Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004596.1 Hibiscus syriacus cultivar Beakdansim tig00010269_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: 55338
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Found at i:403 original size:52 final size:51
Alignment explanation
Indices: 325--427 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 51
315 TGCACCATCT
*
325 TTCCTCAAATAAATGAATCTTCAGTTTCTAAC-ATTCGATTGAGGAATTTCAA
1 TTCCTCAAATAAATGAATCTTCAGTTTCTAACAATT-GA-TGAGAAATTTCAA
*
377 TTCCTCAAATAAATGAATCTTCAGTTTCTATCAATTGATGAGAAATTTCAA
1 TTCCTCAAATAAATGAATCTTCAGTTTCTAACAATTGATGAGAAATTTCAA
428 GATTCATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
51 12 0.25
52 33 0.69
53 3 0.06
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (51 bp):
TTCCTCAAATAAATGAATCTTCAGTTTCTAACAATTGATGAGAAATTTCAA
Found at i:4638 original size:13 final size:13
Alignment explanation
Indices: 4620--4644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4610 AAAACAAGTA
4620 AAACAATCATATG
1 AAACAATCATATG
4633 AAACAATCATAT
1 AAACAATCATAT
4645 ATCACACAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (13 bp):
AAACAATCATATG
Found at i:4825 original size:27 final size:27
Alignment explanation
Indices: 4795--4866 Score: 117
Period size: 27 Copynumber: 2.6 Consensus size: 27
4785 TATTCATAAG
4795 GTTCACGGATCATACGAGTAATCACTA
1 GTTCACGGATCATACGAGTAATCACTA
4822 GTTCACGGATCATACGAGTAATCACTA
1 GTTCACGGATCATACGAGTAATCACTA
* *
4849 GCTCACGGTATCAAACGA
1 GTTCACGG-ATCATACGA
4867 ATCAAGAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 34 0.81
28 8 0.19
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (27 bp):
GTTCACGGATCATACGAGTAATCACTA
Found at i:16899 original size:12 final size:12
Alignment explanation
Indices: 16884--16922 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
16874 AGAAAAGACA
16884 AAGAAAAAAAAT
1 AAGAAAAAAAAT
16896 AAGAAAAAGAAA-
1 AAGAAAAA-AAAT
16908 AAGAAAATAAAAT
1 AAGAAAA-AAAAT
16921 AA
1 AA
16923 AAGGGGGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (12 bp):
AAGAAAAAAAAT
Found at i:16899 original size:18 final size:18
Alignment explanation
Indices: 16864--16919 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
16854 TATTATACTT
*
16864 AAAGAAGAAAAGAAAAGAC
1 AAAGAA-AAAAGAAAAGAA
16883 AAAGAAAAAA-AATAAGAA
1 AAAGAAAAAAGAA-AAGAA
*
16901 AAAG-AAAAAGAAAATAA
1 AAAGAAAAAAGAAAAGAA
16918 AA
1 AA
16920 TAAAAGGGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 13 0.39
18 14 0.42
19 6 0.18
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAGAA
Found at i:16905 original size:6 final size:6
Alignment explanation
Indices: 16871--16914 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
16861 CTTAAAGAAG
*
16871 AAAAG- AAAAGA CAAAGA AAAA-A AATAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA AAA
16915 TAAAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 8 0.24
6 23 0.68
7 3 0.09
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:16910 original size:24 final size:25
Alignment explanation
Indices: 16876--16922 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
16866 AGAAGAAAAG
*
16876 AAAAGACAAAGAAAA-AAAATAAGA
1 AAAAGAAAAAGAAAATAAAATAAGA
16900 AAAAGAAAAAGAAAATAAAATAA
1 AAAAGAAAAAGAAAATAAAATAA
16923 AAGGGGGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (25 bp):
AAAAGAAAAAGAAAATAAAATAAGA
Found at i:17643 original size:21 final size:21
Alignment explanation
Indices: 17601--17645 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17591 GAAATAGAGG
*
17601 AAAAGAGAAAAAAGAAAATGA
1 AAAAGAGAAAAAACAAAATGA
*
17622 AAAAGA-AAAAAACCAAAGTGA
1 AAAAGAGAAAAAA-CAAAATGA
17643 AAA
1 AAA
17646 CCCGAAAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (21 bp):
AAAAGAGAAAAAACAAAATGA
Found at i:17764 original size:13 final size:13
Alignment explanation
Indices: 17746--17770 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17736 TTCCAAACAT
17746 GAGATGAAACCAA
1 GAGATGAAACCAA
17759 GAGATGAAACCA
1 GAGATGAAACCA
17771 TGAGTTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.24, T:0.08
Consensus pattern (13 bp):
GAGATGAAACCAA
Found at i:19494 original size:22 final size:22
Alignment explanation
Indices: 19441--19497 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
19431 GCGAAGAAAT
* **
19441 TTATCCCGAAGGACCATGTAGA
1 TTATTCCGAAGGACCACATAGA
*
19463 TT-GTCTCGAAGGACCACATAGA
1 TTATTC-CGAAGGACCACATAGA
19485 TTATTCCGAAGGA
1 TTATTCCGAAGGA
19498 ACGTGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.89
23 2 0.07
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (22 bp):
TTATTCCGAAGGACCACATAGA
Found at i:23183 original size:2 final size:2
Alignment explanation
Indices: 23176--23202 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23166 TTTTGAACAT
