Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007827.1 Hibiscus syriacus cultivar Beakdansim tig00110166_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: 61083
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2231 original size:80 final size:80
Alignment explanation
Indices: 2104--2254 Score: 257
Period size: 80 Copynumber: 1.9 Consensus size: 80
2094 TGCACAACTG
* *
2104 GCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTACGAACC
1 GCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTACGAACC
2169 ATTCTTGGTGCAACC
66 ATTCTTGGTGCAACC
* * *
2184 GCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTTGCTCCGCCATTTCGTGTGCGAACC
1 GCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTACGAACC
2249 ATTCTT
66 ATTCTT
2255 TGTAACTCGC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.32
Consensus pattern (80 bp):
GCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTACGAACC
ATTCTTGGTGCAACC
Found at i:2555 original size:54 final size:54
Alignment explanation
Indices: 2369--2668 Score: 293
Period size: 54 Copynumber: 5.5 Consensus size: 54
2359 TAGAATTAAC
*
2369 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAA-T
* **
2424 GATTGAGCACCTCTGTGCTT-AATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAG-----CCAAAAT
* ** * * * *
2482 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAAT
*
2536 GATTGAGCACCTCTGTGCTTCAATCGAG-GACTGACACCTCTGTGCAGCC-AACT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGCAGCCAAAAT
* * * * * * * **
2589 AGACTGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCCCTGTGCA-TCGGAAT
1 -GATTGAGCACCTCTGTGCTTCAATCGAGA-GCTGACACCTCTGTGCAGCCAAAAT
*
2644 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
2669 TAAAATCAAG
Statistics
Matches: 202, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
53 3 0.01
54 118 0.58
55 36 0.18
58 20 0.10
59 25 0.12
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAAT
Found at i:2570 original size:113 final size:113
Alignment explanation
Indices: 2372--2582 Score: 352
Period size: 113 Copynumber: 1.9 Consensus size: 113
2362 AATTAACGAT
*
2372 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
2437 TGTGCTTAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
66 TGTGCTTAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
* * * *
2485 TGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGA-TGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
*
2549 TGTGCTTCAATCGAGGACTGACACCTCTGTGCAG
66 TGTGCTT-AATCGAGAACTGACACCTCTGTGCAG
2583 CCAACTAGAC
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
112 21 0.23
113 70 0.77
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (113 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
TGTGCTTAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
Found at i:2573 original size:27 final size:28
Alignment explanation
Indices: 2372--2614 Score: 120
Period size: 27 Copynumber: 8.8 Consensus size: 28
2362 AATTAACGAT
2372 TGAGCACCTCTGTGCTTCAATCGA-GAGC
1 TGAGCACCTCTGTGCTTCAATCGAGGA-C
* * *
2400 TGA-CACCTCTGTG-TAGCCAA--AAGTGAT
1 TGAGCACCTCTGTGCT--TCAATCGAG-GAC
*
2427 TGAGCACCTCTGTGCTT-AATCGAGAAC
1 TGAGCACCTCTGTGCTTCAATCGAGGAC
* *** *
2454 TGA-CACCTCTGTGCAGTTAAAAAAAAATGAC
1 TGAGCACCTCTGTGC--TT--CAATCGAGGAC
**
2485 TGAGCACCTCTGTGCTTCAGCCG-GGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGGA-C
* * *
2513 TGA-CACCTCTGTG-TAGCTAA--GATGAT
1 TGAGCACCTCTGTGCT-TC-AATCGAGGAC
2539 TGAGCACCTCTGTGCTTCAATCGAGGAC
1 TGAGCACCTCTGTGCTTCAATCGAGGAC
** *
2567 TGA-CACCTCTGTGCAGCCAA-CTA-GAC
1 TGAGCACCTCTGTGC-TTCAATCGAGGAC
2593 TGAGCACCTCTGTGCTTCAATC
1 TGAGCACCTCTGTGCTTCAATC
2615 TAAATTCTGG
Statistics
Matches: 160, Mismatches: 30, Indels: 51
0.66 0.12 0.21
Matches are distributed among these distances:
26 31 0.19
27 68 0.43
28 39 0.24
29 1 0.01
30 2 0.01
31 8 0.05
32 11 0.07
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (28 bp):
TGAGCACCTCTGTGCTTCAATCGAGGAC
Found at i:2646 original size:108 final size:110
Alignment explanation
Indices: 2372--2668 Score: 305
Period size: 113 Copynumber: 2.7 Consensus size: 110
2362 AATTAACGAT
* * * * * *
2372 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCCCTGTGCAGCGAAGA-TGATTGAGCACCTC
