Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004021.1 Hibiscus syriacus cultivar Beakdansim tig00008782_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: 58911
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:1748 original size:15 final size:15
Alignment explanation
Indices: 1724--1759 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1714 GAACGATACT
1724 TGAG-AATTTGAAGG
1 TGAGAAATTTGAAGG
1738 TGAGAAATTTGAAGG
1 TGAGAAATTTGAAGG
1753 TGAGAAA
1 TGAGAAA
1760 ATACCATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.25
Consensus pattern (15 bp):
TGAGAAATTTGAAGG
Found at i:2543 original size:15 final size:15
Alignment explanation
Indices: 2523--2554 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2513 GATCAATACC
2523 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2538 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2553 TT
1 TT
2555 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:6367 original size:8 final size:9
Alignment explanation
Indices: 6340--6370 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
6330 AAATGGCAAT
6340 CATTCTTTA
1 CATTCTTTA
6349 CATTCTTTA
1 CATTCTTTA
6358 CATT-TTTA
1 CATTCTTTA
6366 CATTC
1 CATTC
6371 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:9969 original size:36 final size:37
Alignment explanation
Indices: 9902--9972 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
9892 AGATTTGAAA
* *
9902 AAAAAATGAATGAAGAAAGAAAAATGGAAAAAGAGAG
1 AAAAAATGAATGAAAAAAGAAAAATGAAAAAAGAGAG
*
9939 AAAAAATG-TTGAAAAAAGAAAAAAT-AAAAAAGAG
1 AAAAAATGAATGAAAAAAG-AAAAATGAAAAAAGAG
9973 GGTCAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 16 0.53
37 14 0.47
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (37 bp):
AAAAAATGAATGAAAAAAGAAAAATGAAAAAAGAGAG
Found at i:10358 original size:19 final size:19
Alignment explanation
Indices: 10334--10380 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
10324 ATTCAATTTA
* *
10334 TTATTTTTTGAGATTTAAT
1 TTATTTTTTGAAATTCAAT
10353 TTA-TTTTTGAAATTCAAT
1 TTATTTTTTGAAATTCAAT
10371 TTATTCTTTT
1 TTATT-TTTT
10381 ATTTTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 16 0.67
19 4 0.17
20 4 0.17
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (19 bp):
TTATTTTTTGAAATTCAAT
Found at i:11696 original size:113 final size:112
Alignment explanation
Indices: 11487--12283 Score: 922
Period size: 113 Copynumber: 7.0 Consensus size: 112
11477 CAAAGATTCG
11487 AATCCATCATTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAATG-ACTCATCTGAAGA
1 AATCCATCATTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAA-GAACTCATCTGAAGA
* * ** *
11551 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCGAACCTTTTGTTTG
65 AGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC-AACCTTTTGTTTA
* * * *
11600 AATTCATCATTCGATGAATCAACGTTTCCAGAGAAGTTCATAATGAAAAGAACTCATCTGAAGAA
1 AATCCATCATTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA
* * * ** *
11665 GAAAGAAAAAATTCATAATGAGAAAATTTTGTTCAACCTTTTGTTCA
66 GAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTA
* * * *
11712 AATCCAT-A-ACAATGGATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAATA
1 AATCCATCATTCGATGGATCAACATTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
11774 AGGAAGAGGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCA
65 AGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTA
*
11822 AATCCATCACTT-GATGGATCAATATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCA-TTCGATGGATCAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
11886 AGGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTC
64 AAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTA
* * *
11935 AATTCATCACTCGATGGATCAGCATTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTCGATGGATCAACA-TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
12000 AAGAAAGAAGAAGTTCATAATAAGAAGAGCTTGTTCAGCCTTTT-TCTTC
64 AAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGT-TTA
* * *
12049 AATTCATCACTCGATGGATCAGCATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTCGATGGATCAACA-TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
12114 AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGA
65 AGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTG-TTTA
** ** * * *
12163 ATCTATCACAGAATGAGATAGATCAACATCAATTTTTTCTAGAGAAAGTTCATAATAAGAAGAAC
1 A---ATC-CATCATTCGATGGATC-A-A-C-A---TTTCCAGAG-AAGTTCATAATGAGAAGAAC
* *
12228 TCATCTGAAGAAGCAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTCTTGT
54 TCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGT
12284 ATAATCTATC
Statistics
Matches: 598, Mismatches: 63, Indels: 35
0.86 0.09 0.05
Matches are distributed among these distances:
109 1 0.00
110 92 0.15
111 2 0.00
112 37 0.06
113 249 0.42
114 121 0.20
117 2 0.00
118 10 0.02
119 1 0.00
121 1 0.00
122 1 0.00
124 9 0.02
125 72 0.12
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (112 bp):
AATCCATCATTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA
GAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTA
Found at i:12067 original size:227 final size:224
Alignment explanation
Indices: 11491--12278 Score: 957
Period size: 227 Copynumber: 3.5 Consensus size: 224
11481 GATTCGAATC
*
11491 CATCATTCGATGGATCAACATTTCCAGAG-AAGTTCATAATGAGAATG-ACTCATCTGAAGAAGG
1 CATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAA-GAACTCATCTGAAGAAGG
* ** * * *
11554 AAGAAGAAATTCATAATGAGAAGAATTTGTTCGAACCTTTTGT-TTGAATTCATCATTCGATGAA
65 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTC-AACCTTTT-TCTTCAATTCATCACTCGATGGA
* * * * *
11618 TCAACGTTTCCAGAGAAGTTCATAATGAAAAGAACTCATCTGAAGAAGAAAGAAAAAATTCATAA
128 TCAA-TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAGAAGAAGTTCATAA
* ** *
11683 TGAGAAAATTTTGTTCAACCTTTTG-TTCAAATC
192 TGAGAAGAGCTTGTTCAACCTTTTGCTTC-AATT
* * ** *
11716 CAT-A-ACAATGGATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAATAAGGA
1 CATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
11778 AGAGGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC-TCAAATCCATCACTTGATGGATC
66 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTTCTTC-AATTCATCACTCGATGGATC
11842 AATATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAGAAGAAGTTCATAAT
130 AAT-TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAGAAGAAGTTCATAAT
11907 GAGAAGAGCTTGTTCAACCTTTTGCTTCAATT
193 GAGAAGAGCTTGTTCAACCTTTTGCTTCAATT
* *
11939 CATCACTCGATGGATCAGCATTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 CATCACTCGATGGATCAACA-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
12004 AAGAAGAAGTTCATAATAAGAAGAGCTTGTTCAGCCTTTTTCTTCAATTCATCACTCGATGGATC
65 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTTCTTCAATTCATCACTCGATGGATC
12069 AGCATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AAGAAGAAGTTCATAA
130 A--ATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAAGAAGAAGTTCATAA
* *
12133 TGAGAAGAGCTTGTTCAACCTTTTGCATGAA-T
192 TGAGAAGAGCTTGTTCAACCTTTTGCTTCAATT
* * * *
12165 CTATCACAGAATGAGATAGATCAACATCAATTTTTTCTAGAGAAAGTTCATAATAAGAAGAACTC
1 C-ATCAC----T-CGATGGATC-A-A-C-A---TTTCCAGAGAAAGTTCATAATGAGAAGAACTC
*
12230 ATCTGAAGAAGCAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCT
53 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCT
12279 CTTGTATAAT
Statistics
Matches: 489, Mismatches: 47, Indels: 41
0.85 0.08 0.07
Matches are distributed among these distances:
221 1 0.00
222 36 0.07
223 151 0.31
224 5 0.01
225 14 0.03
226 10 0.02
227 168 0.34
228 14 0.03
229 2 0.00
231 1 0.00
232 7 0.01
233 1 0.00
235 1 0.00
236 1 0.00
238 77 0.16
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (224 bp):
CATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTTCTTCAATTCATCACTCGATGGATCA
ATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAGAAGAAGTTCATAATGAG
AAGAGCTTGTTCAACCTTTTGCTTCAATT
Found at i:12218 original size:125 final size:124
Alignment explanation
Indices: 12066--12361 Score: 402
Period size: 125 Copynumber: 2.4 Consensus size: 124
12056 CACTCGATGG
* * *
12066 ATCAGCATTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 ATCAACATTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGCAAGAAGAAGTTCA
* * *
12130 TAATGAGAAGAGCTTGTTCAACCTTTTGCATGAATCTATCACAGAATGAGATAGATCAAC
66 TAATGAGAAGAGCTTGTTCAACCTCTTGCAT-AATCTATCACAAAAGGAGATAGATCAAC
** *
12190 ATCAATTTTTTCTAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGCAAGAAGAAGTTCA
1 ATCAACATTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGCAAGAAGAAGTTCA
* * * *
12255 TAATGAGAAGAGCTTGTTCAACCTCTTGTATAATCTATCATAAAAGGAGATAGATTAGC
66 TAATGAGAAGAGCTTGTTCAACCTCTTGCATAATCTATCACAAAAGGAGATAGATCAAC
* * *
12314 ATTAACATTTTCATA-A-ATA-TTTATAATGAGAAGAACTCATCTGAAGAA
1 ATCAACATTTTC-TAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
12362 TAAGGAGCAG
Statistics
Matches: 151, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
122 27 0.18
123 2 0.01
124 46 0.30
125 76 0.50
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (124 bp):
ATCAACATTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGCAAGAAGAAGTTCA
TAATGAGAAGAGCTTGTTCAACCTCTTGCATAATCTATCACAAAAGGAGATAGATCAAC
Found at i:12651 original size:29 final size:31
Alignment explanation
Indices: 12610--12688 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 31
12600 CTCATTTGAA
* *
12610 TATTATTTATATTATTATTATTATTATAATAT
1 TATTATTAATATTATTATTATTATTATTAT-T
* * **
12642 TATTATTATTATTATTATTTATTATTAATAAA
1 TATTATTAATATTATTA-TTATTATTATTATT
12674 TATTATTACATATTA
1 TATTATTA-ATATTA
12689 CAGGCCCAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 23 0.61
33 15 0.39
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TATTATTAATATTATTATTATTATTATTATT
Found at i:12679 original size:20 final size:19
Alignment explanation
Indices: 12618--12681 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
12608 AATATTATTT
*
12618 ATATTATTATTATTATTATA
1 ATATTATTATTATTAATA-A
12638 ATATTATTATTATT-AT--
1 ATATTATTATTATTAATAA
12654 -TATTATTTATTATTAATAA
1 ATATTA-TTATTATTAATAA
12673 ATATTATTA
1 ATATTATTA
12682 CATATTACAG
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
15 5 0.13
16 8 0.21
17 2 0.05
19 4 0.11
20 19 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTATTATTATTAATAA
Found at i:12681 original size:3 final size:3
Alignment explanation
Indices: 12610--12668 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
12600 CTCATTTGAA
*
12610 TAT TAT T-T ATAT TAT TAT TAT TAT TA- TAA TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12654 TAT TATT TAT TAT TA
1 TAT TA-T TAT TAT TA
12669 ATAAATATTA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
2 3 0.06
3 44 0.86
4 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:15360 original size:12 final size:12
Alignment explanation
Indices: 15343--15370 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
15333 TGTTTCACCA
15343 CAAACACAATCT