23176 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
23203 CCCCTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23389 original size:81 final size:81
Alignment explanation
Indices: 23250--23901 Score: 896
Period size: 81 Copynumber: 8.0 Consensus size: 81
23240 CACTATAATT
* * * * * *
23250 CCTTTATTCTTTTAGTCCATGGTATTTAACCGTTCATTTAAATAGCATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
23315 CAAATGTAAAGTTAGG
66 CAAATGCAAAGTTAGG
* *
23331 CCTATATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTCGCATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
23396 CAAATGCACAGTTAGG
66 CAAATGCAAAGTTAGG
* * *
23412 CCATTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACGGGCATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
23477 CAAATGCACAA-TTAGG
66 CAAATGCA-AAGTTAGG
* * * *
23493 CCTTTATTCTTTTACTCAATGGTATTTAATCGTTCATCTAACTGGCATAATTGACACGTTTCTAT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
23558 CAAATGCATAA-TTAGG
66 CAAATGCA-AAGTTAGG
* * * **
23574 CCTTTATTCTTTTACTCCACAGTATTTAACCGTTCATCTAAATAACATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
* *
23639 CAAATGTACAGTTAGG
66 CAAATGCAAAGTTAGG
* * * * * * *
23655 CCTTTATTCGTTTACTCAACGGTATTTAATCGTTCCTCTAACTGACATAATTTATACCTTTCTCT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
23720 CAAATGCACAGTTAGG
66 CAAATGCAAAGTTAGG
* * *
23736 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGAATAATTGACACCTTTATGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
23801 CAAGTGCACAA-TTAGG
66 CAAATGCA-AAGTTAGG
* * *
23817 CCTTTATTCTTTTACTCAACGGTATTTAATCATTCATCTAACTGACATAATTGACACCTTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
*
23882 CAAATGCACAGTTAGG
66 CAAATGCAAAGTTAGG
23898 CCTT
1 CCTT
23902 AAAGGCACTC
Statistics
Matches: 502, Mismatches: 65, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
80 2 0.00
81 498 0.99
82 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (81 bp):
CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT
CAAATGCAAAGTTAGG
Found at i:23960 original size:68 final size:68
Alignment explanation
Indices: 23849--24239 Score: 525
Period size: 68 Copynumber: 5.8 Consensus size: 68
23839 TATTTAATCA
* * * ** * *
23849 TTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTTAAAGGCACTCAA
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
23914 CCT
66 CCT
* * * * * *
23917 TTCATCTAACTGGCATAAATTATACCTTTCTGTCATTTTCACAGTTAGGCCTCAAAGGCAGTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
23982 CCT
66 CCT
* *** * *
23985 TTCATCGAACCAACATAAATGAAACCTTTCTATAATTTGCACAGTTAGGCCTCAAAGGCACTCAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
24050 CCT
66 CCT
* *
24053 TTCATCTAACTGGCATAAATGACATCTTTCTATCATTTACACAGTTAGGCCTCAAAGGCACAT-A
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCAC-TCA
24117 GCCT
65 GCCT
* *
24121 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
24186 CCT
66 CCT
* * *
24189 TTCATCTAACT-GCATAAATGACACCATTCTGTCATTTGCACAGTTAAGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCT
24240 ATAATCTTTT
Statistics
Matches: 285, Mismatches: 36, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
67 38 0.13
68 246 0.86
69 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
CCT
Found at i:26330 original size:81 final size:80
Alignment explanation
Indices: 25862--26346 Score: 477
Period size: 81 Copynumber: 6.0 Consensus size: 80
25852 AGCTAGTCCA
* * ** * * * * * *
25862 TTATTCTTTTACTTAACAGTGCTTAACCATTCAGT-TAACTAGCACAATTCACACTTTTCTGTGA
1 TTATTCTTTTACTCAACGGTATTTAA-CGTTCA-TCTAACTGGCATAATTGACACCTTTCTGTCA
* * *
25926 ATTGCACTGTTAGGCCA
64 AATGCACAGTTAGGCCT
* * * * * *
25943 TTATCCTTTTACTCAACAGTATTTAACCATTCATATAACTTGCATAATTGTCACCTTTCTGTCAA
1 TTATTCTTTTACTCAACGGTATTTAA-CGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAA
* *
26008 ATTCATAGTTAGGCCT
65 ATGCACAGTTAGGCCT
* * * * *
26024 TTATTCTTTTACTCAGCGGTATTTAACTGTTCATCTAGCTGGCATTATTGACACTTTTCTTTCAA
1 TTATTCTTTTACTCAACGGTATTTAAC-GTTCATCTAACTGGCATAATTGACACCTTTCTGTCAA
* *
26089 ATTCACAATTAGGCCT
65 ATGCACAGTTAGGCCT
* * *
26105 TTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGAAACCTTTATGTCAA
1 TTATTCTTTTACTCAACGGTATTTAA-CGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAA
**
26170 ATGCACAACTAGGCCT
65 ATGCACAGTTAGGCCT
* * *
26186 TGATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGAGACCTTTTTGTCAA
1 TTATTCTTTTACTCAACGGTATTTAAC-GTTCATCTAACTGGCATAATTGACACCTTTCTGTCAA
*
26251 GTGCACAGTTAGGCCT
65 ATGCACAGTTAGGCCT
* * * * * **
26267 TTATTCTTTTACTCATCGATATTTAATCATTCATCTAACTAGAATAATTGACATATTTCTGTCAA
1 TTATTCTTTTACTCAACGGTATTTAA-CGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAA
** *
26332 AAACACATTTAGGCC
65 ATGCACAGTTAGGCC
26347 ATAAAGGCAC
Statistics
Matches: 340, Mismatches: 59, Indels: 10
0.83 0.14 0.02
