Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006982.1 Hibiscus syriacus cultivar Beakdansim tig00017986_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: 90265
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1128 original size:15 final size:15
Alignment explanation
Indices: 1110--1147 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1100 GGAGCAGTAT
1110 GGGCATCAGCAATTG
1 GGGCATCAGCAATTG
1125 GGGCATCAGCAATTG
1 GGGCATCAGCAATTG
1140 GGGCATCA
1 GGGCATCA
1148 CTTGCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.34, T:0.18
Consensus pattern (15 bp):
GGGCATCAGCAATTG
Found at i:5085 original size:80 final size:80
Alignment explanation
Indices: 4946--5323 Score: 598
Period size: 80 Copynumber: 4.7 Consensus size: 80
4936 ACACAACAAA
* * * * * *
4946 AAAGGGAGCCAACCTAAGGATATACCTT-GGATCTACCTAAGGACATCCTTAGATACGTAGGGTT
1 AAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTT
* *
5010 ACCTTAAGAACACAGC
65 ACCTTATGCACACAGC
* * *
5026 AAAGGTAACAAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTA
1 AAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTA
5091 CCTTATGCACACAGC
66 CCTTATGCACACAGC
5106 AAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTA
1 AAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTA
5171 CCTTATGCACACAGC
66 CCTTATGCACACAGC
5186 AAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTA
1 AAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTA
5251 CCTTATGCACACAGC
66 CCTTATGCACACAGC
* * * *
5266 AAAGGGAACCAACCTAAGTATATGCCTTGGG-GCTACCTAAGATATCCTTAGGTCCGTA
1 AAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTA
5324 AGGACTTACA
Statistics
Matches: 279, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
79 25 0.09
80 245 0.88
81 9 0.03
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (80 bp):
AAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTA
CCTTATGCACACAGC
Found at i:7378 original size:17 final size:15
Alignment explanation
Indices: 7333--7369 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
7323 CCAATGGTTA
7333 ATTCTTTTCTCGAAC
1 ATTCTTTTCTCGAAC
7348 ATTCTTTTCTCGAAC
1 ATTCTTTTCTCGAAC
7363 ATTCTTT
1 ATTCTTT
7370 GATCTCGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.51
Consensus pattern (15 bp):
ATTCTTTTCTCGAAC
Found at i:8350 original size:16 final size:17
Alignment explanation
Indices: 8319--8358 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
8309 GGTCAATTGT
*
8319 GGTCAACGCTGGTCAAC
1 GGTCAACGCAGGTCAAC
8336 GGTCAACG-AGGTCAAC
1 GGTCAACGCAGGTCAAC
*
8352 AGTCAAC
1 GGTCAAC
8359 ATTCGACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (17 bp):
GGTCAACGCAGGTCAAC
Found at i:10529 original size:80 final size:80
Alignment explanation
Indices: 10389--10778 Score: 572
Period size: 80 Copynumber: 4.9 Consensus size: 80
10379 GCTTGCCCTC
* ** * *
10389 AGCACACAGCAAAAAGGGGAGCC-ACCTAAGGATATACCTT-GGATCTACCTAAGGACATCCTTA
1 AGCACACAGC--AAA-GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTA
* *
10452 GATACGTAGGGTTACCTTA
62 GGTCCGTAGGGTTACCTTA
*
10471 AGAACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTC
1 AGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTC
10536 CGTAGGGTTACCTTA
66 CGTAGGGTTACCTTA
10551 TA-CACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGT
1 -AGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGT
10615 CCGTAGGGTTACCTTA
65 CCGTAGGGTTACCTTA
* * * *
10631 TGCACACAGTAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATAGCCTTAGGTC
1 AGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTC
10696 CGTAGGGTTACCTTA
66 CGTAGGGTTACCTTA
* * *
10711 TGCACACAGCAAAGGGAACCAACTTAAGGATATACCTT-GGGCCTACCTAAGATATCCTTAGGTC
1 AGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTC
10775 CGTA
66 CGTA
10779 AGGACTTACA
Statistics
Matches: 286, Mismatches: 18, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
79 33 0.12
80 234 0.82
81 10 0.03
82 9 0.03
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (80 bp):
AGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTC
CGTAGGGTTACCTTA
Found at i:12953 original size:63 final size:63
Alignment explanation
Indices: 12831--12974 Score: 173
Period size: 63 Copynumber: 2.3 Consensus size: 63
12821 ATGCACATGA
** * *
12831 AGTGCATCGATGCACTCTGATAAAATAAAAACATCGAATGCCATTAGTGCATCGATGCATAAGG
1 AGTGCATCGATGCAC-CCCATAAAATAAAAACATCAAATGCCATTAGTGCACCGATGCATAAGG
* * ** *
12895 AGTGCATCGATGCACCCCATTAAATACAAACATCAAATGTGATTCA-TGCACCGATGCATAAGT
1 AGTGCATCGATGCACCCCATAAAATAAAAACATCAAATGCCATT-AGTGCACCGATGCATAAGG
*
12958 AGTGCATCGATACACCC
1 AGTGCATCGATGCACCC
12975 GTTAAGGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
63 53 0.77
64 16 0.23
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (63 bp):
AGTGCATCGATGCACCCCATAAAATAAAAACATCAAATGCCATTAGTGCACCGATGCATAAGG
Found at i:13407 original size:21 final size:20
Alignment explanation
Indices: 13382--13427 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
13372 TGATACCGGT
13382 ATGTGAATATTGAAAAGAATC
1 ATGTGAATA-TGAAAAGAATC
* * *
13403 ATGTGTATATGAAATGAATT
1 ATGTGAATATGAAAAGAATC
13423 ATGTG
1 ATGTG
13428 CTATATGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (20 bp):
ATGTGAATATGAAAAGAATC
Found at i:13432 original size:21 final size:20
Alignment explanation
Indices: 13382--13435 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
13372 TGATACCGGT
*
13382 ATGTGAATATTGAAAAGAATC
1 ATGTGTATA-TGAAAAGAATC
* *
13403 ATGTGTATATGAAATGAATT
1 ATGTGTATATGAAAAGAATC
13423 ATGTGCTATATGA
1 ATGTG-TATATGA
13436 GAAGTGATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (20 bp):