1 CAAACACAATCT
15355 CAAACACAATCT
1 CAAACACAATCT
15367 CAAA
1 CAAA
15371 ACTCACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (12 bp):
CAAACACAATCT
Found at i:15510 original size:24 final size:24
Alignment explanation
Indices: 15482--15533 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
15472 GTGAGTACTA
**
15482 GTCAGTATTCGAAATTTGATCTTG
1 GTCAGTACCCGAAATTTGATCTTG
* *
15506 GTCAGTACCCGAACTTTGATGTTG
1 GTCAGTACCCGAAATTTGATCTTG
15530 GTCA
1 GTCA
15534 ATACTCGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (24 bp):
GTCAGTACCCGAAATTTGATCTTG
Found at i:17854 original size:18 final size:18
Alignment explanation
Indices: 17819--17854 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17809 AAGAAAAAGG
*
17819 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
*
17837 AAATCAAAATCCCTATCA
1 AAATCAAAATCCCAATCA
17855 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:18279 original size:14 final size:14
Alignment explanation
Indices: 18262--18298 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
18252 ATCAAATTAA
18262 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
18276 ACAACTCAACTTTT
1 ACAAATCAACATTT
18290 ACAAATCAA
1 ACAAATCAA
18299 TTAAACAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:19761 original size:21 final size:21
Alignment explanation
Indices: 19737--19831 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
19727 GAGGGACCCA
*
19737 TTGAACGATGACAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
* * * *
19758 TTGAATGGTGGGAAGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
* *
19779 TTGAACGGTGAGAGGAGCCTC
1 TTGAACGATGAGAGGGGCCTC
* * *
19800 TTGAATGAT-AGGAGGTGTCTC
1 TTGAACGATGA-GAGGGGCCTC
19821 TTGAACGATGA
1 TTGAACGATGA
19832 CAGGTGAATC
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (21 bp):
TTGAACGATGAGAGGGGCCTC
Found at i:19783 original size:42 final size:41
Alignment explanation
Indices: 19713--19835 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 41
19703 GTGAATCGAG
* *
19713 CTCTTAAATGGTGGGAGGGACC-CATTGAACGATGACAGGGGC
1 CTCTTGAATGGTGGGAGGG-CCTC-TTGAACGATGACAGGAGC
* *
19755 CTCTTGAATGGTGGGAAGGGCCTCTTGAACGGTGAGAGGAGC
1 CTCTTGAATGGTGGG-AGGGCCTCTTGAACGATGACAGGAGC
* * *
19797 CTCTTGAATGATAGGAGGTGTCTCTTGAACGATGACAGG
1 CTCTTGAATGGTGGGAGG-GCCTCTTGAACGATGACAGG
19836 TGAATCAGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 3 0.04
42 61 0.88
43 5 0.07
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGCCTCTTGAACGATGACAGGAGC
Found at i:21559 original size:14 final size:14
Alignment explanation
Indices: 21540--21571 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
21530 ACGCGAAAAT
21540 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
21554 GAAAATCGCAACGC
1 GAAAATCGCAACGA
21568 GAAA
1 GAAA
21572 CTAAAATCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.06
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:21982 original size:20 final size:21
Alignment explanation
Indices: 21957--22014 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
21947 TCTGAGAGAT
21957 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
21977 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
* *
21999 GAAGATGGGGACGGAT
1 GGAGAT-GAGACGGAT
22015 GTCACCGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 6 0.18
22 27 0.82
ACGTcount: A:0.24, C:0.14, G:0.43, T:0.19
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:21991 original size:22 final size:22
Alignment explanation
Indices: 21964--22014 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
21954 GATGGAGATA
*
21964 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGAAGATGGG
*
21986 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGCCGAAGATGGG
22008 GACGGAT
1 GACGGAT
22015 GTCACCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGGG
Found at i:22199 original size:20 final size:20
Alignment explanation
Indices: 22174--22269 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 20
22164 TAAACGCGCT
22174 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
**
22194 TTGCGAATTTGA-TTATCGTA
1 TTGCGAATTTGACTT-TCGCG
* *
22214 TTGCAAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGCG
** *
22234 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGACTTTC-GCG
22255 TTGCGAATTTGACTT
1 TTGCGAATTTGACTT
22270 CTGTGTTGTA
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
19 2 0.03
20 42 0.70
21 16 0.27
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:22277 original size:20 final size:20
Alignment explanation
Indices: 22174--22297 Score: 94
Period size: 20 Copynumber: 6.2 Consensus size: 20
22164 TAAACGCGCT
*
22174 TTGCGAATTTGACTT-TCGCG
1 TTGCGAATTTGACTTCT-GTG
* *
22194 TTGCGAATTTGA-TTATCGTA
1 TTGCGAATTTGACTTCT-GTG
* *
22214 TTGCAAATTTGACTATC-GCG
1 TTGCGAATTTGACT-TCTGTG
* *
22234 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTG-ACTTCTGTG
22255 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
* *
22275 TTG-TACATTTGACTTATGTG
1 TTGCGA-ATTTGACTTCTGTG
22295 TTG
1 TTG
22298 TGATTTACAG
Statistics
Matches: 85, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
19 3 0.04
20 65 0.76
21 16 0.19
22 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:22342 original size:21 final size:21
Alignment explanation
Indices: 22318--22383 Score: 114
Period size: 21 Copynumber: 3.1 Consensus size: 21
22308 ATTCACGTTC
22318 CGAATTTGGAAAATTGCAACG
1 CGAATTTGGAAAATTGCAACG
22339 CGAATTTGGAAAATTGCAACG
1 CGAATTTGGAAAATTGCAACG
* *
22360 CGAATTTGGAAAATCGCAATG
1 CGAATTTGGAAAATTGCAACG
22381 CGA
1 CGA
22384 TTTATATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (21 bp):
CGAATTTGGAAAATTGCAACG
Found at i:24429 original size:3 final size:3
Alignment explanation
Indices: 24421--24479 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
24411 TATGTAACCA
24421 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
24469 TAT TAT TAT TA
1 TAT TAT TAT TA
24480 GTAGTAGTAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:24838 original size:27 final size:27
Alignment explanation
Indices: 24808--24864 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
24798 ATTATTATAG
24808 TTAACTTATAGACATTGATTATACAAA
1 TTAACTTATAGACATTGATTATACAAA
24835 TTAACTTATAGACATTGATTATACAAA
1 TTAACTTATAGACATTGATTATACAAA
24862 TTA
1 TTA
24865 TATGGTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (27 bp):
TTAACTTATAGACATTGATTATACAAA
Found at i:39461 original size:2 final size:2
Alignment explanation
Indices: 39450--39518 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
39440 AAAAGGCGAT
39450 TA TA -A 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
39491 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
39519 GCCAAACTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41341 original size:134 final size:134
Alignment explanation
Indices: 41114--42034 Score: 1068
Period size: 134 Copynumber: 6.9 Consensus size: 134
41104 GTCGAACTCA
* ** * *
41114 ATTCAATCTTCTCTGAGTGACAGTGGAATGAATCAA-CTCATCCAGATCTGATATTCCCTCCAGA
1 ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTC-CCCAGATCTGATATTCCCTCCAGA
* * *
41178 AGAAGAAGAACATATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTAACAGTGGAACAAGTCTA
65 AGAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