Matches are distributed among these distances:
80 3 0.01
81 335 0.99
82 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (80 bp):
TTATTCTTTTACTCAACGGTATTTAACGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAA
TGCACAGTTAGGCCT
Found at i:26413 original size:68 final size:68
Alignment explanation
Indices: 26335--26686 Score: 465
Period size: 68 Copynumber: 5.2 Consensus size: 68
26325 CTGTCAAAAA
* * * * *
26335 CACATTTAGGCCAT-AAAGGCACTCAACCTTTCATCTAACTGGCATAAATTACACATTTCTATCA
1 CACAGTTAGGCC-TCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCA
*
26399 TATG
65 TTTG
* * * * * *
26403 CACAGTTAGGCCTCAAAGGCAGTTAGCCTTTCATCGAACTAGCATAAATGAAACTTTTCTATAAT
1 CACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCAT
26468 TTG
66 TTG
* * * *
26471 CACAGTTAGGCCTCAAAGGCACTCAGACTTTCATCTGACTGGCATAAATGACATCTTTCTATCAT
1 CACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCAT
*
26536 TTA
66 TTG
* *
26539 CACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGATACCTTTCTGTCAT
1 CACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCAT
26604 TTG
66 TTG
* * *
26607 CACAGTTAGGCCTTAAAGGAACTTAGCCTTTCATCTAACT-GCATAAATGACACCTTTCTGTCAT
1 CACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCAT
26671 TTG
66 TTG
**
26674 CACAACTAGGCCT
1 CACAGTTAGGCCT
26687 GTAATCTTTT
Statistics
Matches: 249, Mismatches: 34, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
67 38 0.15
68 211 0.85
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (68 bp):
CACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCAT
TTG
Found at i:28416 original size:81 final size:81
Alignment explanation
Indices: 28309--28793 Score: 558
Period size: 81 Copynumber: 6.0 Consensus size: 81
28299 AGCTAGTCCA
* * ** * ** * *
28309 TTATTCTTTTACTTAACAGTGCTTAACCATTCAGCTAACCAGCACAATTGACACTTTTCTGTGAA
1 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
* * *
28374 TTGCACTGTTAGGCCA
66 ATGCACAGTTAGGCCT
* * * * *
28390 TTATCCTTTTACTCAACAGTATTTAACCATTCATCTAACTTGCATAATTGTCACCTTTCTGTCAA
1 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
* *
28455 ATTCATAGTTAGGCCT
66 ATGCACAGTTAGGCCT
** * * *
28471 TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAGCTGGCATTATTGACACTTTTCTATCAA
1 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
*
28536 ATGCACAATTAGGCCT
66 ATGCACAGTTAGGCCT
* * * * *
28552 TTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGAAACCTTTATGTCAA
1 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
**
28617 ATGCACAACTAGGCCT
66 ATGCACAGTTAGGCCT
* ** *
28633 TGATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGAGACATTTT-TGTCA
1 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACAC-TTTTCTGTCA
*
28697 AGTGCACAGTTAGGCCT
65 AATGCACAGTTAGGCCT
* * * *
28714 TTATTCTTTTACTCATCGATATTTAATCATTCATCTAACTGGCATAATTGACACATTTCTGTCAA
1 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
** *
28779 AAACACATTTAGGCC
66 ATGCACAGTTAGGCC
28794 ATAAAGGAAC
Statistics
Matches: 344, Mismatches: 58, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
80 3 0.01
81 338 0.98
82 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
ATGCACAGTTAGGCCT
Found at i:28868 original size:68 final size:68
Alignment explanation
Indices: 28743--29133 Score: 428
Period size: 68 Copynumber: 5.8 Consensus size: 68
28733 TATTTAATCA
* * * **** * *
28743 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAAAACACATTTAGGCCAT-AAAGGAACTCA
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCC-TCAAAGGCACTCA
*
28807 ACCT
65 GCCT
* ** * * * *
28811 TTCATCTAACTGGCATAAATTACATATTTCTATCATATGCACAGTTAGACCTCAAAGGCAGTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
28876 CCT
66 CCT
* * * *
28879 TTCAT-TGAACTAGCATAAATGAAACTTTTCTATAATTTGCACAGTTAGGCCTCAAAGGCACTCA
1 TTCATCT-AACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCA
*
28943 GACT
65 GCCT
* * * *
28947 TTCATCTGACTGGCATAAATGACACCTTTCTATCATTTACATAGTTAGGCCTTAAAGGCACTCAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
29012 CCT
66 CCT
* * * * * *
29015 TTCATCTAACTGGCATAAATGATACCTTTCTGTCATTTGTACAGTTAGGCCTTAAAGGAACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
29080 CCT
66 CCT
* **
29083 TTCATCTAACT-GCATAAATGACACCTTTCTGTCATTTGCACAACTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCT
29134 GTAATCTTTT
Statistics
Matches: 275, Mismatches: 45, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
67 38 0.14
68 236 0.86
69 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTATCATTTGCACAGTTAGGCCTCAAAGGCACTCAG
CCT
Found at i:30860 original size:81 final size:81
Alignment explanation
Indices: 30753--31236 Score: 522
Period size: 81 Copynumber: 6.0 Consensus size: 81
30743 AGCTAGTCTA
* ** * ** * *
30753 TTATTCTTTTACTTAACAGTGCTTAACCATTCAGCTAACCAGCACAATTGACACTTTTCTGTGAA
1 TTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