ATGTGTATATGAAAAGAATC
Found at i:13562 original size:18 final size:18
Alignment explanation
Indices: 13539--13611 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
13529 AGGGATATAC
13539 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
13557 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
* * *
13576 CAATAGTCCTTTGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
13595 AGTGGTCCTTCAGGACA
1 AGTGGTCCTTCGGGACA
13612 AATACTGAAC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
18 27 0.64
19 4 0.10
20 11 0.26
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:16623 original size:22 final size:24
Alignment explanation
Indices: 16595--16643 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
16585 ATATTTTATA
16595 TATATTAAATTA-AAAATAT-TTT
1 TATATTAAATTATAAAATATATTT
* *
16617 TATATTAACTTATTAAATATATTT
1 TATATTAAATTATAAAATATATTT
16641 TAT
1 TAT
16644 TGTTAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 6 0.26
24 6 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATTAAATTATAAAATATATTT
Found at i:16631 original size:25 final size:27
Alignment explanation
Indices: 16602--16665 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 27
16592 ATATATATTA
16602 AATTAAAAATATTTTTA-TATTAACTT
1 AATTAAAAATATTTTTATTATTAACTT
* *
16628 -ATTAAATATA-TTTTATTGTTAACTT
1 AATTAAAAATATTTTTATTATTAACTT
16653 AATTTAAAAATAT
1 AA-TTAAAAATAT
16666 ATATTTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.16
25 17 0.55
26 1 0.03
27 8 0.26
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (27 bp):
AATTAAAAATATTTTTATTATTAACTT
Found at i:16688 original size:30 final size:31
Alignment explanation
Indices: 16633--16691 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
16623 AACTTATTAA
*
16633 ATATATTTTATTGTTAACTTAATTTAAAAAT
1 ATATATTTTATTGTTAAATTAATTTAAAAAT
*
16664 ATATATTTTA-TGTTAAATTTATTTAAAA
1 ATATATTTTATTGTTAAATTAATTTAAAA
16692 GTATGACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (31 bp):
ATATATTTTATTGTTAAATTAATTTAAAAAT
Found at i:16843 original size:31 final size:31
Alignment explanation
Indices: 16800--16868 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
16790 ACCCATGATA
*
16800 ACCACATTTTAATTAAATAAAAACAAAAGTG
1 ACCATATTTTAATTAAATAAAAACAAAAGTG
*
16831 ACCATATTTTAATTAAATAAAAACGAAAGTG
1 ACCATATTTTAATTAAATAAAAACAAAAGTG
*
16862 ATCATAT
1 ACCATAT
16869 CTTACGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (31 bp):
ACCATATTTTAATTAAATAAAAACAAAAGTG
Found at i:17254 original size:31 final size:31
Alignment explanation
Indices: 17219--17296 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
17209 TCAAAAGACA
* * **
17219 TAAGTTTTTATCACTTATGTTATTGTTTTAT
1 TAAGTTTTGATCACTTATATTATCATTTTAT
*
17250 TAAGTTTTGGTCACTTATATTATCATTTTAT
1 TAAGTTTTGATCACTTATATTATCATTTTAT
* *
17281 TAAGTTTGGGTCACTT
1 TAAGTTTTGATCACTT
17297 GGACATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (31 bp):
TAAGTTTTGATCACTTATATTATCATTTTAT
Found at i:18147 original size:2 final size:2
Alignment explanation
Indices: 18142--18166 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18132 CAAGCATAAT
18142 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
18167 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18171 original size:2 final size:2
Alignment explanation
Indices: 18166--18212 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
18156 ACACACACAC
18166 AT AT AT AT AT 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 AT AT AT AT AT
18208 AT AT A
1 AT AT A
18213 CACACACACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18433 original size:22 final size:24
Alignment explanation
Indices: 18408--18453 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
18398 CATTTATATT
18408 CATTCACATATA-CAT-TAACATA
1 CATTCACATATATCATGTAACATA
*
18430 CATTCATATATATCATGTAACATA
1 CATTCACATATATCATGTAACATA
18454 TGCAATCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 3 0.14
24 7 0.33
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (24 bp):
CATTCACATATATCATGTAACATA
Found at i:18660 original size:23 final size:23
Alignment explanation
Indices: 18634--18679 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18624 CACCACAGCT
*
18634 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* *
18657 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
18680 TACAAGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:24398 original size:21 final size:21
Alignment explanation
Indices: 24347--24399 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
24337 ATTCTGACTA
24347 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
24368 TCACGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
24389 TCGCAATGCGA
1 TCGCATTGCGA
24400 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:24414 original size:20 final size:20
Alignment explanation
Indices: 24389--24521 Score: 212
Period size: 20 Copynumber: 6.7 Consensus size: 20
24379 TTTTCCTAAT
24389 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
24409 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
24429 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
24449 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
24469 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
24489 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
24509 TCGCAACGCGAAT
1 TCGCAATGCGAAT
24522 CTGACTATCG
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:24743 original size:22 final size:22
Alignment explanation
Indices: 24718--24783 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
24708 GGCGACATCC