*
41243 CCTCA
130 CCTCG
* *
41248 ATTTAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCCAGATATGATATTCCCTCCAGAA
1 ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCCAGATCTGATATTCCCTCCAGAA
* *
41313 GAAGCATAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTGC
66 GAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGC
41378 CTCG
131 CTCG
* ** *
41382 ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCCATATCTTCTATTCCCTTCA-AA
1 ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCCAGATCTGATATTCCCTCCAGAA
* * * * * *
41446 AAAG-ATAAACAAATCCCTCTTTTTCAAGATTTTATATTCCCTGAGTAACAGTGGAGCAAGT-TG
66 GAAGCA-GAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
* *
41509 GCTTG
130 CCTCG
* * * * * * * *
41514 ATTCAATTTTCCATGAGTGACAA-GAAATGAATCGACGTCCCCATATCTTATATTCCCTCTAGAA
1 ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCCAGATCTGATATTCCCTCCAGAA
* * * * *
41578 GAAGCGGAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACACTGGAACAAGTCTGG
66 GAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGC
41643 CTCG
131 CTCG
* * * * * * *
41647 ATTCAATCTTCCCTAAGTGATAGCAGAATGAATCAACGTCCCCATATATGATATTCCCTCCAGAA
1 ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCCAGATCTGATATTCCCTCCAGAA
* * * ** * *
41712 GAAGCGGAATAAATCTATATCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTTC
66 GAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGC
*
41777 C-CTT
131 CTC-G
* ** * * * *
41781 ATTCAATCTTCCCTGAGTGATAGTGGAATGGATCAATCTCCCCTAGATATAATATTCCCTCCAGA
1 ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCC-AGATCTGATATTCCCTCCAGA
* * * *
41846 AGAAGCAAAACATATCCCTCTCTTTGAAGATTTGATATTCCCTGAGTCACGGTGGAACAAGTCTG
65 AGAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
41911 CCTCG
130 CCTCG
* ** * ** * *
41916 ATTCAATCTTCCCTGAGTGAAAATAGAATGGAT-AAACTCCATCAGATCTTATATTCCCTCCAGA
1 ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCC-CCAGATCTGATATTCCCTCCAGA
* *
41980 AGAAGCAGAACATATCCCTCTCTTTCAAGA--TAATATTCCCTGAGTGACAGTGGAA
65 AGAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAA
42035 TGGATCAACC
Statistics
Matches: 682, Mismatches: 95, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
131 32 0.05
132 103 0.15
133 79 0.12
134 359 0.53
135 108 0.16
136 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (134 bp):
ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCCAGATCTGATATTCCCTCCAGAA
GAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGC
CTCG
Found at i:41607 original size:265 final size:263
Alignment explanation
Indices: 41114--42034 Score: 1049
Period size: 269 Copynumber: 3.5 Consensus size: 263
41104 GTCGAACTCA
* * * * *
41114 ATTCAATCTTCTCTGAGTGACAGTGGAATGAATCAACTCATCCAGATCTGATATTCCCTCCAGAA
1 ATTCAATCTTCCCTGAGTGACAGCGGAATGAATCAAGTC-CCCATATCTGATATTCCCTCCAGAA
* *
41179 GAAGAAGAACATATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTAACAGTGGAACAAGTCTAC
65 GAAGAA-AACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT-TAC
* * * *
41244 CTCAATTTAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCCAGATATGATATTCCCTCC
128 CT-TATTCAATCTTCCCTGAGTGACAA-GGAATGAATCAACGTCCCCAGATATAATATTCCCTCC
* *
41309 AGAAGAAGCATAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGT
191 AGAAGAAGCAAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
41374 CTGCCTCG
256 CTGCCTCG
* ** *
41382 ATTCAATCTTCCCTGAGTGACAACGGAATGAATCAATGTCCCCATATCTTCTATTCCCTTCA-AA
1 ATTCAATCTTCCCTGAGTGACAGCGGAATGAATCAA-GTCCCCATATCTGATATTCCCTCCAGAA
* * * * **
41446 AAAGATAAACAAATCCCTCTTTTTCAAGATTTTATATTCCCTGAGTAACAGTGGAGCAAGTTGGC
65 GAAGA-AAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTTACC
* * * * * * * *
41511 TTGATTCAATTTTCCATGAGTGACAAGAAATGAATCGACGTCCCCATATCTTATATTCCCTCTAG
129 TT-ATTCAATCTTCCCTGAGTGACAAGGAATGAATCAACGTCCCCAGATATAATATTCCCTCCAG
** * * *
41576 AAGAAGCGGAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACACTGGAACAAGTCT
193 AAGAAGCAAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
*
41641 GGCTCG
258 GCCTCG
* * * *
41647 ATTCAATCTTCCCTAAGTGATAGCAGAATGAATCAACGTCCCCATATATGATATTCCCTCCAGAA
1 ATTCAATCTTCCCTGAGTGACAGCGGAATGAATCAA-GTCCCCATATCTGATATTCCCTCCAGAA
** * ** * *
41712 GAAGCGGAATAAATCTATATCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTTC
65 GAAG-AAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG--TTA
* * *
41777 CCTTATTCAATCTTCCCTGAGTGATAGTGGAATGGATCAATC-TCCCCTAGATATAATATTCCCT
127 CCTTATTCAATCTTCCCTGAGTGACA-AGGAATGAATCAA-CGTCCCC-AGATATAATATTCCCT
* * *
41841 CCAGAAGAAGCAAAACATATCCCTCTCTTTGAAGATTTGATATTCCCTGAGTCACGGTGGAACAA
189 CCAGAAGAAGCAAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
41906 GTCTGCCTCG
254 GTCTGCCTCG
* *** * * * * * *
41916 ATTCAATCTTCCCTGAGTGAAAATAGAATGGATAAACTCCATCAGATCTTATATTCCCTCCAGAA
1 ATTCAATCTTCCCTGAGTGACAGCGGAATGAATCAAGTCC-CCATATCTGATATTCCCTCCAGAA
* * * *
41981 GAAGCAGAACATATCCCTCTCTTTCAAGA--TAATATTCCCTGAGTGACAGTGGAA
65 GAAG-AAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAA
42035 TGGATCAACC
Statistics
Matches: 547, Mismatches: 95, Indels: 23
0.82 0.14 0.03
Matches are distributed among these distances:
265 149 0.27
266 74 0.14
267 97 0.18
268 73 0.13
269 154 0.28
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (263 bp):
ATTCAATCTTCCCTGAGTGACAGCGGAATGAATCAAGTCCCCATATCTGATATTCCCTCCAGAAG
AAGAAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTTACCTT
ATTCAATCTTCCCTGAGTGACAAGGAATGAATCAACGTCCCCAGATATAATATTCCCTCCAGAAG
AAGCAAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCC
TCG
Found at i:42036 original size:91 final size:91
Alignment explanation
Indices: 41924--42125 Score: 246
Period size: 92 Copynumber: 2.2 Consensus size: 91
41914 CGATTCAATC
* * * * * *
41924 TTCCCTGAGTGAAAATAGAATGGAT-AAACT-CCATCAGATCTTATATTCCCTCCAGAAGAAGCA
1 TTCCCTGAGTGACAGTAGAATGGATCAAACTCCCCT-AAATATGATATTCCCTCCAGAAGAAGCA
41987 GAACATATCCCTCTCTTTCAAGATAATA
65 GAACATATCCCTCTCTTTCAAGAT-ATA
* * *
42015 TTCCCTGAGTGACAGTGGAATGGATCAACCTCCCCTAAATATGATATTCCCTTCAGAAGAAGCAG
1 TTCCCTGAGTGACAGTAGAATGGATCAAACTCCCCTAAATATGATATTCCCTCCAGAAGAAGCAG
* * *
42080 AATATATCCCTCTCTTTGAAGATTTA
66 AACATATCCCTCTCTTTCAAGATATA
* *
42106 TTCCCTAAGTCACAGTAGAA
1 TTCCCTGAGTGACAGTAGAA
42126 CAAGTCTACC
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
91 41 0.44
92 50 0.53
93 3 0.03
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (91 bp):
TTCCCTGAGTGACAGTAGAATGGATCAAACTCCCCTAAATATGATATTCCCTCCAGAAGAAGCAG
AACATATCCCTCTCTTTCAAGATATA
Found at i:42226 original size:223 final size:226
Alignment explanation
Indices: 41789--42259 Score: 700
Period size: 223 Copynumber: 2.1 Consensus size: 226
41779 TTATTCAATC
* *
41789 TTCCCTGAGTGATAGTGGAATGGATCAATCTCCCCTAGATATAATATTCCCTCCAGAAGAAGCAA
1 TTCCCTGAGTGATAGTGGAATGGATCAACCTCCCCTAAATATAATATTCCCTCCAGAAGAAGCAA
* * * *
41854 AACATATCCCTCTCTTTGAAGATTTGATATTCCCTGAGTCACGGTGGAACAAGTCTGCCTCGATT
66 AACATATCCCTCTCTTTGAAGATTT-ATATTCCCTAAGTCACAGTAGAACAAGTCTACCTCGATT
* * *
41919 CAATCTTCCCTGAGTGAAAATAGAATGGATAAACTCCATCAGATCTTATATTCCCTCCAGAAGAA
130 CAATCTTCCCTGAGTGAAAATAAAATGGATAAACTCCATCAGATATGATATTCCCTCCAGAAGAA
*
41984 GCAGAACATATCCCTCTCTTTCAAGA-TAATA
195 GCAGAACATATCACTCTCTTTCAAGATTAATA
* * * *
42015 TTCCCTGAGTGACAGTGGAATGGATCAACCTCCCCTAAATATGATATTCCCTTCAGAAGAAGCAG