* * *
30818 TTGCACTGTTAGGCCA
66 ATGCACAGTTAGGCCT
* * *
30834 TTATCCTTTTACTCAACAGTATTTAACCATTCATCTAACTTGCATAATTGTCACTTTTCTGTCAA
1 TTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
* *
30899 ATTCATAGTTAGGCCT
66 ATGCACAGTTAGGCCT
* * * ** * *
30915 TTATTCTTTAACTCAGCAGTTTTTAACTGTTCATCTAGCTGGCATTATTGACACTTTTCTGTCAA
1 TTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
*
30980 ATGCACAATTAGGCCT
66 ATGCACAGTTAGGCCT
* * * * * * *
30996 TTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGAAACCTTTATGTCAA
1 TTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
**
31061 ATGCACAACTAGGCCT
66 ATGCACAGTTAGGCCT
* * ** * *
31077 TGATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTGAGACCTTT-TGTCAA
1 TTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
*
31141 GTGCACAGTTAGGCCT
66 ATGCACAGTTAGGCCT
* ** *
31157 TTATTCTTTTACTCATC-GATATTTAATTATTCATCTAACTGGCATAATTGACACATTTCTGTCA
1 TTATTCTTTTACTCAACAG-TATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCA
** *
31221 AAAACACATTTAGGCC
65 AATGCACAGTTAGGCC
31237 ATAAAGGCAC
Statistics
Matches: 342, Mismatches: 59, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
79 1 0.00
80 69 0.20
81 272 0.80
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (81 bp):
TTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATTGACACTTTTCTGTCAA
ATGCACAGTTAGGCCT
Found at i:31302 original size:68 final size:67
Alignment explanation
Indices: 31186--31368 Score: 195
Period size: 68 Copynumber: 2.7 Consensus size: 67
31176 TATTTAATTA
* * **** * * *
31186 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAAAACACATTTAGGCCATAAAGGCACTCAA
1 TTCATCTAACTGGCATAAATGACACATTTCTATCATTTGCACAGTTAGGCC-TAAAGGCACTTAG
31251 CCT
65 CCT
* * *
31254 TTCATCTAACTGGCATAAATTACACATTTCTATCATATGCACAGTTAGGCCTCAAAGGCAGTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTATCATTTGCACAGTTAGGCCT-AAAGGCACTTAG
31319 CCT
65 CCT
* * * * *
31322 TTCATCGAACTAGCATAAATGAAACTTTTCTATAATTTGCACAGTTA
1 TTCATCTAACTGGCATAAATGACACATTTCTATCATTTGCACAGTTA
31369 TAATTTGCAC
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
67 1 0.01
68 96 0.99
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (67 bp):
TTCATCTAACTGGCATAAATGACACATTTCTATCATTTGCACAGTTAGGCCTAAAGGCACTTAGC
CT
Found at i:31372 original size:15 final size:15
Alignment explanation
Indices: 31352--31383 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
31342 GAAACTTTTC
31352 TATAATTTGCACAGT
1 TATAATTTGCACAGT
31367 TATAATTTGCACAGT
1 TATAATTTGCACAGT
31382 TA
1 TA
31384 GGCCTCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (15 bp):
TATAATTTGCACAGT
Found at i:31407 original size:151 final size:151
Alignment explanation
Indices: 31225--31519 Score: 434
Period size: 151 Copynumber: 2.0 Consensus size: 151
31215 CTGTCAAAAA
* *
31225 CACATTTAGGCCATAAAGGCACTCAACCTTTCATCTAACTGGCATAAATTACA-CATTTCTATCA
1 CACAGTTAGGCCATAAAGGCACTCAACCTTTCATCTAACTGGCATAAATGACATC-TTTCTATCA
* * *
31289 TATGCACAGTTAGGCCTCAAAGGCAGTTAGCCTTTCATCGAACTAGCATAAATGAAACTTTTCTA
65 TATACACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCGAACTAGCATAAATGAAACCTTTCTA
31354 TAATTTGCACAGTTATAATTTG
130 TAATTTGCACAGTTATAATTTG
*
31376 CACAGTTAGGCC-TCAAAGGCACTCAGA-CTTTCATCTGACTGGCATAAATGACATCTTTCTATC
1 CACAGTTAGGCCAT-AAAGGCACTCA-ACCTTTCATCTAACTGGCATAAATGACATCTTTCTATC
* * * *
31439 ATTTACACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGATACCTTTCT
64 ATATACACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCGAACTAGCATAAATGAAACCTTTCT
* *
31504 GTCATTTGCACAGTTA
129 ATAATTTGCACAGTTA
31520 GGCCTTAAAG
Statistics
Matches: 129, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
150 1 0.01
151 126 0.98
152 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (151 bp):
CACAGTTAGGCCATAAAGGCACTCAACCTTTCATCTAACTGGCATAAATGACATCTTTCTATCAT
ATACACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCGAACTAGCATAAATGAAACCTTTCTAT
AATTTGCACAGTTATAATTTG
Found at i:31435 original size:83 final size:83
Alignment explanation
Indices: 31291--31451 Score: 227
Period size: 83 Copynumber: 1.9 Consensus size: 83
31281 TTCTATCATA
* * *
31291 TGCACAGTTAGGCCTCAAAGGCAGTTAGCCTTTCATCGAACTAGCATAAATGAAACTTTTCTATA
1 TGCACAGTTAGGCCTCAAAGGCACTCAGACTTTCATCGAACTAGCATAAATGAAACTTTTCTATA
*
31356 ATTTGCACAGTTATAATT
66 ATTTACACAGTTATAATT
* *
31374 TGCACAGTTAGGCCTCAAAGGCACTCAGACTTTCATCTG-ACTGGCATAAATGACA-TCTTTCTA
1 TGCACAGTTAGGCCTCAAAGGCACTCAGACTTTCATC-GAACTAGCATAAATGAAACT-TTTCTA
*
31437 TCATTTACACAGTTA
64 TAATTTACACAGTTA
31452 GGCCTCAAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
82 1 0.01
83 67 0.97
84 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (83 bp):
TGCACAGTTAGGCCTCAAAGGCACTCAGACTTTCATCGAACTAGCATAAATGAAACTTTTCTATA
ATTTACACAGTTATAATT
Found at i:31476 original size:219 final size:218