24718 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
24740 GTCCCCATCTCTGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
24762 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
24784 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:25180 original size:39 final size:39
Alignment explanation
Indices: 25121--25249 Score: 152
Period size: 39 Copynumber: 3.3 Consensus size: 39
25111 CGATTATGTC
25121 GTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTTCGT
* **
25160 GTTGTGATTTTCATTTCGCGTTGCGATAGTCAAATTC-T
1 GTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTTCGT
** * * **
25198 CGTTGCGATAGTCATTTTCGTGTTACGATTTTCATTTTCGT
1 -GTTGCGATTTTCA-TTTCGCGTTGCGATAGTCATTTTCGT
25239 GTTGCGATTTT
1 GTTGCGATTTT
25250 AAGTTTCAGA
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
38 1 0.01
39 44 0.60
40 27 0.37
41 1 0.01
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (39 bp):
GTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTTCGT
Found at i:25247 original size:20 final size:20
Alignment explanation
Indices: 25121--25249 Score: 120
Period size: 20 Copynumber: 6.5 Consensus size: 20
25111 CGATTATGTC
*
25121 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
**
25140 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
* *
25160 GTTGTGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
** **
25179 GTTGCGATAGTCAAATTC-T
1 GTTGCGATTTTCATTTTCGT
**
25198 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
*
25219 GTTACGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
25239 GTTGCGATTTT
1 GTTGCGATTTT
25250 AAGTTTCAGA
Statistics
Matches: 88, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
19 26 0.30
20 61 0.69
21 1 0.01
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:25256 original size:20 final size:20
Alignment explanation
Indices: 25213--25256 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
25203 CGATAGTCAT
* *
25213 TTTCGTGTTACGATTTTCAT
1 TTTCGTGTTACGATTTTAAG
*
25233 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
25253 TTTC
1 TTTC
25257 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:27158 original size:20 final size:20
Alignment explanation
Indices: 27133--27289 Score: 101
Period size: 20 Copynumber: 8.5 Consensus size: 20
27123 AGAATAGTTT
*
27133 ACTATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
27153 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
27173 ACTATCGCAAT--G-AGA-G
1 ACTATCGCAATGCGAAAATG
27189 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
27206 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
27222 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
27240 ACTATCGAAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
** *
27260 ACTATTACAATGC-AAATTTG
1 ACTATCGCAATGCGAAA-ATG
27280 ACTATCGCAA
1 ACTATCGCAA
27290 CGAAAGAATC
Statistics
Matches: 109, Mismatches: 13, Indels: 30
0.72 0.09 0.20
Matches are distributed among these distances:
14 15 0.14
16 9 0.08
17 8 0.07
18 4 0.04
19 10 0.09
20 63 0.58
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:27361 original size:20 final size:20
Alignment explanation
Indices: 27336--27407 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
27326 GATTCTCTCG
* *
27336 TTGCGATAGTAAAATCCGCA
1 TTGCGATAGTCAAATTCGCA
27356 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
*
27376 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCA
27396 TTGCGATAGTCA
1 TTGCGATAGTCA
27408 TTTTCGCGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:27947 original size:18 final size:19
Alignment explanation
Indices: 27908--27949 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
27898 CTCACCTGTC
27908 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
27929 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
27947 ATC
1 ATC
27950 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:29414 original size:14 final size:14
Alignment explanation
Indices: 29395--29430 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29385 ATTGTTTAAT
29395 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
29409 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
29423 TGATTTGT
1 TGATTTGT
29431 TTAATTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:29586 original size:33 final size:34
Alignment explanation
Indices: 29536--29631 Score: 104
Period size: 33 Copynumber: 2.9 Consensus size: 34
29526 AAAACAGACT
* ** * *
29536 ATCGCAACGCGGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGCGGAAATGAAAATCACAACGAGAGA
29570 ATCGCAATGC-GAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCACAACGAGAGA
*** *
29603 ATCGCAATGTAAAAATGAAAATCGCAACG
1 ATCGCAATGCGGAAATGAAAATCACAACG
29632 CGAAACCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.53
34 25 0.47
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCACAACGAGAGA
Found at i:29624 original size:34 final size:33
Alignment explanation
Indices: 29564--29631 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
29554 CTATCGCAAT
**
29564 GAGAGAATCGCAATGCGAAATGAAAATCACAAC
1 GAGAGAATCGCAATGAAAAATGAAAATCACAAC
*
29597 GAGAGAATCGCAATGTAAAAATGAAAATCGCAAC
1 GAGAGAATCGCAATG-AAAAATGAAAATCACAAC
29631 G
1 G
29632 CGAAACCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 15 0.48
34 16 0.52
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.13
Consensus pattern (33 bp):
GAGAGAATCGCAATGAAAAATGAAAATCACAAC
Found at i:29653 original size:19 final size:20
Alignment explanation
Indices: 29631--29695 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
29621 AAATCGCAAC
*
29631 GCGA-AACCATTTTCGCGTT