2437 TGTGCTT-AATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
65 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG---AAAAAAAATGAC
* ** * * *
2485 TGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGATGATTGAGCACCTCT
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCCCTGTGCAGCGAAGATGATTGAGCACCTCT
* ** **
2550 GTGCTTCAATCGAGGACTGACACCTCTGTGCAG-CCAACTA-GAC
66 GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
* * * * * *
2593 TGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCCCTGTGCATCGGA-ATGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAAA-GCTGACACCCCTGTGCAGCGAAGATGATTGAGCACCTC
*
2657 TGTGCTACAATC
65 TGTGCTTCAATC
2669 TAAAATCAAG
Statistics
Matches: 159, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
108 50 0.31
109 18 0.11
112 21 0.13
113 70 0.44
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (110 bp):
TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCCCTGTGCAGCGAAGATGATTGAGCACCTCT
GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
Found at i:4914 original size:21 final size:20
Alignment explanation
Indices: 4889--4928 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4879 GTTAAACATA
4889 TAAATTAATCAAAAAATAATT
1 TAAA-TAATCAAAAAATAATT
* *
4910 TAAATATTTAAAAAATAAT
1 TAAATAATCAAAAAATAAT
4929 AATATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATAATCAAAAAATAATT
Found at i:5051 original size:2 final size:2
Alignment explanation
Indices: 5044--5078 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5034 CCAATCATTA
5044 TC TC TC TC TC 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 TC TC TC TC TC T
5079 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5083 original size:2 final size:2
Alignment explanation
Indices: 5078--5120 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5068 TCTCTCTCTC
5078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5120 T
1 T
5121 CACCATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8470 original size:13 final size:13
Alignment explanation
Indices: 8445--8482 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
8435 AGTACATGTG
*
8445 AACAGT-AACAGT
1 AACAGTGAATAGT
8457 AACAGTGAATAGT
1 AACAGTGAATAGT
*
8470 AATAGTGAATAGT
1 AACAGTGAATAGT
8483 GACGATGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (13 bp):
AACAGTGAATAGT
Found at i:11617 original size:45 final size:45
Alignment explanation
Indices: 11540--11792 Score: 353
Period size: 45 Copynumber: 5.6 Consensus size: 45
11530 TTGTTGTAAG
* *
11540 CATCTTGCATTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* ** *
11585 TATCATGCACTGTAGGTCTTATGGATGGCCCGAAGGCTTTGAAAA
1 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* *
11630 CATCTTGCACTATAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
*
11675 CATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* ** * *
11720 CATCCTGCACTGTAGGTCTTATGGATGACTCGAAGGTTTTGAAAA
1 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
* * *
11765 CATTATGCACTGAAGGTCTTACATATGA
1 CATCATGCACTGTAGGTCTTACAGATGA
11793 GCAAAATATT
Statistics
Matches: 184, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 184 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (45 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAA
Found at i:11782 original size:135 final size:135
Alignment explanation
Indices: 11540--11792 Score: 411
Period size: 135 Copynumber: 1.9 Consensus size: 135
11530 TTGTTGTAAG
* *
11540 CATCTTGCATTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCATGCACTGTAGGTCTT
1 CATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGTAGGTCTT
*
11605 ATGGATGGCCCGAAGGCTTTGAAAACATCTTGCACTATAGGTCTTACAGATGACCCGAAGGCTTT
66 ATGGATGACCCGAAGGCTTTGAAAACATCTTGCACTATAGGTCTTACAGATGACCCGAAGGCTTT
11670 GAAAA
131 GAAAA
*
11675 CATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCCTGCACTGTAGGTCTT
1 CATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGTAGGTCTT
* * *
11740 ATGGATGACTCGAAGGTTTTGAAAACAT-TATGCACTGA-AGGTCTTACATATGA
66 ATGGATGACCCGAAGGCTTTGAAAACATCT-TGCACT-ATAGGTCTTACAGATGA
11793 GCAAAATATT
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