Alignment explanation
Indices: 31186--31582 Score: 555
Period size: 219 Copynumber: 1.8 Consensus size: 218
31176 TATTTAATTA
* * *
31186 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAAAACACATTTAGGCCATAAAGGCACTCAA
1 TTCATCTAACTGGCATAAATGACACATTTCTATCAAAAACACAGTTAGGCCATAAAGGCACTCAA
* * *
31251 CCTTTCATCTAACTGGCATAAATTACACATTTCTATCATATGCACAGTTAGGCCTCAAAGGCAGT
66 CCTTTCATCTAACTGGCATAAATGACACATTTCTATCATATGCACAGTTAGGCCTCAAAGGAACT
*
31316 TAGCCTTTCATCGAACTAGCATAAATGAAACTTTTCTATAATTTGCACAGTTATAATTTGCACAG
131 TAGCCTTTCATCGAACT-GCATAAATGAAACCTTTCTATAATTTGCACAGTTATAATTTGCACAG
31381 TTAGGCCTCAAAGGCACTCAGACT
195 TTAGGCCTCAAAGGCACTCAGACT
* *** *
31405 TTCATCTGACTGGCATAAATGACATC-TTTCTATCATTTACACAGTTAGGCC-TCAAAGGCACTT
1 TTCATCTAACTGGCATAAATGACA-CATTTCTATCAAAAACACAGTTAGGCCAT-AAAGGCACTC
* * * * * *
31468 AGCCTTTCATCTAACTGGCATAAATGATACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGAA
64 AACCTTTCATCTAACTGGCATAAATGACACATTTCTATCATATGCACAGTTAGGCCTCAAAGGAA
* * * *
31533 CTTAGCCTTTCATCTAACTGCATAAATGACACCTTTCTGTCATTTGCACA
129 CTTAGCCTTTCATCGAACTGCATAAATGAAACCTTTCTATAATTTGCACA
31583 ACTAGGCCTG
Statistics
Matches: 154, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
218 28 0.18
219 125 0.81
220 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (218 bp):
TTCATCTAACTGGCATAAATGACACATTTCTATCAAAAACACAGTTAGGCCATAAAGGCACTCAA
CCTTTCATCTAACTGGCATAAATGACACATTTCTATCATATGCACAGTTAGGCCTCAAAGGAACT
TAGCCTTTCATCGAACTGCATAAATGAAACCTTTCTATAATTTGCACAGTTATAATTTGCACAGT
TAGGCCTCAAAGGCACTCAGACT
Found at i:31485 original size:68 final size:68
Alignment explanation
Indices: 31371--31591 Score: 336
Period size: 68 Copynumber: 3.3 Consensus size: 68
31361 CACAGTTATA
* * * *
31371 ATTTGCACAGTTAGGCCTCAAAGGCACTCAGACTTTCATCTGACTGGCATAAATGACATCTTTCT
1 ATTTGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCT
*
31436 ATC
66 GTC
* *
31439 ATTTACACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGATACCTTTCT
1 ATTTGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCT
31504 GTC
66 GTC
* *
31507 ATTTGCACAGTTAGGCCTTAAAGGAACTTAGCCTTTCATCTAACT-GCATAAATGACACCTTTCT
1 ATTTGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCT
31571 GTC
66 GTC
**
31574 ATTTGCACAACTAGGCCT
1 ATTTGCACAGTTAGGCCT
31592 GTAATCTTTT
Statistics
Matches: 140, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 37 0.26
68 103 0.74
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (68 bp):
ATTTGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCT
GTC
Found at i:31921 original size:54 final size:54
Alignment explanation
Indices: 31797--31943 Score: 165
Period size: 54 Copynumber: 2.7 Consensus size: 54
31787 ACATCTATTT
* * * * *
31797 CCCATACAGAAGTTCATACACTTAGTATGAATTTCTTAGTTCGCACCTATAGTG
1 CCCATACAAAAGTTCATACACTTAGTATGAATTTCTTAATTTGCAACTAAAGTG
** *
31851 CCCATTTTAAAA-TTCATACACTTAGTTTGAATTTCTTATATTTGCATAC-AAAGTG
1 CCCA-TACAAAAGTTCATACACTTAGTATGAATTTCTTA-ATTTGCA-ACTAAAGTG
*
31906 -CCATACAAAAGTTCATACGCTTAGTATGAATTTCTTAA
1 CCCATACAAAAGTTCATACACTTAGTATGAATTTCTTAA
31944 ATTTTTGCAC
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
53 6 0.08
54 56 0.73
55 14 0.18
56 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (54 bp):
CCCATACAAAAGTTCATACACTTAGTATGAATTTCTTAATTTGCAACTAAAGTG
Found at i:33272 original size:81 final size:81
Alignment explanation
Indices: 33187--33761 Score: 821
Period size: 81 Copynumber: 7.1 Consensus size: 81
33177 AAGGCATAGC
* * * *
33187 TAGGCCATTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAGTTGGCACATTT
1 TAGGCCTTTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
* *
33252 CTGCCAAATGCACAGT
66 CTGTCAAATGCACAAT
*
33268 TAGGCCTTTATTCTTTTACTCAACGATGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
1 TAGGCCTTTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
*
33333 CTGTCAAATGCATAAT
66 CTGTCAAATGCACAAT
* * *
33349 TAGGCCTTTATTCTTTTCCTCAAC-AGTATTTAACCGTTCATCTAACTTGAATAATTGACACCTT
1 TAGGCCTTTATTCTTTTACTCAACGA-TATTTAACCGTTCATCTAACTGGCATAATTGACACCTT
*
33413 TCTGTCAAATGCACATT
65 TCTGTCAAATGCACAAT
* * * * *
33430 TATGCCTTTATTATTTTACTCAAC-AGTATTTAGCCATTCATCTAACTGGCATAATAGACACCTT
1 TAGGCCTTTATTCTTTTACTCAACGA-TATTTAACCGTTCATCTAACTGGCATAATTGACACCTT
* * *
33494 TATGTCAAATACATAAT
65 TCTGTCAAATGCACAAT
* * * *
33511 TAGGCCTTTATTGTTTTACTCAACGGTATTTAACCGTTTATCTAACTGGCATAATTGACACATTT
1 TAGGCCTTTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
*
33576 CTGTCAAATGCACAGT
66 CTGTCAAATGCACAAT
** * *
33592 TAGGCCTTTATTCTTTTACTCAACGGCATTTAACCGTTCATCTAACTGTCATAATTGAGACCTTT
1 TAGGCCTTTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
* *
33657 CTGTCAAGTGCACGAT
66 CTGTCAAATGCACAAT
*
33673 TAGGCCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
1 TAGGCCTTTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