1 GCGATAACCATTTCCGCGTT
**
29650 GCGATAGTCATTTCCGCGTT
1 GCGATAACCATTTCCGCGTT
** *
29670 GCGATAGTCATTTCCGTGTT
1 GCGATAACCATTTCCGCGTT
29690 GCGATA
1 GCGATA
29696 GTCATATTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 4 0.10
20 37 0.90
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (20 bp):
GCGATAACCATTTCCGCGTT
Found at i:29667 original size:20 final size:20
Alignment explanation
Indices: 29638--29719 Score: 121
Period size: 20 Copynumber: 4.1 Consensus size: 20
29628 AACGCGAAAC
*
29638 CATTTTCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGT
29658 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGT
*
29678 CATTTCCGTGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGT
*
29698 CATATT-CGCGTTACGATAGT
1 CAT-TTCCGCGTTGCGATAGT
29718 CA
1 CA
29720 AATGAATTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
20 55 0.96
21 2 0.04
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGT
Found at i:33039 original size:20 final size:20
Alignment explanation
Indices: 33013--33060 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
33003 GAAATTCAGT
33013 ATTGCGATAGTCAGAA-TCGC
1 ATTGCGATAGTCA-AATTCGC
*
33033 GTTGCGATAGTCAAATTCGC
1 ATTGCGATAGTCAAATTCGC
33053 ATTGCGAT
1 ATTGCGAT
33061 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (20 bp):
ATTGCGATAGTCAAATTCGC
Found at i:33100 original size:21 final size:21
Alignment explanation
Indices: 33076--33121 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
33066 TATTCGCATT
33076 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
33097 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
33118 GCGA
1 GCGA
33122 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:39506 original size:31 final size:31
Alignment explanation
Indices: 39464--39667 Score: 145
Period size: 31 Copynumber: 6.7 Consensus size: 31
39454 TATGCCACTC
* * *
39464 GGATTCGGATTTAGACTTGAGTGCTGGGTTT
1 GGATTCGGACTTAAAGTTGAGTGCTGGGTTT
* * * *
39495 GGATTCAGATTTAAAGTTGAGT-CTTAGGTTA
1 GGATTCGGACTTAAAGTTGAGTGC-TGGGTTT
* * * *
39526 GTAATCGGACTTAAAGTTGAGTGCCGGGTTC
1 GGATTCGGACTTAAAGTTGAGTGCTGGGTTT
**
39557 GGATTCGGACTTAAAGTTGAGTATTGGGTTT
1 GGATTCGGACTTAAAGTTGAGTGCTGGGTTT
* * *
39588 GGATTC--A--GAAAGTTGAGT-ATTGGTTT
1 GGATTCGGACTTAAAGTTGAGTGCTGGGTTT
* *
39614 CGGATTCAGACTTAAAGTTGAGT-TTCGGGTTT
1 -GGATTCGGACTTAAAGTTGAGTGCT-GGGTTT
*
39646 GGATTTAGG-CTTAAAGTTGAGT
1 GGA-TTCGGACTTAAAGTTGAGT
39668 TTCGGGTTCA
Statistics
Matches: 138, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
26 6 0.04
27 16 0.12
29 2 0.01
30 1 0.01
31 104 0.75
32 9 0.07
ACGTcount: A:0.24, C:0.09, G:0.31, T:0.37
Consensus pattern (31 bp):
GGATTCGGACTTAAAGTTGAGTGCTGGGTTT
Found at i:39607 original size:27 final size:28
Alignment explanation
Indices: 39568--39650 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 28
39558 GATTCGGACT
39568 TAAAGTTGAGTATTGGGTTTGGATTCAG
1 TAAAGTTGAGTATTGGGTTTGGATTCAG
39596 -AAAGTTGAGTATT-GGTTTCGGATTCAG
1 TAAAGTTGAGTATTGGGTTT-GGATTCAG
39623 ACTTAAAGTTGAGT-TTCGGGTTTGGATT
1 ---TAAAGTTGAGTATT-GGGTTTGGATT
39651 TAGGCTTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
26 5 0.10
27 21 0.44
30 2 0.04
31 15 0.31
32 5 0.10
ACGTcount: A:0.24, C:0.06, G:0.30, T:0.40
Consensus pattern (28 bp):
TAAAGTTGAGTATTGGGTTTGGATTCAG
Found at i:39668 original size:31 final size:31
Alignment explanation
Indices: 39489--39675 Score: 151
Period size: 31 Copynumber: 6.2 Consensus size: 31
39479 CTTGAGTGCT
**
39489 GGGTTTGGATTCAGATTTAAAGTTGAGTCTT-
1 GGGTTTGGATTCAGGCTTAAAGTTGAGT-TTC
* * * * **
39520 AGGTTAGTAATC-GGACTTAAAGTTGAGTGCC
1 GGGTTTGGATTCAGG-CTTAAAGTTGAGTTTC
*
39551 GGGTTCGGATTC-GGACTTAAAGTTGAGTATT-
1 GGGTTTGGATTCAGG-CTTAAAGTTGAGT-TTC
39582 GGGTTTGGATTCA-G---AAAGTTGAGTATT-
1 GGGTTTGGATTCAGGCTTAAAGTTGAGT-TTC
*
39609 -GGTTTCGGATTCAGACTTAAAGTTGAGTTTC
1 GGGTTT-GGATTCAGGCTTAAAGTTGAGTTTC
*
39640 GGGTTTGGATTTAGGCTTAAAGTTGAGTTTC
1 GGGTTTGGATTCAGGCTTAAAGTTGAGTTTC
39671 GGGTT
1 GGGTT
39676 CAATTATGTG
Statistics
Matches: 127, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
26 5 0.04
27 20 0.16
30 3 0.02
31 94 0.74
32 5 0.04
ACGTcount: A:0.23, C:0.09, G:0.31, T:0.37
Consensus pattern (31 bp):
GGGTTTGGATTCAGGCTTAAAGTTGAGTTTC
Found at i:42082 original size:14 final size:14
Alignment explanation
Indices: 42060--42089 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42050 TTTATAGATC
42060 ATATAAATTTTCTG
1 ATATAAATTTTCTG
*
42074 ATATGAATTTTCTG
1 ATATAAATTTTCTG
42088 AT
1 AT
42090 TGAGCGTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (14 bp):
ATATAAATTTTCTG
Found at i:44039 original size:55 final size:55
Alignment explanation
Indices: 43958--44102 Score: 236
Period size: 55 Copynumber: 2.6 Consensus size: 55
43948 ATTATTTGAG
* *
43958 TGTGTATCGGTACACTGAGGAGTGTATCGATATCCTCAAAACATTGAATGTCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATT
* * *
44013 TGTGTATCGGTACACTGAGGAGTGTATCGGTACCCTCAAAACATCGAGTGTTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATT
*
44068 TGTGTATCGGTACATTGAGGAGTGTATCGATACCC
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCC
44103 CCAAGTATGA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 83 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATT
Found at i:44878 original size:44 final size:44
Alignment explanation
Indices: 44825--44911 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
44815 AGTCGAGGGT
* *
44825 CTATGTGGTCCTTCGGGACAAATATGTGGCACTTCGGTGCAAAC
1 CTATGTGGTCCTTCGGGACAAATATATGGCACTTCGATGCAAAC
*
44869 CTATGTGGTCCTTCGGGACAATTATATGGCACTTCGATGCAAA
1 CTATGTGGTCCTTCGGGACAAATATATGGCACTTCGATGCAAA
