTA T-TA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA
5335 AATAATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 29 0.78
4 8 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5309 original size:26 final size:24
Alignment explanation
Indices: 5249--5329 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 24
5239 TTTGCCAGTT
*
5249 TATAATATTATATATTATTAACTATA
1 TATAATA-TATATATTATT-ATTATA
**
5275 TATTTTATATATACGTTATTATTATA
1 TATAATATATATA--TTATTATTATA
5301 TATAATATATTATTATTATTATTATA
1 TATAATATA-TA-TATTATTATTATA
5327 TAT
1 TAT
5330 TATTAAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.13
26 31 0.67
27 7 0.15
28 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (24 bp):
TATAATATATATATTATTATTATA
Found at i:5311 original size:17 final size:17
Alignment explanation
Indices: 5272--5342 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
5262 ATTATTAACT
5272 ATATATT-TTATATATA
1 ATATATTATTATATATA
*
5288 CGT-TATTATTATATATA
1 -ATATATTATTATATATA
*
5305 ATATATTATTATTATTATT
1 ATATATTATTA-TA-TATA
5324 ATATATTATTA-A-ATA
1 ATATATTATTATATATA
5339 ATAT
1 ATAT
5343 TACAAGCCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
15 6 0.13
16 5 0.11
17 19 0.41
18 2 0.04
19 14 0.30
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
ATATATTATTATATATA
Found at i:5343 original size:26 final size:26
Alignment explanation
Indices: 5260--5344 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
5250 ATAATATTAT
* *
5260 ATATTATTAACTATATATT-TTATAT-
1 ATATTATT-ATTATATATTATTAAATA
* *
5285 ATACGTTATTATTATATA-TAATATATTA
1 ATA--TTATTATTATATATTATTA-AATA
*
5313 TTATTATTATTATATATTATTAAATA
1 ATATTATTATTATATATTATTAAATA
5339 ATATTA
1 ATATTA
5345 CAAGCCAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
25 4 0.09
26 30 0.65
27 10 0.22
28 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (26 bp):
ATATTATTATTATATATTATTAAATA
Found at i:6634 original size:26 final size:25
Alignment explanation
Indices: 6603--6668 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
6593 ATTTTAAGAC
6603 TAATTATAATATTAGTATAAT-TATA
1 TAATTATAATATTA-TATAATCTATA
*
6628 TATATTATGATAACTT-TATAATCTATA
1 TA-ATTATAAT-A-TTATATAATCTATA
*
6655 TAATTTTAATATTA
1 TAATTATAATATTA
6669 AATATAATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
24 2 0.06
25 3 0.09
26 19 0.58
27 7 0.21
28 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (25 bp):
TAATTATAATATTATATAATCTATA
Found at i:6640 original size:18 final size:18
Alignment explanation
Indices: 6585--6668 Score: 56
Period size: 18 Copynumber: 4.8 Consensus size: 18
6575 TTTTCATCAT
* *
6585 TAATTAT-TATTTTAAGA
1 TAATTATATATATTATGA
6602 CTAATTATA-ATATTA-GTA
1 -TAATTATATATATTATG-A
6620 TAATTATATATATTATGA
1 TAATTATATATATTATGA
6638 TAACTT-TATA-ATCTAT-A
1 TAA-TTATATATAT-TATGA
*
6655 TAATTTTA-ATATTA
1 TAATTATATATATTA
6669 AATATAATAG
Statistics
Matches: 57, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
16 5 0.09
17 19 0.33
18 30 0.53
19 3 0.05
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (18 bp):
TAATTATATATATTATGA
Found at i:7850 original size:2 final size:2
Alignment explanation
Indices: 7804--7830 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7794 GGATATGATG
7804 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 T
7831 GATTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12698 original size:5 final size:5
Alignment explanation
Indices: 12682--12713 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
12672 TAAAAAAAAT
12682 TCGGG TTCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG -TCGGG TCGGG TCGGG TCGGG TCGGG T