*
33738 CTATCAAATGCACAAT
66 CTGTCAAATGCACAAT
33754 TAGGCCTT
1 TAGGCCTT
33762 AAAGGCACCC
Statistics
Matches: 439, Mismatches: 53, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
80 1 0.00
81 438 1.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (81 bp):
TAGGCCTTTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
CTGTCAAATGCACAAT
Found at i:33825 original size:68 final size:68
Alignment explanation
Indices: 33709--34085 Score: 454
Period size: 68 Copynumber: 5.6 Consensus size: 68
33699 TATTTAACCG
* * ** * **
33709 TTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAATTAGGCCTTAAAGGCACCCAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAG
33774 CCT
66 CCT
* *
33777 TTCATCTAACTGGCATAAA-GTACACCTTTCTGTCATTTGCAAAGTTAGGCCTTAAAGGAACTTA
1 TTCATCTAACTGGCATAAATG-ACACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTA
33841 GCCT
65 GCCT
* * * * * * * *
33845 TTCATCGAACTGGCATAAATGAAAACTTT-TCATAATTTGCACAGTTAGTCCTCAAAGGCACTCA
1 TTCATCTAACTGGCATAAATGACACCTTTCT-GTCATTTGCACAGTTAGGCCTTAAAGGCACTTA
*
33909 ACCT
65 GCCT
* * * * * * * *
33913 TTCATCTAACTGGCATAAATGAAATCTTTCGGTCATTTACACAGATAGGCCTCAAAGGAACTTAT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAG
33978 CCT
66 CCT
* *
33981 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCTCAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAG
34046 CCT
66 CCT
*
34049 TTCATCTAACT-GTATAAATGACACCTTTCTGTCATTT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTT
34086 ACAGACCTAG
Statistics
Matches: 262, Mismatches: 43, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
67 26 0.10
68 235 0.90
69 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAG
CCT
Found at i:35806 original size:81 final size:81
Alignment explanation
Indices: 35678--36210 Score: 564
Period size: 81 Copynumber: 6.6 Consensus size: 81
35668 GCTTTTTAGT
* * * * * * * * * * **
35678 TAACTTGCATATTTGACACTTTTATGTCCAAGGCATAGCTAGTCCATTATTCTTTTACTCAACAA
1 TAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTTTATTCTTTTACTCAACGG
** *
35743 TGCTTAACCATTCAGC
66 TATTTAACCATTCATC
* * * * * * * * * *
35759 TAACCGACATAATTGACACCTTTCTGCCAATTGTATAGTTAGGCCATTATCCTTTTATTCAATGG
1 TAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTTTATTCTTTTACTCAACGG
**
35824 TATTTAACTGTTCATC
66 TATTTAACCATTCATC
* * * *
35840 TAACTGGCATAATTGACACCTTTATGCCAAATGCACAGTTATGCCTTTATTCTTTTACTCAACGA
1 TAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTTTATTCTTTTACTCAACGG
35905 TATTTAACCATTCATC
66 TATTTAACCATTCATC
* * **
35921 TAACTGGCATAATTGACACAC-TTCTGTCAAATGCACAATTAGGCCTTTATTATTTTACTCAATA
1 TAACTGGCATAATTGACAC-CTTTCTGTCAAATGCACAGTTAGGCCTTTATTCTTTTACTCAACG
*
35985 GTATTTAACCATTCAAC
65 GTATTTAACCATTCATC
* * ** * *
36002 TAACTTGCATAATTAACATATTTCTGTCAAATCCACATTTAGGCCTTTATTCTTTTACTCAACGG
1 TAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTTTATTCTTTTACTCAACGG
*
36067 TATTTAACCGTTCATC
66 TATTTAACCATTCATC
* * * * * *
36083 TAACTGGCATAATTGAGACATTTCTGTCAAGTGCAGAGTTAGACCTTTATTCTTTTACTCAGCGG
1 TAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTTTATTCTTTTACTCAACGG
36148 TATTTAACCATTCATC
66 TATTTAACCATTCATC
* * * * *
36164 TAATTGGAATAATTGACATCTTTCCGTCAAATGCACAGTTATGCCTT
1 TAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTT
36211 AAAGGCACTC
Statistics
Matches: 372, Mismatches: 78, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
81 371 1.00
82 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.38
Consensus pattern (81 bp):
TAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTTTATTCTTTTACTCAACGG
TATTTAACCATTCATC
Found at i:36287 original size:68 final size:68
Alignment explanation
Indices: 36153--36537 Score: 430
Period size: 68 Copynumber: 5.7 Consensus size: 68
36143 AGCGGTATTT
* * * * * * ** * *
36153 AACCATTCATCTAATTGGAATAATTGACATCTTTCCGTCAAATGCACAGTTATGCCTTAAAGGCA
1 AACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCA
36218 CTC
66 CTC
* * * * * *
36221 AAACTTTAATCTAACTAGCATAAATTACACCTTTCTGTTATTTGCACAGTTAGGCCTCAAAAGCA
1 AACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCA
*
36286 CTT
66 CTC
* * * * * * *
36289 AGCCTTTCATCGAATTGGCATAAGTGAAACCTTTCTATAATTTGCACAGTTAGGCCTCAAAGGCA
1 AACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCA
36354 CTC
66 CTC
* * * * * *
36357 AACCTTTCATCTAATTGGCATAAATGACATCTTTCTGTCAGTTACACAATTATGCCTCAAAGGCA
1 AACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCA
*
36422 CTT
66 CTC
* * * *
36425 AGCTTTTCATCTAACTGGCATAAATGACACCTTTCTTTCATTTGCACAGTTAGGCCTTAAAGGCA
1 AACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCA
*
36490 CTT
66 CTC
*
36493 AGCCTTTCATCTAACT-GCATAAATGACACCTTTCTGTCATTTGCA
1 AACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCA
36538 GACCTAGGCC
Statistics
Matches: 263, Mismatches: 54, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