44912 TTACGAGCTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (44 bp):
CTATGTGGTCCTTCGGGACAAATATATGGCACTTCGATGCAAAC
Found at i:44882 original size:23 final size:22
Alignment explanation
Indices: 44825--44889 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 22
44815 AGTCGAGGGT
44825 CTATGTGGTCCTTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
44847 -TATGTGG-CACTTCGGTG-CAAA
1 CTATGTGGTC-CTTCGG-GACAAA
44868 CCTATGTGGTCCTTCGGGACAA
1 -CTATGTGGTCCTTCGGGACAA
44890 TTATATGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
20 1 0.03
21 17 0.46
22 2 0.05
23 16 0.43
24 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGGACAAA
Found at i:47286 original size:55 final size:55
Alignment explanation
Indices: 47218--47362 Score: 236
Period size: 55 Copynumber: 2.6 Consensus size: 55
47208 ATTGTTTGAG
*
47218 TGTGTATCGGTACACTGAGGAGTGTATCGATATCCTCAAAACATCGAATGTCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATT
* * * *
47273 TGTGTATCAGTACACTGAGAAGTGTATCGATACCCTCAAAACATCGAGTGTTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATT
*
47328 TGTGTATCGGTACATTGAGGAGTGTATCGATACCC
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCC
47363 CCCAAGTATG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 82 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGTCATT
Found at i:48113 original size:21 final size:21
Alignment explanation
Indices: 48087--48127 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
48077 GTCGAGGGTC
48087 TATGTGGTCCTTCGGGACAAT
1 TATGTGGTCCTTCGGGACAAT
48108 TATGTGGTCCTTCGGGACAA
1 TATGTGGTCCTTCGGGACAA
48128 ATATATGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAT
Found at i:48141 original size:21 final size:21
Alignment explanation
Indices: 48087--48165 Score: 74
Period size: 21 Copynumber: 3.7 Consensus size: 21
48077 GTCGAGGGTC
*
48087 TATGTGGTC-CTTCGGGACAAT
1 TATGTGG-CACTTCGGGACAAA
48108 TATGTGGTC-CTTCGGGACAAA
1 TATGTGG-CACTTCGGGACAAA
*
48129 TATATGGCACTTCGGTG-CAAA
1 TATGTGGCACTTCGG-GACAAA
48150 CCTATGTGGCACTTCG
1 --TATGTGGCACTTCG
48166 ATGAAAATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.02
21 36 0.71
22 1 0.02
23 13 0.25
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (21 bp):
TATGTGGCACTTCGGGACAAA
Found at i:51281 original size:20 final size:20
Alignment explanation
Indices: 51256--51348 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
51246 TTTTCCCAAT
51256 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
51276 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
51296 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
51317 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
51338 TCGCAATGCGA
1 TCGCAATGCGA
51349 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:51298 original size:41 final size:41
Alignment explanation
Indices: 51253--51348 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
51243 CGATTTTCCC
51253 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
51294 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
51335 AAATCGCAATGCGA
1 AATTCGCAATGCGA
51349 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:51302 original size:21 final size:20
Alignment explanation
Indices: 51256--51348 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
51246 TTTTCCCAAT
*
51256 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
51276 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
51296 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
51317 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
51338 TCGCAATGCGA
1 TCGCAATGCGA
51349 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:51361 original size:41 final size:41
Alignment explanation
Indices: 51275--51409 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
51265 GAATAAGTAA
* * *
51275 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
51316 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
51357 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
51398 TTCGCAACGCGA
1 ATCGCAACGCGA
51410 TTTACTTAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:51383 original size:21 final size:20
Alignment explanation
Indices: 51334--51384 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
51324 GCGAATTGGG
* *
51334 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
51354 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
51375 AAAATCGCAA
1 AAAATCGCAA
51385 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:51416 original size:18 final size:19
Alignment explanation
Indices: 51379--51416 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
51369 TAATAAAAAA
51379 TCGCAACGAGATACTTACTT
1 TCGCAACGAGATA-TTACTT
*
51399 TCGCAACGCGAT-TTACTT
1 TCGCAACGAGATATTACTT
51417 AGCGCCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
TCGCAACGAGATATTACTT
Found at i:51989 original size:19 final size:19
Alignment explanation
Indices: 51965--52009 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
51955 GCAACGAGAT
*
51965 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
51984 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
52003 AATCGCA
1 AATCGCA
52010 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:52027 original size:19 final size:19
Alignment explanation
Indices: 52005--52189 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
51995 GAAACCAAAA
*
52005 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
52024 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
52043 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