12714 TTAGGGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:13400 original size:55 final size:56
Alignment explanation
Indices: 13313--13420 Score: 173
Period size: 55 Copynumber: 1.9 Consensus size: 56
13303 CTTATTCGAG
* *
13313 ATTTGATTAAGATGTGGAGACATGAAATGAATTAAGATGAATCCTTCTTGTGAATT
1 ATTTGATTAAGATGTGGAGACATGAAAGGAATTAAGATAAATCCTTCTTGTGAATT
* *
13369 ATTTGATT-AGATGTGGAGACATGAAAGGAATTAGGATAAATCCTTTTTGTGA
1 ATTTGATTAAGATGTGGAGACATGAAAGGAATTAAGATAAATCCTTCTTGTGA
13421 TGTGTTCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
55 40 0.83
56 8 0.17
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (56 bp):
ATTTGATTAAGATGTGGAGACATGAAAGGAATTAAGATAAATCCTTCTTGTGAATT
Found at i:14156 original size:41 final size:41
Alignment explanation
Indices: 14099--14201 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
14089 TCACGAATTT
* *
14099 TTAAATCCTTCGGGTCATCTGTAAGTCCTTCGAG-CATGATG
1 TTAAATCCTTAGGGTCATCTGTAAGTCCTTCGAGCCA-GATC
* * *
14140 TTAAAACCTTAGGGTCATCTGTCAGTCTTTCGAGCCAGATC
1 TTAAATCCTTAGGGTCATCTGTAAGTCCTTCGAGCCAGATC
*
14181 ATAAATCCTTAGGGTCATCTG
1 TTAAATCCTTAGGGTCATCTG
14202 CCAAACCTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 52 0.96
42 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (41 bp):
TTAAATCCTTAGGGTCATCTGTAAGTCCTTCGAGCCAGATC
Found at i:14255 original size:18 final size:18
Alignment explanation
Indices: 14232--14270 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
14222 TGGCTCACAT
14232 AATGTAAGATTACCAAGG
1 AATGTAAGATTACCAAGG
* *
14250 AATGTAATATTACCAGGG
1 AATGTAAGATTACCAAGG
14268 AAT
1 AAT
14271 AGGATTACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (18 bp):
AATGTAAGATTACCAAGG
Found at i:22578 original size:22 final size:22
Alignment explanation
Indices: 22553--22600 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
22543 ACGTCGTCCG
22553 GTTCTTCCGACCTG-TCGGACCA
1 GTTCTTCCGACC-GATCGGACCA
22575 GTTCTTCCGACCGATCGGACCA
1 GTTCTTCCGACCGATCGGACCA
22597 GTTC
1 GTTC
22601 GACCGGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.15, C:0.35, G:0.23, T:0.27
Consensus pattern (22 bp):
GTTCTTCCGACCGATCGGACCA
Found at i:24110 original size:23 final size:23
Alignment explanation
Indices: 24084--24128 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24074 TGTGTTTTCT
24084 TTTTAAAAATATATATAATTTTA
1 TTTTAAAAATATATATAATTTTA
* * *
24107 TTTTTAAATTTTATATAATTTT
1 TTTTAAAAATATATATAATTTT
24129 TTAAAATATT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAAAAATATATATAATTTTA
Found at i:27445 original size:21 final size:23
Alignment explanation
Indices: 27421--27466 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
27411 TCATAAAAAT
27421 AATTTT-TAA-ATACAAAAGTAA
1 AATTTTCTAATATACAAAAGTAA
* *
27442 AATTTTCTAATATTCAGAAGTAA
1 AATTTTCTAATATACAAAAGTAA
27465 AA
1 AA
27467 CAAATTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 12 0.57
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.35
Consensus pattern (23 bp):
AATTTTCTAATATACAAAAGTAA
Found at i:28100 original size:31 final size:31
Alignment explanation
Indices: 28022--28106 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
28012 GGAATGCCTT
*
28022 GGGGCCCGAGAGCCTACCCAAGAAAGTTACTC
1 GGGGCCC-AGAGCCTACCCAAGAAAGATACTC
* *
28054 AGGG-CCACGAGGCCTACCCAAGAATGAT-CTC
1 GGGGCCCA-GA-GCCTACCCAAGAAAGATACTC
*
28085 GGGGCCTCAGAGCCTATCCAAG
1 GGGGCC-CAGAGCCTACCCAAG
28107 GGTTGTCTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
30 1 0.02
31 20 0.45
32 21 0.48
33 2 0.05
ACGTcount: A:0.27, C:0.32, G:0.28, T:0.13
Consensus pattern (31 bp):