134 1 0.01
135 107 0.98
136 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (135 bp):
CATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGTAGGTCTT
ATGGATGACCCGAAGGCTTTGAAAACATCTTGCACTATAGGTCTTACAGATGACCCGAAGGCTTT
GAAAA
Found at i:12956 original size:54 final size:54
Alignment explanation
Indices: 12857--12964 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
12847 ATAATCACTA
* * *
12857 GTTCATAAAACATTTGTCAACACATTCATCCTTTATTGTGTCTTCT-GTCCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTAG-CCAGAT
* * *
12911 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCCTGTGGCTTCTAGCCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTAGCCAGAT
12965 TTCTCAATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 46 0.98
55 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (54 bp):
GTTCATAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTAGCCAGAT
Found at i:18325 original size:12 final size:13
Alignment explanation
Indices: 18301--18348 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
18291 GAAAAGATGC
*
18301 AAATATAAAATGA
1 AAATGTAAAATGA
18314 AAATGT-AAATGA
1 AAATGTAAAATGA
*
18326 AAATATAAAAATGA
1 AAATGT-AAAATGA
18340 AAATG-AAAA
1 AAATGTAAAA
18349 CATAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 15 0.50
13 5 0.17
14 10 0.33
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (13 bp):
AAATGTAAAATGA
Found at i:18338 original size:20 final size:20
Alignment explanation
Indices: 18313--18356 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
18303 ATATAAAATG
* *
18313 AAAATGTAAATGAAAATATA
1 AAAATGAAAATGAAAACATA
18333 AAAATGAAAATGAAAACATA
1 AAAATGAAAATGAAAACATA
18353 AAAA
1 AAAA
18357 ATGCAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.18
Consensus pattern (20 bp):
AAAATGAAAATGAAAACATA
Found at i:21428 original size:18 final size:17
Alignment explanation
Indices: 21388--21429 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
21378 TAAAGTATTG
21388 AAAAATAAAGGACAATA
1 AAAAATAAAGGACAATA
21405 ATAAAATAAAATGG-CAATA
1 A-AAAAT-AAA-GGACAATA
21424 AAAAAT
1 AAAAAT
21430 GACCAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 10 0.45
19 9 0.41
20 2 0.09
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.17
Consensus pattern (17 bp):
AAAAATAAAGGACAATA
Found at i:22681 original size:3 final size:3
Alignment explanation
Indices: 22673--22703 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
22663 TATATTTATT
22673 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
22704 ATAAGATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:22692 original size:16 final size:16
Alignment explanation
Indices: 22673--22707 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
22663 TATATTTATT
22673 TAATAATAATAATAAA
1 TAATAATAATAATAAA
22689 TAATAATAATAATAAA
1 TAATAATAATAATAAA
22705 TAA
1 TAA
22708 GATCAGGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATAATAATAATAAA
Found at i:22707 original size:13 final size:13
Alignment explanation
Indices: 22674--22700 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22664 ATATTTATTT
22674 AATAATAATAATA
1 AATAATAATAATA
22687 AATAATAATAATA
1 AATAATAATAATA
22700 A
1 A
22701 TAAATAAGAT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:25085 original size:57 final size:59
Alignment explanation
Indices: 24951--25151 Score: 162
Period size: 58 Copynumber: 3.5 Consensus size: 59
24941 ATAATGTTAT
* * * * * * * * *
24951 TCAATTTATCATTTGTTTACATAAAAC-ATATACTAATAGTA-TTTCACATATCATCAC
1 TCAAATTATCATTTATTCACATAGAACAATATACTCATAGCATTTTCATATAGCATTAC
* * * *
25008 -CTAAATTTATTATTTATTCACATAAAACAAT-TACTTATAGCATTTT-ATATTGCATTAC
1 TC-AAA-TTATCATTTATTCACATAGAACAATATACTCATAGCATTTTCATATAGCATTAC
* * * ** *
25066 TCAACTTATCATTTATTCACATAGAAC-GTATACTCATGGTTTTTTCATATAGCATTAT
1 TCAAATTATCATTTATTCACATAGAACAATATACTCATAGCATTTTCATATAGCATTAC
*
25124 TCAAATTATCATTTATTCCCATAGAACA
1 TCAAATTATCATTTATTCACATAGAACA
25152 TATTCACATA
Statistics
Matches: 114, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
56 2 0.02
57 33 0.29
58 73 0.64
59 6 0.05
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (59 bp):
TCAAATTATCATTTATTCACATAGAACAATATACTCATAGCATTTTCATATAGCATTAC