67 28 0.11
68 235 0.89
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (68 bp):
AACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCA
CTC
Found at i:36815 original size:54 final size:55
Alignment explanation
Indices: 36757--36900 Score: 173
Period size: 55 Copynumber: 2.6 Consensus size: 55
36747 GATCTATTTT
* * * * *
36757 CCATACGGAAATTCATACACTTATTTTGAATTTCTCA-GTCCGCACCCATAGTGC
1 CCATACAGAAATTCATACACTTAGTATGAATTTCTCATGTCCGCACACAAAGTGC
* * * **
36811 CCATACTGAAATTCATACACTTAGTATGAATTTCTTATTTTTGCACACAAAGTGC
1 CCATACAGAAATTCATACACTTAGTATGAATTTCTCATGTCCGCACACAAAGTGC
* *
36866 CTATACAGAAGTTCATACACTTAGTATGAATTTCT
1 CCATACAGAAATTCATACACTTAGTATGAATTTCT
36901 TAAATATTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
54 33 0.43
55 44 0.57
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (55 bp):
CCATACAGAAATTCATACACTTAGTATGAATTTCTCATGTCCGCACACAAAGTGC
Found at i:38132 original size:5 final size:5
Alignment explanation
Indices: 38122--38149 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
38112 TATATGCCAT
38122 TCATA TCATA TCATA TCATA TCATA TCA
1 TCATA TCATA TCATA TCATA TCATA TCA
38150 CATTACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
TCATA
Found at i:38333 original size:81 final size:80
Alignment explanation
Indices: 38278--38663 Score: 504
Period size: 81 Copynumber: 4.8 Consensus size: 80
38268 TGCTTAATCA
* * *
38278 TTCAGCTAACCGGCATAATTGACACCTTTCTGCTAATTGCACAGTTTGGTCATTATCCTTTTACT
1 TTCATCTAACCGGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGG-CATTATCCTTTTACT
38343 CAACGGTATTTAACTG
65 CAACGGTATTTAACTG
* *
38359 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGGCAATTATCCTTTTATT
1 TTCATCTAACCGGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGGC-ATTATCCTTTTACT
*
38424 CAACGGTATTTAACCG
65 CAACGGTATTTAACTG
* ** * *
38440 TTCATTTAACCAACATAATTGACACTTTTCTACCAATTGCACAGTTAGGCTATTATCCTTTTACT
1 TTCATCTAACCGGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGGC-ATTATCCTTTTACT
38505 CAACGGTATTTAACTG
65 CAACGGTATTTAACTG
** *
38521 TTCATCTAATTGGCATAATTGACACCTTTCTTCCAATTGCACAGTTAGGCCATTATCCTTTTACT
1 TTCATCTAACCGGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGG-CATTATCCTTTTACT
*
38586 CAACGGTATTTAAATG
65 CAACGGTATTTAACTG
* * ** * * ** *
38602 TTTACCTAACTAGCATAATTGACA-TTTTCTACCAATTGCATGGTTAGGCCATTATCATTTTA
1 TTCATCTAACCGGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGG-CATTATCCTTTTA
38664 TTTTGGACTA
Statistics
Matches: 271, Mismatches: 32, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
80 34 0.13
81 236 0.87
82 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.38
Consensus pattern (80 bp):
TTCATCTAACCGGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGGCATTATCCTTTTACTC
AACGGTATTTAACTG
Found at i:38946 original size:54 final size:54
Alignment explanation
Indices: 38800--39216 Score: 475
Period size: 54 Copynumber: 7.7 Consensus size: 54
38790 ATTTATTAGG
* * *
38800 ATGCACA-TGTAGTGCCTATATGG-TAGTTCATCAACTCATGATGAATTTCAT-GA
1 ATGCACACT-TAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTTCGTGGA
* ** *
38853 ATTTGAACAAATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGA
1 A--TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGA
* * *
38909 ATGCACACTTAGTGCCTATACGATTATTCATCAACTCATGATGAATTCCGTGGA
1 ATGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGA
* *
38963 ATGCACACTTAGTGCCTGTACGGTTATTCATAAACTCATGATGAATTTCATGGA
1 ATGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGA
* ** * *
39017 ATGTACACTTAGTGAATGTACGGTTATTCATCAACTCTTGATGAA-TTCTTTGGA
1 ATGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTC-GTGGA
* * * *
39071 ATGCACAGTTAGTTCCTGTATGGTTATTCATCAACTCATGATGAATTTTGTGGA
1 ATGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGA
* * * *
39125 TTTGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGT-AA
1 -ATGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGA
* * *
39179 ATTTGCACACATAGTTCCTGTACGGTTATTCATTAACT
1 A--TGCACACTTAGTGCCTGTACGGTTATTCATCAACT
39217 TATATTAATA
Statistics
Matches: 310, Mismatches: 44, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
53 4 0.01
54 182 0.59
55 119 0.38
56 5 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (54 bp):
ATGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGA
Found at i:39575 original size:19 final size:22
Alignment explanation
Indices: 39536--39584 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 22
39526 CCATCATGGA
39536 ATCGATACTACTATACTACGGT
1 ATCGATACTACTATACTACGGT
39558 ATCGATACT-CTAT-C-ACGGT
1 ATCGATACTACTATACTACGGT
*
39577 ACCGATAC
1 ATCGATAC
39585 CATTTTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.46
20 1 0.04
21 4 0.15
22 9 0.35
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (22 bp):