GGGGCCCAGAGCCTACCCAAGAAAGATACTC
Found at i:30524 original size:22 final size:22
Alignment explanation
Indices: 30496--30549 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
30486 CAGTTAACGA
30496 TCAGACCGGTCAAAGTCAACAG
1 TCAGACCGGTCAAAGTCAACAG
* *
30518 TCAGACCGATCAAAGTCAACGG
1 TCAGACCGGTCAAAGTCAACAG
30540 TCAGACCGGT
1 TCAGACCGGT
30550 AAACGGGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (22 bp):
TCAGACCGGTCAAAGTCAACAG
Found at i:30589 original size:13 final size:13
Alignment explanation
Indices: 30571--30597 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30561 CTCAGTCAAG
30571 TCAATGAGTTGAC
1 TCAATGAGTTGAC
30584 TCAATGAGTTGAC
1 TCAATGAGTTGAC
30597 T
1 T
30598 TAGCCGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (13 bp):
TCAATGAGTTGAC
Found at i:31590 original size:2 final size:2
Alignment explanation
Indices: 31583--31614 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31573 AATAATATGA
31583 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
31615 CTTATATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37289 original size:21 final size:22
Alignment explanation
Indices: 37265--37305 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
37255 ACAAGTGTAG
*
37265 TAATTGTCAA-ATAAATAAACC
1 TAATTCTCAATATAAATAAACC
*
37286 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
37306 TAAAACAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACC
Found at i:38094 original size:18 final size:18
Alignment explanation
Indices: 38071--38105 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38061 TTAGCGTTGT
38071 GAAAAG-AAAATAATGAAA
1 GAAAAGTAAAA-AATGAAA
38089 GAAAAGTAAAAAATGAA
1 GAAAAGTAAAAAATGAA
38106 GGGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (18 bp):
GAAAAGTAAAAAATGAAA
Found at i:38286 original size:54 final size:53
Alignment explanation
Indices: 38195--38332 Score: 221
Period size: 54 Copynumber: 2.7 Consensus size: 53
38185 ATTTATAACT
38195 AAAAAGTTCTAAGTAAATAAATGACTAATTCCTAATCAAACTAAAAATGCTAC
1 AAAAAGTTCTAAGTAAATAAATGACTAATTCCTAATCAAACTAAAAATGCTAC
*
38248 CAAAAGTTCTAAGTAAATAAAATGACTAATTCCTAATCAAACTAAAAATGCTAC
1 AAAAAGTTCTAAGTAAAT-AAATGACTAATTCCTAATCAAACTAAAAATGCTAC
*
38302 AAAAAGTTCTAA-T--A-AAATAACTAATTCCTAA
1 AAAAAGTTCTAAGTAAATAAATGACTAATTCCTAA
38333 ATAAAATAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
49 16 0.20
51 1 0.01
53 18 0.22
54 46 0.57
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (53 bp):
AAAAAGTTCTAAGTAAATAAATGACTAATTCCTAATCAAACTAAAAATGCTAC
Found at i:43681 original size:6 final size:6
Alignment explanation
Indices: 43670--43694 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43660 TCTTTCAACT
43670 ACTTCC ACTTCC ACTTCC ACTTCC A
1 ACTTCC ACTTCC ACTTCC ACTTCC A
43695 TTTAATCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.48, G:0.00, T:0.32
Consensus pattern (6 bp):
ACTTCC
Found at i:44288 original size:28 final size:29
Alignment explanation
Indices: 44256--44316 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
44246 TATGACTCTC
44256 ATTTTAAATT-AGTCACTAAA-TTTTGAAT
1 ATTTTAAATTCAGTCAC-AAATTTTTGAAT
* * *
44284 ATTTTAATTTCATTCTCAAATTTTTGAAT
1 ATTTTAAATTCAGTCACAAATTTTTGAAT
44313 ATTT
1 ATTT
44317 CAATTTTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (29 bp):
ATTTTAAATTCAGTCACAAATTTTTGAAT
Found at i:44331 original size:28 final size:29
Alignment explanation
Indices: 44276--44331 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
44266 AGTCACTAAA
* *
44276 TTTTGAATATTTTAATTTCATTCTCAAAT
1 TTTTGAATATTTCAATTTCATTCCCAAAT
*
44305 TTTTGAATATTTCAATTTTA-TCCCAAA