52062 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
52082 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
52098 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
52115 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
52129 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
52148 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
52168 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
52188 TC
1 TC
52190 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:52082 original size:39 final size:38
Alignment explanation
Indices: 52005--52094 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
51995 GAAACCAAAA
* *
52005 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
52043 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
52082 TCGCGTTGCGATT
1 TCGCGTTGCGATT
52095 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:52114 original size:33 final size:33
Alignment explanation
Indices: 52077--52164 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
52067 GTTGCGATTT
* *
52077 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
52110 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
52143 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
52165 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:52166 original size:20 final size:20
Alignment explanation
Indices: 52132--52189 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
52122 GCGATTCTCT
**
52132 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
52152 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
52172 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
52190 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:54270 original size:42 final size:42
Alignment explanation
Indices: 54190--54282 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
54180 GCCCGACTCA
* * **
54190 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTACAAGAGGCC
* * *
54232 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTACAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTACAAGAGGCC
* *
54274 ACTGTCATC
1 CCTATCATC
54283 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTACAAGAGGCC
Found at i:55688 original size:14 final size:14
Alignment explanation
Indices: 55669--55704 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
55659 ATTGTTTAAT
55669 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
55683 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
55697 TGATTTGT
1 TGATTTGT
55705 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:55885 original size:19 final size:19
Alignment explanation
Indices: 55863--55980 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
55853 CGAAATTAAA
55863 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
55882 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
55897 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
55915 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
55930 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
55948 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
55967 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
55981 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:55909 original size:33 final size:33
Alignment explanation
Indices: 55867--55960 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
55857 ATTAAATTCG
55867 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
55900 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
55933 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
55961 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:59755 original size:14 final size:14
Alignment explanation
Indices: 59736--59772 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59726 CATCAATTAA
59736 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
59750 ACAAATCATCTTTT
1 ACAAATCAACATTT
59764 ACAAATCAA
1 ACAAATCAA
59773 TTAAACAATC
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:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:60157 original size:20 final size:20
Alignment explanation
Indices: 60132--60179 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
60122 CATTCATTGA
*
60132 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
60152 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
60172 TTATCGCA
1 CTATCGCA
60180 CGAGAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:60247 original size:19 final size:19
Alignment explanation
Indices: 60225--60272 Score: 89
Period size: 18 Copynumber: 2.6 Consensus size: 19
60215 CGATTTCTCG
60225 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
60244 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
60262 TTGCGATTTTC
1 TTGCGATTTTC
60273 TCGTTGCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:60255 original size:18 final size:18
Alignment explanation
Indices: 60207--60270 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
60197 GAAATGAAAA
60207 TCGCATTGCGATTTC---
1 TCGCATTGCGATTTCATT
60222 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
60239 TCGCATTGCGATTTCATT
1 TCGCATTGCGATTTCATT
60257 TCGCATTGCGATTT
1 TCGCATTGCGATTT
60271 TCTCGTTGCG
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.14
14 4 0.09
15 3 0.07
17 3 0.07
18 21 0.49
19 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:62300 original size:20 final size:19
Alignment explanation
Indices: 62265--62331 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
62255 CGAAACTTAA
62265 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
62284 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