Found at i:30666 original size:24 final size:24
Alignment explanation
Indices: 30638--30742 Score: 124
Period size: 24 Copynumber: 4.4 Consensus size: 24
30628 AAAAATACCG
30638 CGTAGAATTTGCACTGAAGTGACA
1 CGTAGAATTTGCACTGAAGTGACA
*
30662 CGTAGAATTTGCACTGAAGTGCCA
1 CGTAGAATTTGCACTGAAGTGACA
* *
30686 CGTAGAATATGCACTGAAGTGCCA
1 CGTAGAATTTGCACTGAAGTGACA
* *
30710 CATAGATTTTGTC-CTGAAG-GACCA
1 CGTAGAATTTG-CACTGAAGTGA-CA
*
30734 CATAGAATT
1 CGTAGAATT
30743 GTCCCGAAGG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
23 1 0.01
24 70 0.97
25 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (24 bp):
CGTAGAATTTGCACTGAAGTGACA
Found at i:30751 original size:23 final size:24
Alignment explanation
Indices: 30707--30757 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
30697 CACTGAAGTG
* *
30707 CCACATAGATTTTGTCCTGAAGGA
1 CCACATAGATATTGTCCCGAAGGA
30731 CCACATAGA-ATTGTCCCGAAGGA
1 CCACATAGATATTGTCCCGAAGGA
30754 CCAC
1 CCAC
30758 GCAAAACCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (24 bp):
CCACATAGATATTGTCCCGAAGGA
Found at i:30969 original size:58 final size:59
Alignment explanation
Indices: 30855--31049 Score: 179
Period size: 57 Copynumber: 3.4 Consensus size: 59
30845 ATTATTATTC
* * *
30855 AATTTATCATTTGTTTACATAAAATATATATACTCATAGTATTTCACATAGCATTACCTA
1 AATTTATCATTTATTCACATAAAATATATATACTCATAGTATTTCACATAGAATTA-CTA
* * * *
30915 AATTTATTATTTATTCACATAAAATA-AT-TACTCATA-TCATTTCATATCGAATTACTC
1 AATTTATCATTTATTCACATAAAATATATATACTCATAGT-ATTTCACATAGAATTACTA
* * * * * *
30972 AACTTATCATTTATTCACAT-AGA-ACATATACTCATAGTTTTTCATATA-ACATTATTCA
1 AATTTATCATTTATTCACATAAAATATATATACTCATAGTATTTCACATAGA-ATTACT-A
*
31030 AA-TTATCATTTATTCCCATA
1 AATTTATCATTTATTCACATA
31050 TAACATATTC
Statistics
Matches: 113, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
55 1 0.01
56 5 0.04
57 58 0.51
58 24 0.21
59 2 0.02
60 23 0.20
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.43
Consensus pattern (59 bp):
AATTTATCATTTATTCACATAAAATATATATACTCATAGTATTTCACATAGAATTACTA
Found at i:33717 original size:12 final size:12
Alignment explanation
Indices: 33677--33718 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
33667 AATTACATCT
*
33677 TTAAAA-TTTAT
1 TTAAAATTTTAA
33688 TTAAAATTTTAAA
1 TTAAAATTTT-AA
*
33701 ATAAAATTTTAA
1 TTAAAATTTTAA
33713 TTAAAA
1 TTAAAA
33719 ATAATATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 6 0.23
12 10 0.38
13 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTAAAATTTTAA
Found at i:41983 original size:23 final size:22
Alignment explanation
Indices: 41940--41991 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
41930 TTTATTTTTA
*
41940 AATTAGTATATTTTCTTTAAA-
1 AATTATTATATTTTCTTTAAAT
*
41961 AAGTTATTATATTTTTTTATAAAT
1 AA-TTATTATATTTTCTT-TAAAT
41985 AATTATT
1 AATTATT
41992 TAAAATAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.08
22 13 0.50
23 9 0.35
24 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
AATTATTATATTTTCTTTAAAT
Found at i:42036 original size:23 final size:23
Alignment explanation
Indices: 41983--42059 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
41973 TTTTTTATAA
*
41983 ATAATTATTTAAAATAAT-GTTAT
1 ATAATTA-TTAAAATAATATTTAT
**
42006 ATTTTTATTAAAATAATATTTAT
1 ATAATTATTAAAATAATATTTAT
42029 ATAATTATTATATAATTAA-ATTTAT
1 ATAATTATTA-A-AA-TAATATTTAT
42054 -TAATTA
1 ATAATTA
42060 ATTATTTGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 10 0.22
23 17 0.38
24 7 0.16
25 8 0.18
26 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
ATAATTATTAAAATAATATTTAT
Found at i:42040 original size:34 final size:36
Alignment explanation
Indices: 41955--42041 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 36
41945 GTATATTTTC
*
41955 TTTAAAA-AGTTATTATATTTTTTTATAAATAATTA
1 TTTAAAATAATTATTATATTTTTTTATAAATAATTA
*
41990 TTTAAAATAA-TGTTATATTTTTATTA-AAATAA-TA
1 TTTAAAATAATTATTATATTTTT-TTATAAATAATTA
*
42024 TTT-ATATAATTATTATAT
1 TTTAAAATAATTATTATAT
42042 AATTAAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
33 5 0.11
34 12 0.27
35 24 0.53
36 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (36 bp):
TTTAAAATAATTATTATATTTTTTTATAAATAATTA