ATCGATACTACTATACTACGGT
Found at i:44908 original size:80 final size:81
Alignment explanation
Indices: 44616--45019 Score: 536
Period size: 80 Copynumber: 5.0 Consensus size: 81
44606 CATTATAATT
* *** * *
44616 CCTTTATTC-TTTACTCCACGGTATTTAAATTTTCATCTAACTAGCATAATTGACACATTTTTAT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGT
*
44680 CAAATGCACGGTTAGG
66 CAAATGCACAGTTAGG
* *
44696 CCTTTATTCTTTTACTCAACGGTATTTAACTGTTCATATAACTAGCATAATTGACACA-TT-TGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGT
* *
44759 CAAATCCATAGTTAGG
66 CAAATGCACAGTTAGG
* *
44775 CCTTTATTCTTTTACTCAATGGTATTTAACAGTTCATCTAACTAGCATAATTGACACATTTCTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGT
44840 CAAATGCACAGTTAGG
66 CAAATGCACAGTTAGG
* * * *
44856 CCTTTATCCTTTTACTC-ACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTTTGT
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGT
*
44920 CAAATGCACAATTAGG
66 CAAATGCACAGTTAGG
* * *
44936 CCTTTATTC-TTTACTCAACGGTATTTAAACTTTCATCTAACT-G-ATTTAATTGGCATC-TTTC
1 CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCA--TAATTGACA-CATTTC
44997 TGTCAAATGCACAGTTAGG
63 TGTCAAATGCACAGTTAGG
45016 CCTT
1 CCTT
45020 AAAGGAACTT
Statistics
Matches: 291, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
78 1 0.00
79 78 0.27
80 134 0.46
81 78 0.27
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (81 bp):
CCTTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACATTTCTGT
CAAATGCACAGTTAGG
Found at i:45076 original size:68 final size:68
Alignment explanation
Indices: 44965--45290 Score: 454
Period size: 68 Copynumber: 4.8 Consensus size: 68
44955 GGTATTTAAA
*** * * * ** * *
44965 CTTTCATCTAACTGATTTAATTGGCATCTTTCTGTCAAATGCACAGTTAGGCCTTAAAGGAACTT
1 CTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTT
*
45030 AAC
66 AGC
*
45033 CTTTCATCTAAGTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTT
1 CTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTT
45098 AGC
66 AGC
* ** * * * * *
45101 CTTTCATCTAACTAGCATAAACAACACCTTTCTTTCATTTACATAGTTAAGCCTCAAAGGCACTC
1 CTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTT
45166 AGC
66 AGC
*
45169 CTTTCATCTAACTGGTATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTT
1 CTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTT
45234 AGC
66 AGC
*
45237 CTTTCATCTAACTGGCATAAATGACACCTTTCTGTGATTTGCACAGTTAGGCCT
1 CTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCT
45291 ACAATTTTTA
Statistics
Matches: 226, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 226 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (68 bp):
CTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTT
AGC
Found at i:45582 original size:54 final size:55
Alignment explanation
Indices: 45508--45643 Score: 177
Period size: 55 Copynumber: 2.5 Consensus size: 55
45498 TCCTATACGG
** *
45508 AAATTCATACACTTAGTATGAATTTCTCA-GTTCGCAC-CTATGGTGCCCATACTA
1 AAATTCATACACTTAGTATGAATTTCTCATGTTCGCACAC-AAAGTGCCCATACAA
* * * **
45562 AAATTCATACGCTTATTATGAATTTCTTATGTTTTCACACAAAGTGCCCATACAA
1 AAATTCATACACTTAGTATGAATTTCTCATGTTCGCACACAAAGTGCCCATACAA
45617 AAATTCATACACTTAGTATGAATTTCT
1 AAATTCATACACTTAGTATGAATTTCT
45644 TAAATTTTTG
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
54 26 0.37
55 43 0.61
56 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (55 bp):
AAATTCATACACTTAGTATGAATTTCTCATGTTCGCACACAAAGTGCCCATACAA
Found at i:46166 original size:94 final size:95
Alignment explanation
Indices: 45989--46210 Score: 290
Period size: 94 Copynumber: 2.3 Consensus size: 95
45979 TTGCTCTATA
** *
45989 GTATCGATATCCC-TACCATGGTATTAATACTACTATACTATGGTACCAATACTCCCTTCCAGTA
1 GTATCGATA-CCCTTACCATGGTATCGATACTACTATACTATGGTACCAATACCCCCTTCCAGTA
* *
46053 TCGATACTAATTTTTGATTCGATATTGCA-TG
65 TCGATACTAATTTTAGATTCGA-AGTGCACTG
* * *
46084 GTATCGATACCCTTACCATGGTATCGATACTACTATA-TTTGGTACCGATACCCCCTTCCGGTAT
1 GTATCGATACCCTTACCATGGTATCGATACTACTATACTATGGTACCAATACCCCCTTCCAGTAT
* *
46148 CGATACCT-ATTTTAGATTCGACGTGGACTG
66 CGATA-CTAATTTTAGATTCGAAGTGCACTG
*
46178 GTATCGCTACCCTTACCATGGTATCGATACTAC
1 GTATCGATACCCTTACCATGGTATCGATACTAC
46211 CTCATCGGTA
Statistics
Matches: 113, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
93 3 0.03
94 77 0.68
95 33 0.29
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACTATACTATGGTACCAATACCCCCTTCCAGTAT
CGATACTAATTTTAGATTCGAAGTGCACTG
Found at i:46220 original size:20 final size:21
Alignment explanation
Indices: 46197--46252 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
46187 CCCTTACCAT
*
46197 GGTATCGATACTACCT-CATC
1 GGTATCGATACTACCTGAATC
* **
46217 GGTATCAATACTAATTGAATC
1 GGTATCGATACTACCTGAATC
*
46238 AGTATCGATACTACC
1 GGTATCGATACTACC
46253 AGCTAATTCA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (21 bp):
GGTATCGATACTACCTGAATC
Done.