62304 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
62323 ATCGCAACG
1 ATCGCAACG
62332 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:62339 original size:14 final size:14
Alignment explanation
Indices: 62320--62377 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
62310 ATGCGAAATG
62320 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
62334 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
62350 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
62366 AAAATCGCAACG
1 AAAATCGCAACG
62378 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:62362 original size:32 final size:33
Alignment explanation
Indices: 62304--62382 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
62294 GGAAATGGCT
*
62304 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
62337 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
62369 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
62383 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:62430 original size:14 final size:14
Alignment explanation
Indices: 62411--62450 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
62401 TTCCATTTCG
62411 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
62425 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
62439 CGTTGCGATTTT
1 CGTTGCGATTTT
62451 CATTTCGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:62505 original size:20 final size:20
Alignment explanation
Indices: 62451--62494 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
62441 TTGCGATTTT
*
62451 CATTTC-GCATTGCGATAGC
1 CATTTCTGCGTTGCGATAGC
*
62470 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCGTTGCGATAGC
62490 CATTT
1 CATTT
62495 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCTGCGTTGCGATAGC
Found at i:62798 original size:18 final size:18
Alignment explanation
Indices: 62772--62813 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
62762 GTCGATCAGA
* *
62772 TGATGGCTCTAGGTGAGG
1 TGATAGCTCTAGGCGAGG
*
62790 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTAGGCGAGG
62808 TGATAG
1 TGATAG
62814 GTGATGGCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.12, G:0.43, T:0.26
Consensus pattern (18 bp):
TGATAGCTCTAGGCGAGG
Found at i:62877 original size:85 final size:84
Alignment explanation
Indices: 62726--62896 Score: 333
Period size: 85 Copynumber: 2.0 Consensus size: 84
62716 ATGTGAAAGA
62726 ATAGGTGATGGCTGTCGTTGTGGAGGTGTATAGCGGGTCGATCAGATGATGGCTCTAGGTGAGGT
1 ATAGGTGATGGCTGTCGTTGTGGAGGTGTATAGCGGGTCGATCAGATGATGGCTCTAGGTGAGGT
62791 GATAGCTCTGGGCGAGGTG
66 GATAGCTCTGGGCGAGGTG
62810 ATAGGTGATGGCTGTCGTTGTGGAGGTGTATAGCCGGGTCGATCAGATGATGGCTCTAGGTGAGG
1 ATAGGTGATGGCTGTCGTTGTGGAGGTGTATAG-CGGGTCGATCAGATGATGGCTCTAGGTGAGG
62875 TGATAGCTCTGGGCGAGGTG
65 TGATAGCTCTGGGCGAGGTG
62895 AT
1 AT
62897 GGCTCCCGAA
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 33 0.38
85 53 0.62
ACGTcount: A:0.18, C:0.12, G:0.42, T:0.27
Consensus pattern (84 bp):
ATAGGTGATGGCTGTCGTTGTGGAGGTGTATAGCGGGTCGATCAGATGATGGCTCTAGGTGAGGT
GATAGCTCTGGGCGAGGTG
Found at i:62883 original size:18 final size:18
Alignment explanation
Indices: 62857--62901 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
62847 GTCGATCAGA
*
62857 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
62875 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
62893 TGATGGCTC
1 TGATGGCTC
62902 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:64244 original size:20 final size:20
Alignment explanation
Indices: 64219--64272 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
64209 AATAGTTTCT
64219 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
64239 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
64259 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
64273 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:64757 original size:20 final size:20
Alignment explanation
Indices: 64732--64825 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
64722 GATTATGTAT
64732 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
64752 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
64772 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
64793 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
64813 TATCGCATTGCGA
1 TATCGCGTTGCGA
64826 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:64797 original size:41 final size:41
Alignment explanation
Indices: 64752--64829 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
64742 CGAAAGTCAG
* * *
64752 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
64793 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
64830 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:64826 original size:20 final size:20
Alignment explanation
Indices: 64712--64826 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
64702 CGCTTTGAAA
*
64712 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
64733 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
64753 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
64773 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
64794 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
64814 ATCGCATTGCGAT
1 ATCGCATTGCGAT
64827 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:64845 original size:41 final size:41
Alignment explanation
Indices: 64752--64865 Score: 106
Period size: 41 Copynumber: 2.8 Consensus size: 41
64742 CGAAAGTCAG
* * * ** *
64752 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
64793 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
* **