Found at i:43517 original size:42 final size:42
Alignment explanation
Indices: 43458--43552 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
43448 TATGAGGTCT
* * *
43458 CAGGGGTACATGCCCAGTCCACCAGTTCAGATGCCACCTCTG
1 CAGGGGTACATGCCCAGTCCAACAGTTCAGATGCCACCACTA
* * *
43500 CAGGGGTATATGCCCAGTCCAACATTTCATATGCCACCACTA
1 CAGGGGTACATGCCCAGTCCAACAGTTCAGATGCCACCACTA
*
43542 CAGGGTTACAT
1 CAGGGGTACAT
43553 TCCTAGACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22
Consensus pattern (42 bp):
CAGGGGTACATGCCCAGTCCAACAGTTCAGATGCCACCACTA
Found at i:43611 original size:21 final size:20
Alignment explanation
Indices: 43541--43611 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
43531 TGCCACCACT
43541 ACAGGGTTACATTCCTAGACC
1 ACAGGGTTACATTCCTAG-CC
* * * *
43562 ACAGGGATACATACCCATCC
1 ACAGGGTTACATTCCTAGCC
*
43582 -CGTAAGGTTACATTCCTAGCC
1 AC--AGGGTTACATTCCTAGCC
43603 AACAGGGTT
1 -ACAGGGTT
43612 TTATTACACC
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 32 0.89
23 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (20 bp):
ACAGGGTTACATTCCTAGCC
Found at i:44088 original size:18 final size:19
Alignment explanation
Indices: 44067--44111 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
44057 TTTTATGTTT
44067 TTAAAATTCAAATT-CAAC
1 TTAAAATTCAAATTCCAAC
* * *
44085 TTAATATTCTAATTCCAAT
1 TTAAAATTCAAATTCCAAC
44104 TTAAAATT
1 TTAAAATT
44112 GTATTCGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAAATTCAAATTCCAAC
Found at i:44133 original size:49 final size:49
Alignment explanation
Indices: 44070--44198 Score: 181
Period size: 49 Copynumber: 2.7 Consensus size: 49
44060 TATGTTTTTA
* **
44070 AAATTCAAAT-TCAACTTAATATTCTAATTCCAATTTAAAATTGTATTCG
1 AAATTC-AATGTCAACTTAATATTCCAATTAAAATTTAAAATTGTATTCG
*
44119 AAATTCAATGTCAACTTCATATTCCAATTAAAATTTAAAATTGTATTCG
1 AAATTCAATGTCAACTTAATATTCCAATTAAAATTTAAAATTGTATTCG
* *
44168 AAATTCAAAGT-AACTTTATATTCCAATTAAA
1 AAATTCAATGTCAACTTAATATTCCAATTAAA
44199 GTTCATAATG
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
48 22 0.30
49 51 0.70
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (49 bp):
AAATTCAATGTCAACTTAATATTCCAATTAAAATTTAAAATTGTATTCG
Found at i:44189 original size:24 final size:24
Alignment explanation
Indices: 44113--44190 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
44103 TTTAAAATTG
* *
44113 TATTCGAAATTCAATGTCAACTTCA
1 TATTCGAAATTCAAAGT-AACTTTA
* * * ** *
44138 TATTC-CAATTAAAATTTAAAATTG
1 TATTCGAAATTCAAA-GTAACTTTA
44162 TATTCGAAATTCAAAGTAACTTTA
1 TATTCGAAATTCAAAGTAACTTTA
44186 TATTC
1 TATTC
44191 CAATTAAAGT
Statistics
Matches: 37, Mismatches: 14, Indels: 5
0.66 0.25 0.09
Matches are distributed among these distances:
24 24 0.65
25 13 0.35
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (24 bp):
TATTCGAAATTCAAAGTAACTTTA
Found at i:46764 original size:20 final size:21
Alignment explanation
Indices: 46729--46771 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
46719 TTTCAATCAT
**
46729 TTTCATATTATTTATT-TATA
1 TTTCATATTAACTATTATATA
46749 TTTCATATTAACTATTATATA
1 TTTCATATTAACTATTATATA
46770 TT
1 TT
46772 CCTTATGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTCATATTAACTATTATATA
Found at i:47811 original size:26 final size:25
Alignment explanation
Indices: 47781--47906 Score: 76
Period size: 25 Copynumber: 5.0 Consensus size: 25
47771 ATCGAACCTT
*
47781 ACCTTAAACCACTTTAACCTACACAA
1 ACCTTAAACCACTTTAACCTA-AAAA
* * * * *
47807 TCCTT-GACCACTCTCACATTAAAAA
1 ACCTTAAACCACTTTAAC-CTAAAAA
*
47832 ACCCTAAACCACTTTAACCTACAAAA
1 ACCTTAAACCACTTTAACCTA-AAAA
* * * *
47858 TCCTT-CACCACTTTCACCTTAACAA
1 ACCTTAAACCACTTTAACC-TAAAAA
* * *
47883 ACCCTATACAACTTTAACCTAAAA
1 ACCTTAAACCACTTTAACCTAAAA
47907 TCACTCCAAC
Statistics
Matches: 72, Mismatches: 23, Indels: 11
0.68 0.22 0.10
Matches are distributed among these distances:
25 38 0.53
26 34 0.47
ACGTcount: A:0.40, C:0.34, G:0.01, T:0.25
Consensus pattern (25 bp):
ACCTTAAACCACTTTAACCTAAAAA
Found at i:47861 original size:51 final size:51
Alignment explanation
Indices: 47785--47903 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
47775 AACCTTACCT
* *
47785 TAAACCACTTTAACCTACACAATCCTTGACCACTCTCACATTAAAAAACCC