1 TTTTGAATATTTCAATTTCATTCCCAAA
44332 CTATAGGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTTGAATATTTCAATTTCATTCCCAAAT
Found at i:44503 original size:29 final size:29
Alignment explanation
Indices: 44456--44533 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
44446 TAAATTTGCG
44456 GATGAAATTGAAAGATTCAAAAGTTTAGA
1 GATGAAATTGAAAGATTCAAAAGTTTAGA
* * * * *
44485 GATGAATTTGGAAGCTTCAAAAGTTTTGG
1 GATGAAATTGAAAGATTCAAAAGTTTAGA
* *
44514 GATGAAATTAAAATATTCAA
1 GATGAAATTGAAAGATTCAA
44534 GAATTTAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (29 bp):
GATGAAATTGAAAGATTCAAAAGTTTAGA
Found at i:44672 original size:41 final size:41
Alignment explanation
Indices: 44615--44696 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
44605 TCATATACAT
*
44615 ATGATGTAGTTAACCCTATCTAATATTTAATTAATAAAATA
1 ATGATGTAGTTAACCCTATCAAATATTTAATTAATAAAATA
44656 ATGATGTAGTTAACCCTATCAAATATTTAATTAATAAAATA
1 ATGATGTAGTTAACCCTATCAAATATTTAATTAATAAAATA
44697 TTATAAATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (41 bp):
ATGATGTAGTTAACCCTATCAAATATTTAATTAATAAAATA
Found at i:45391 original size:30 final size:30
Alignment explanation
Indices: 45357--45429 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
45347 AAGCAGAAGC
45357 AGAAGCAGGAGTAGAGAGACAAGGAGACGA
1 AGAAGCAGGAGTAGAGAGACAAGGAGACGA
* * *
45387 AGAAGCAGGAGTAGAGAGAGAAGGAGGCGG
1 AGAAGCAGGAGTAGAGAGACAAGGAGACGA
45417 AGAAGCAGGAGTA
1 AGAAGCAGGAGTA
45430 CGAGTAGGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.44, C:0.08, G:0.44, T:0.04
Consensus pattern (30 bp):
AGAAGCAGGAGTAGAGAGACAAGGAGACGA
Found at i:50903 original size:10 final size:10
Alignment explanation
Indices: 50888--50913 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
50878 CATTTCGACC
50888 AAAAAAATAA
1 AAAAAAATAA
50898 AAAAAAATAA
1 AAAAAAATAA
50908 AAAAAA
1 AAAAAA
50914 TATATGGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:64175 original size:24 final size:24
Alignment explanation
Indices: 64125--64212 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 24
64115 TATATCAAAA
* *
64125 ATCAAAACATAATTCAGGTCAGAT
1 ATCATAACAGAATTCAGGTCAGAT
*
64149 ATCATAACAGAATTTAGGTCA-AGT
1 ATCATAACAGAATTCAGGTCAGA-T
* * * * *
64173 ATCATATCAGAATCCAAGTTAGGT
1 ATCATAACAGAATTCAGGTCAGAT
*
64197 ATCATAACACAATTCA
1 ATCATAACAGAATTCA
64213 AATCGAAAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.02
24 49 0.98
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.27
Consensus pattern (24 bp):
ATCATAACAGAATTCAGGTCAGAT
Found at i:65279 original size:24 final size:24
Alignment explanation
Indices: 65229--65316 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
65219 TATATCAAAA
* * *
65229 ATCAAAACATAATTCATGTC-AGAT
1 ATCAGAACAGAATCCATGTCAAG-T
*
65253 ATCATAACAGAATCCATGTCAAGT
1 ATCAGAACAGAATCCATGTCAAGT
*
65277 ATCAGATCAGAATCCATGTCAAGT
1 ATCAGAACAGAATCCATGTCAAGT
*
65301 ATCAGATCAGAATCCA
1 ATCAGAACAGAATCCA
65317 AATCGGAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 56 0.97
25 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAGAACAGAATCCATGTCAAGT
Found at i:74394 original size:60 final size:60
Alignment explanation
Indices: 74309--74456 Score: 183
Period size: 60 Copynumber: 2.5 Consensus size: 60
74299 GATTCTTATC
* * * * *
74309 TAAATTGGT-CTCTAAACTTTTGAACATTTTAATTTCATTCTTAAACTAT-AACTCTTATTA
1 TAAATTGGTCCCCT-AACTTTTGAACATTTCAAATTCATCCTCAAACTATGAAC-CTTATTA
*
74369 TAAATTGGTCCCCTAACTTTTGAACATTTCAAATTCATCCTCAAACTATGAACCTTATTC
1 TAAATTGGTCCCCTAACTTTTGAACATTTCAAATTCATCCTCAAACTATGAACCTTATTA
* * *
74429 TAAGTTAGTCCCCAAACTTTTGAACATT