64835 T-TCGCGTTGCGAT-TTACTTATCGCATTGCGA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGA
64866 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
40 14 0.24
41 43 0.73
42 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:64863 original size:19 final size:20
Alignment explanation
Indices: 64813--64865 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
64803 CGATAGTCAG
*
64813 TATCGCATTGCGATTTTCCC
1 TATCGCATTGCGATTTTACC
* * *
64833 AATTCGCGTTGCGA-TTTACT
1 TA-TCGCATTGCGATTTTACC
64853 TATCGCATTGCGA
1 TATCGCATTGCGA
64866 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 10 0.38
20 6 0.23
21 10 0.38
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (20 bp):
TATCGCATTGCGATTTTACC
Found at i:66215 original size:22 final size:21
Alignment explanation
Indices: 66181--66221 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
66171 ATAATTATTT
66181 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
66202 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
66222 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:69681 original size:42 final size:42
Alignment explanation
Indices: 69618--69742 Score: 171
Period size: 42 Copynumber: 3.0 Consensus size: 42
69608 CAACTGAGTC
*
69618 ATTAGGTGAATTATT-AGAATTTCCAATAGGATTATTAGAAGT
1 ATTAGGTGAATCATTGA-AATTTCCAATAGGATTATTAGAAGT
* * *
69660 ATTAAGTGAATCATTGAAATTTCCAATAGAATTATTAAAAGT
1 ATTAGGTGAATCATTGAAATTTCCAATAGGATTATTAGAAGT
* * *
69702 ATTAGGTGAATCATTGGAATTTACAATCGGATTATTAGAAG
1 ATTAGGTGAATCATTGAAATTTCCAATAGGATTATTAGAAG
69743 GTTTAACCGG
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 71 0.99
43 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (42 bp):
ATTAGGTGAATCATTGAAATTTCCAATAGGATTATTAGAAGT
Found at i:69983 original size:14 final size:14
Alignment explanation
Indices: 69964--69993 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
69954 TATGTTGTTG
69964 ACTTGTTATTTCTC
1 ACTTGTTATTTCTC
69978 ACTTGTTATTTCTC
1 ACTTGTTATTTCTC
69992 AC
1 AC
69994 AATCAACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.07, T:0.53
Consensus pattern (14 bp):
ACTTGTTATTTCTC
Found at i:70850 original size:16 final size:16
Alignment explanation
Indices: 70829--70861 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
70819 TAATAAATAA
70829 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
70845 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
70861 A
1 A
70862 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:70956 original size:16 final size:16
Alignment explanation
Indices: 70931--70991 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
70921 TAATAAATAA
*
70931 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
70947 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
70963 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
70979 ACGAACATAAACG
1 ACGAACATAAACG
70992 TTGGAGACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.56, C:0.21, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:71756 original size:24 final size:24
Alignment explanation
Indices: 71729--71814 Score: 136
Period size: 24 Copynumber: 3.6 Consensus size: 24
71719 ATAAATGAAT
* * *
71729 GAACATAAACGAATATAATCGAAC
1 GAACATAAACGAACATAACCAAAC
71753 GAACATAAACGAACATAACCAAAC
1 GAACATAAACGAACATAACCAAAC
71777 GAACATAAACGAACATAACCAAAC
1 GAACATAAACGAACATAACCAAAC
*
71801 GAACATAACCGAAC
1 GAACATAAACGAAC
71815 GTTCACGAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.56, C:0.23, G:0.10, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCAAAC
Found at i:71800 original size:14 final size:14
Alignment explanation
Indices: 71759--71815 Score: 77
Period size: 14 Copynumber: 4.4 Consensus size: 14
71749 GAACGAACAT
71759 AAACGAACATAACC
1 AAACGAACATAACC
71773 AAACGAACAT----
1 AAACGAACATAACC
71783 AAACGAACATAACC
1 AAACGAACATAACC
71797 AAACGAACATAACC
1 AAACGAACATAACC
*
71811 GAACG
1 AAACG
71816 TTCACGAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 10 0.26
14 28 0.74
ACGTcount: A:0.56, C:0.26, G:0.11, T:0.07
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:71813 original size:10 final size:10
Alignment explanation
Indices: 71750--71794 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
71740 AATATAATCG
71750 AACGAACATA
1 AACGAACATA
71760 AACGAACATAACCA
1 AACGAACAT----A
71774 AACGAACATA
1 AACGAACATA
71784 AACGAACATA
1 AACGAACATA
71794 A
1 A
71795 CCAAACGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 21 0.68
14 10 0.32
ACGTcount: A:0.60, C:0.22, G:0.09, T:0.09
Consensus pattern (10 bp):
AACGAACATA
Found at i:73791 original size:30 final size:31
Alignment explanation
Indices: 73734--73800 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
73724 TCATGTGTCG
*
73734 AATTGATATTTCATCTCAAACTTAAAATT-A
1 AATTAATATTTCATCTCAAACTTAAAATTCA
* *
73764 AATTAATATTTTATCT-AAATTTCAAAATTCA
1 AATTAATATTTCATCTCAAACTT-AAAATTCA
73795 AATTAA
1 AATTAA
73801 AAATCAACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 20 0.62
31 7 0.22
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.42
Consensus pattern (31 bp):
AATTAATATTTCATCTCAAACTTAAAATTCA
Found at i:82510 original size:19 final size:19
Alignment explanation
Indices: 82457--82516 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
82447 ATATAATTCA
82457 TTTTATTTTTAAAAA-ATAT
1 TTTTA-TTTTAAAAATATAT
* *
82476 TTTTAATATAACAAATATAT
1 TTTTATTTTAA-AAATATAT
* *
82496 TTTTATTTTCAAAATCTAT
1 TTTTATTTTAAAAATATAT
82515 TT
1 TT
82517 CAGTAAAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 4 0.12
19 17 0.52
20 12 0.36
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTATTTTAAAAATATAT
Done.