1 TAAACCACTTTAACCTACAAAATCCTTCACCACTCTCACATTAAAAAACCC
* * *
47836 TAAACCACTTTAACCTACAAAATCCTTCACCACTTTCACCTTAACAAACCC
1 TAAACCACTTTAACCTACAAAATCCTTCACCACTCTCACATTAAAAAACCC
* *
47887 TATACAACTTTAACCTA
1 TAAACCACTTTAACCTA
47904 AAATCACTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.39, C:0.34, G:0.01, T:0.26
Consensus pattern (51 bp):
TAAACCACTTTAACCTACAAAATCCTTCACCACTCTCACATTAAAAAACCC
Found at i:47867 original size:25 final size:25
Alignment explanation
Indices: 47782--47876 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
47772 TCGAACCTTA
*
47782 CCTTAAACCACTTTAACCTACACAAT
1 CCTT-AACCACTTTAACCTACAAAAT
* * * * * *
47808 CCTTGACCACTCTCACATTAAAAAAC
1 CCTTAACCACTTTAAC-CTACAAAAT
*
47834 CCTAAACCACTTTAACCTACAAAAT
1 CCTTAACCACTTTAACCTACAAAAT
* *
47859 CCTTCACCACTTTCACCT
1 CCTTAACCACTTTAACCT
47877 TAACAAACCC
Statistics
Matches: 51, Mismatches: 17, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
25 30 0.59
26 21 0.41
ACGTcount: A:0.36, C:0.37, G:0.01, T:0.26
Consensus pattern (25 bp):
CCTTAACCACTTTAACCTACAAAAT
Found at i:48726 original size:11 final size:11
Alignment explanation
Indices: 48710--48735 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48700 TCAGGAAATG
48710 CGACTAATATA
1 CGACTAATATA
48721 CGACTAATATA
1 CGACTAATATA
48732 CGAC
1 CGAC
48736 ATTACCGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (11 bp):
CGACTAATATA
Found at i:49428 original size:23 final size:23
Alignment explanation
Indices: 49347--49422 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
49337 ACAGGTAAAA
* *
49347 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
49370 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
49393 ATATAATGTAATAGATAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
49416 ATATAAT
1 ATATAAT
49423 AAAATATGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:49607 original size:23 final size:23
Alignment explanation
Indices: 49574--49624 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
49564 CAAAACATAT
**
49574 TAGGTACCGCTTATATAATGTAA
1 TAGGTACCGCTTATATAATAAAA
*
49597 TAGGTAGCGCTTATATAATAAAA
1 TAGGTACCGCTTATATAATAAAA
49620 TAGGT
1 TAGGT
49625 TAATTACTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (23 bp):
TAGGTACCGCTTATATAATAAAA
Found at i:49615 original size:106 final size:109
Alignment explanation
Indices: 49358--49624 Score: 369
Period size: 106 Copynumber: 2.5 Consensus size: 109
49348 TATGATGTAA
* * * *
49358 TAGGTAGCACTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGATAGCGCTTATATAAT
1 TAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGC-TATATAAT
* *
49423 AAAATATGTTAATTACTAGAAACATTATCAAGCACAATAACATAT
65 AAAATAGGTTAATTACTAGAAACATAATCAAGCACAATAACATAT
* * * * *
49468 TAGGTACCGCTTATATAATTTAATAAGTAACGCTAATATAATGTAATAGGTAGTG-T-TATAATA
1 TAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGCTATATAATA
* *
49531 AAATAGGTTAATTATTGGAAACATAATCAAGCACAA-AACATAT
66 AAATAGGTTAATTACTAGAAACATAATCAAGCACAATAACATAT
**
49574 TAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGT
1 TAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGT
49625 TAATTACTGG
Statistics
Matches: 138, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
106 52 0.38
107 39 0.28
108 1 0.01
110 46 0.33
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (109 bp):
TAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGCTATATAATA
AAATAGGTTAATTACTAGAAACATAATCAAGCACAATAACATAT
Found at i:49627 original size:86 final size:87
Alignment explanation
Indices: 49494--49719 Score: 352
Period size: 87 Copynumber: 2.6 Consensus size: 87
49484 AATTTAATAA
*
49494 GTAACGCTAATATAATGTAATAGGTAGTG--T-TATAATAAAATAGGTTAATTATTGGAAACATA
1 GTAACGCTTATATAATGTAATAGGTAGTGCTTATATAATAAAATAGGTTAATTATTGGAAACATA
49556 ATCAAGCACAA-AACATATTAG
66 ATCAAGCACAATAACATATTAG
* * * * *
49577 GTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAATATT
1 GTAACGCTTATATAATGTAATAGGTAGTGCTTATATAATAAAATAGGTTAATTATTGGAAACATA
*
49642 ATTAAGCACAATAACATATTAG
66 ATCAAGCACAATAACATATTAG
*
49664 GTAACACTTATATAATGTAATAGGTAGTGCTTATATAATAAAATAGGTTAATTATT
1 GTAACGCTTATATAATGTAATAGGTAGTGCTTATATAATAAAATAGGTTAATTATT
49720 TAATTTGTTA
Statistics