1 TTCCCTGAGTGATAGTGGAATGGATCAACCTCCCCTAAATATAATATTCCCTCCAGAAGAAGCAA
*
42080 AATATATCCCTCTCTTTGAAGA-TT-TATTCCCTAAGTCACAGTAGAACAAGTCTACCTCGATTC
66 AACATATCCCTCTCTTTGAAGATTTATATTCCCTAAGTCACAGTAGAACAAGTCTACCTCGATTC
* * * *
42143 AATCTTCCCTGAGTGAAAATAAAATGTATCAACTCC-CCTTGATATGATATTCCCTCCAGAAGAA
131 AATCTTCCCTGAGTGAAAATAAAATGGATAAACTCCATC-AGATATGATATTCCCTCCAGAAGAA
42207 GC-GAAACATATCACTCTCTTTCAAGATTTAATA
195 GCAG-AACATATCACTCTCTTTCAAGA-TTAATA
42240 TTCCCTGAGTGATAGTGGAA
1 TTCCCTGAGTGATAGTGGAA
42260 CAAGTCTGCC
Statistics
Matches: 221, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
222 2 0.01
223 113 0.51
225 26 0.12
226 80 0.36
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (226 bp):
TTCCCTGAGTGATAGTGGAATGGATCAACCTCCCCTAAATATAATATTCCCTCCAGAAGAAGCAA
AACATATCCCTCTCTTTGAAGATTTATATTCCCTAAGTCACAGTAGAACAAGTCTACCTCGATTC
AATCTTCCCTGAGTGAAAATAAAATGGATAAACTCCATCAGATATGATATTCCCTCCAGAAGAAG
CAGAACATATCACTCTCTTTCAAGATTAATA
Found at i:42303 original size:41 final size:41
Alignment explanation
Indices: 42246--42341 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
42236 AATATTCCCT
* *
42246 GAGTGATAGTGGAACAAGTCTGCCTCAAATAAATCTTCCTG
1 GAGTGATAGTGGAACAAGTCTGACTCAAATAAATCTTCATG
* * *
42287 GAGTGACAGTGGAACAAGTCTGACTCGAATCAATCTTCATG
1 GAGTGATAGTGGAACAAGTCTGACTCAAATAAATCTTCATG
42328 GAGTGATAGTGGAA
1 GAGTGATAGTGGAA
42342 TGGATCAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (41 bp):
GAGTGATAGTGGAACAAGTCTGACTCAAATAAATCTTCATG
Found at i:42545 original size:19 final size:19
Alignment explanation
Indices: 42518--42554 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42508 TTTTTTATCA
* *
42518 TATTTAATATTATTATTAT
1 TATTGAATACTATTATTAT
42537 TATTGAATACTATTATTA
1 TATTGAATACTATTATTA
42555 ACTAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
TATTGAATACTATTATTAT
Found at i:49931 original size:8 final size:8
Alignment explanation
Indices: 49918--49958 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
49908 CTCATTTTCA
49918 GAGAATTT
1 GAGAATTT
49926 GAGAATTT
1 GAGAATTT
*
49934 -AGAGTTT
1 GAGAATTT
49941 GAGAATTT
1 GAGAATTT
49949 GAGAATTT
1 GAGAATTT
49957 GA
1 GA
49959 AAGCTTGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:49943 original size:15 final size:16
Alignment explanation
Indices: 49918--49958 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
49908 CTCATTTTCA
49918 GAGAATTTGAGAATTT
1 GAGAATTTGAGAATTT
*
49934 -AGAGTTTGAGAATTT
1 GAGAATTTGAGAATTT
49949 GAGAATTTGA
1 GAGAATTTGA
49959 AAGCTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (16 bp):
GAGAATTTGAGAATTT
Found at i:50376 original size:128 final size:128
Alignment explanation
Indices: 50038--50492 Score: 815
Period size: 128 Copynumber: 3.6 Consensus size: 128
50028 ACTATTCACA
*
50038 TGAAGGCGCGTTCCAGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
50103 TTATGTCACTCATGTCCCTCGGAGACACTATTCATATAAGTACCTATTATTTCTCA-GGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
50165 TGAAGGCGCGTTCCCGGGGGCGCGCCTT-CATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
50229 TTATGTCACTCATGTCCCTCGGGGATACTATTCATATCATTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
50292 TGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
50357 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTTAGGAGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
50420 TGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
50485 TTATGTCA
66 TTATGTCA
50493 TCAGAATCCC
Statistics
Matches: 314, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
126 88 0.28
127 60 0.19
128 166 0.53
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Done.