1 TAAATTGGTCCCCTAACTTTTGAACATT
74457 CCAATGATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
60 71 0.92
61 6 0.08
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (60 bp):
TAAATTGGTCCCCTAACTTTTGAACATTTCAAATTCATCCTCAAACTATGAACCTTATTA
Found at i:81824 original size:20 final size:20
Alignment explanation
Indices: 81799--81889 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
81789 TAAATTAAAT
*
81799 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
81819 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
81839 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
81851 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
81871 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
81890 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:81914 original size:53 final size:52
Alignment explanation
Indices: 81798--81947 Score: 275
Period size: 53 Copynumber: 2.9 Consensus size: 52
81788 CTAAATTAAA
*
81798 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
81850 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
81903 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
81948 GTTGCTAATT
Statistics
Matches: 96, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 10 0.10
52 35 0.36
53 51 0.53
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:81929 original size:20 final size:20
Alignment explanation
Indices: 81904--81943 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
81894 TCTATTAGTT
*
81904 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
81924 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
81944 TTCTGTTGCT
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:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:86366 original size:20 final size:19
Alignment explanation
Indices: 86340--86429 Score: 70
Period size: 20 Copynumber: 5.1 Consensus size: 19
86330 CTAAATTAAA
*
86340 TATTAGATAGGATCAGTTT
1 TATTAGATAGAATCAGTTT
86359 TAATTAGATAGAATCAGTTT
1 T-ATTAGATAGAATCAGTTT
* *
86379 TATT---T--TATTAG--T
1 TATTAGATAGAATCAGTTT
*
86391 TATTAGATAGGATCA-TTT
1 TATTAGATAGAATCAGTTT
86409 TAATTAGATAGAATCAGTTT
1 T-ATTAGATAGAATCAGTTT
86429 T
1 T
86430 TTATTTATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 19
0.69 0.08 0.24
Matches are distributed among these distances:
12 5 0.09
14 4 0.07
15 1 0.02
16 1 0.02
17 3 0.05
18 2 0.04
19 17 0.31
20 22 0.40
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (19 bp):
TATTAGATAGAATCAGTTT
Found at i:86416 original size:19 final size:20
Alignment explanation
Indices: 86392--86429 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
86382 TTTATTAGTT
*
86392 ATTAGATAGGATCA-TTTTA
1 ATTAGATAGAATCAGTTTTA
86411 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
86430 TTATTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:86437 original size:51 final size:51
Alignment explanation
Indices: 86340--86482 Score: 231
Period size: 51 Copynumber: 2.8 Consensus size: 51
86330 CTAAATTAAA
*
86340 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTAT-TTTATTAGT
1 TATTAGATAGGATCA-TTTTAATTAGATAGAATCAGTTTTTTATTTATTAGT
86391 TATTAGATAGGATCATTTTAATTAGATAGAATCAGTTTTTTATTTATTAGT
1 TATTAGATAGGATCATTTTAATTAGATAGAATCAGTTTTTTATTTATTAGT
86442 TATTAGATAGGAT--TTTTAATTAGATAGAATCA-TTTTATTAT
1 TATTAGATAGGATCATTTTAATTAGATAGAATCAGTTTT-TTAT
86483 GTTGCTAATT
Statistics
Matches: 89, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
48 4 0.04
49 23 0.26
50 25 0.28
51 37 0.42
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (51 bp):
TATTAGATAGGATCATTTTAATTAGATAGAATCAGTTTTTTATTTATTAGT
Done.