Matches: 128, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
83 26 0.20
85 1 0.01
86 39 0.30
87 62 0.48
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (87 bp):
GTAACGCTTATATAATGTAATAGGTAGTGCTTATATAATAAAATAGGTTAATTATTGGAAACATA
ATCAAGCACAATAACATATTAG
Found at i:50009 original size:39 final size:38
Alignment explanation
Indices: 49966--50071 Score: 105
Period size: 39 Copynumber: 2.8 Consensus size: 38
49956 AATAAACAAT
49966 ATTATTATTAAAATTATTATTTATGTAAATATAAGAATA
1 ATTATTATTAAAA-TATTATTTATGTAAATATAAGAATA
** *
50005 ATTATTAAAAAAAAATAATATTT-T-TAAAATATAAGAATA
1 ATTATT--ATTAAAATATTATTTATGT-AAATATAAGAATA
*
50044 A-T-TTATT-TAATATTATTTATGTAAATAT
1 ATTATTATTAAAATATTATTTATGTAAATAT
50072 TATTATTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
34 9 0.16
35 8 0.15
36 1 0.02
37 2 0.04
38 2 0.04
39 21 0.38
40 7 0.13
41 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (38 bp):
ATTATTATTAAAATATTATTTATGTAAATATAAGAATA
Found at i:50043 original size:19 final size:19
Alignment explanation
Indices: 49992--50043 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
49982 TTATTTATGT
49992 AAATATAAGAATAATTATTA
1 AAATATAAGAAT-ATTATTA
* * * *
50012 AAAAAAAATAATATTTTTA
1 AAATATAAGAATATTATTA
50031 AAATATAAGAATA
1 AAATATAAGAATA
50044 ATTTATTTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AAATATAAGAATATTATTA
Found at i:50055 original size:20 final size:20
Alignment explanation
Indices: 49993--50056 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 20
49983 TATTTATGTA
49993 AATATAAGAATAA-TTA-TT
1 AATATAAGAATAATTTATTT
* *
50011 AA-AAAAAAATAATATT-TTT
1 AATATAAGAATAAT-TTATTT
50030 AAAATATAAGAATAATTTATTT
1 --AATATAAGAATAATTTATTT
50052 AATAT
1 AATAT
50057 TATTTATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
17 8 0.23
18 2 0.06
19 4 0.11
20 5 0.14
21 4 0.11
22 12 0.34
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
AATATAAGAATAATTTATTT
Found at i:50129 original size:29 final size:30
Alignment explanation
Indices: 50097--50158 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
50087 TATCTATAAT
*
50097 TTTA-TAAATAAAAAATTATGAT-TATTATA
1 TTTATTAAA-AAAAAATTATGATAAATTATA
* *
50126 TTTATTAAAATAAAATTATTATAAATTATA
1 TTTATTAAAAAAAAATTATGATAAATTATA
50156 TTT
1 TTT
50159 TTTATAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTATTAAAAAAAAATTATGATAAATTATA
Found at i:50443 original size:21 final size:21
Alignment explanation
Indices: 50419--50461 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
50409 TACCGGAAAT
*
50419 GTTAAAAACATTAATGTTTTA
1 GTTAAAAACAATAATGTTTTA
* *
50440 GTTAGAAATAATAATGTTTTA
1 GTTAAAAACAATAATGTTTTA
50461 G
1 G
50462 GTAATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (21 bp):
GTTAAAAACAATAATGTTTTA
Found at i:50891 original size:27 final size:26
Alignment explanation
Indices: 50826--50892 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
50816 ATTTATGTAA
50826 ATATTTTATT-AAAAATTATATCTAT
1 ATATTTTATTAAAAAATTATATCTAT
*
50851 A-ATTTATAAATAAAAAATTATGAT-TATT
1 ATATTT-T-ATTAAAAAATTAT-ATCTA-T
50879 ATATTTTATTAAAA
1 ATATTTTATTAAAA
50893 TAAAATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
24 4 0.12
25 2 0.06
26 2 0.06
27 17 0.50
28 5 0.15
29 4 0.12
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (26 bp):
ATATTTTATTAAAAAATTATATCTAT
Found at i:51492 original size:198 final size:197
Alignment explanation
Indices: 51020--51686 Score: 950
Period size: 198 Copynumber: 3.4 Consensus size: 197
51010 CACATATGTT
* * * * *
51020 ACATCGAAACAGATAATTATAATGTAATAGCTAAATTTACAATGTAACCAGTATAAATATACCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGT-ACCGGTAGAAATATACCGG
* * * **
51085 TTTTATGAGAGAATAGGTCTACATAATGTATCGACACAAATTTGAA--AAGTGTCGATA-TATTT
65 TTTTATGAGAAAATAGGTCTACATAATGTATCGACAC--GTTTTAAGTTTGTGTCGATACT-TTT
*
51147 TGTCCAGAATGAATGACAAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGA
127 T-TCCAGAATGAATG-CCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGA
51212 TCCCAAAA
190 TCCCAAAA
* * * *
51220 ATATCGAAACCGATAATTACAATGTAATATGTAAATTTATAATGTACTCGGTAGAAATATATCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAC-CGGTAGAAATATACCGG
* *
51285 TTTTATGAGAAAATAGATCTACATAATGTATCGACACGTTTTAAGTTTGCGTCGATACTTTTTTC
65 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTC
*
51350 CAGAATGAATGTCCAACGAGGTGCACGCATAAAGTATCGATACATTTATTAAAAGTATCGATCCC
130 CAGAATGAATG-CCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
51415 AAAA
194 AAAA
*
51419 A-ATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACTCGGTAGAAATATACCAG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAC-CGGTAGAAATATACCGG
51483 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTC
65 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTC
* * * *
51548 CAAAATGAATGCCAACGAGGTGCACGCATAAAATGTCGATACATTTA--AAATGTATCCATCCCA
130 CAGAATGAATGCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
51611 AAA
195 AAA
* * * * *
51614 ACATCGAAACCAATAATTATAATGTAATAGGTAAATTTGCAATGTTGCCGGTATAAATATACCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATG-TACCGGTAGAAATATACCGG
51679 TTTTATGA
65 TTTTATGA
51687 TAGAATATGT
Statistics
Matches: 425, Mismatches: 36, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
195 18 0.04
196 62 0.15
197 36 0.08
198 137 0.32
199 71 0.17
200 100 0.24
201 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (197 bp):
ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCGGTAGAAATATACCGGT
TTTATGAGAAAATAGGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTCC
AGAATGAATGCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAA
AA
Found at i:51746 original size:23 final size:23
Alignment explanation
Indices: 51690--51746 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
51680 TTTATGATAG
*
51690 AATATGTCAATATAAGCGCTACAT
1 AATATGT-TATATAAGCGCTACAT
* ** *
51714 ATTACATTATATAAGCGCTACCT
1 AATATGTTATATAAGCGCTACAT
51737 AATATGTTAT
1 AATATGTTAT
51747 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (23 bp):
AATATGTTATATAAGCGCTACAT
Found at i:51804 original size:87 final size:87
Alignment explanation
Indices: 51699--51938 Score: 374
Period size: 87 Copynumber: 2.8 Consensus size: 87
51689 GAATATGTCA
* *
51699 ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATATTT
51764 CCAGTAATTAACCTATTTTATT
66 CCAGTAATTAACCTATTTTATT
* ** *
51786 ATATAAGCGCTGCCTATTACATTATATAAATGTTACCTAATATGTTATTATGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATATTT
*
51851 CTAGTAATTAACCTATTTTATT
66 CCAGTAATTAACCTATTTTATT
* * * *
51873 ATATAAGTGCTACCTATTACATTAT-TAAGCGCTACCTAATTTGTTATTTTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATATTT
51937 CC
66 CC
51939 GGTTAAATGA
Statistics
Matches: 137, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 34 0.25
87 103 0.75
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATATTT
CCAGTAATTAACCTATTTTATT
Found at i:51887 original size:23 final size:22
Alignment explanation
Indices: 51861--51920 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
51851 CTAGTAATTA
*
51861 ACCTATTTTATTATATAAGTGCT
1 ACCTATTTTATTAT-TAAGCGCT
**
51884 ACCTATTACATTATTAAGCGCT
1 ACCTATTTTATTATTAAGCGCT
* *
51906 ACCTAATTTGTTATT
1 ACCTATTTTATTATT
51921 TTACTTGATA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (22 bp):
ACCTATTTTATTATTAAGCGCT
Found at i:54324 original size:48 final size:48
Alignment explanation
Indices: 54212--54324 Score: 108
Period size: 48 Copynumber: 2.4 Consensus size: 48
54202 ATTTGGTATG
* *
54212 ATTAAACATGTATTATCATTTGATTTATGAGTGGGATTAACTTGATATT
1 ATTAAACATGTATTATCATTTGATTTATGAGTGAGATTAACTT-ATATA
* * * *
54261 ATTAAA-GTGTGTTATCATTTGATTTACT-AGTGATATTGA-TT-TACTCA
1 ATTAAACATGTATTATCATTTGATTTA-TGAGTGAGATTAACTTATA-T-A
54308 ATTAAACATGTATTATC
1 ATTAAACATGTATTATC
54325 GTATAAATAG
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
45 2 0.04
46 1 0.02
47 8 0.15
48 34 0.65
49 7 0.13
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (48 bp):
ATTAAACATGTATTATCATTTGATTTATGAGTGAGATTAACTTATATA
Found at i:60902 original size:17 final size:18
Alignment explanation
Indices: 60875--60912 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
60865 TTCATCATAA
**
60875 TATTCTTAAATTTATTTT
1 TATTCTTAAATAAATTTT
60893 TATT-TTAAATAAATTTT
1 TATTCTTAAATAAATTTT
60910 TAT
1 TAT
60913 AAATATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTCTTAAATAAATTTT
Done.