Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002780.1 Hibiscus syriacus cultivar Beakdansim tig00005731_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: 62449
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:10 original size:5 final size:5
Alignment explanation
Indices: 1--101 Score: 195
Period size: 5 Copynumber: 20.4 Consensus size: 5
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
51 AACAT AACAT AACAT AACAT AAC-T AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT AACAT
100 AA
1 AA
102 TGCTAGAGTA
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.04
5 91 0.96
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AACAT
Found at i:485 original size:21 final size:21
Alignment explanation
Indices: 461--511 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
451 TTGGGATTGG
461 TCTTTTCGGTC-GAGGGATCGA
1 TCTTTT-GGTCTGAGGGATCGA
**
482 TCTTTTTTTCTGAGGGATCGA
1 TCTTTTGGTCTGAGGGATCGA
503 TCCTTTTGG
1 T-CTTTTGG
512 AAATGGATCG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.43
Consensus pattern (21 bp):
TCTTTTGGTCTGAGGGATCGA
Found at i:497 original size:92 final size:92
Alignment explanation
Indices: 378--549 Score: 254
Period size: 92 Copynumber: 1.9 Consensus size: 92
368 ATCCTTTCTT
* * *
378 TCGAGGGATTAATCTTTTTCCCCGAGGGATCGATCCTTTTGAAAAGGGATTGATCCTTTGCACAA
1 TCGAGGGATCAATCTTTTTCCCCGAGGGATCGATCCTTTTGAAAAGGGATCGATCCTTTGCAAAA
*
443 CAGAAAGTTTGGGATTGGTCTTTTCGG
66 CAAAAAGTTTGGGATTGGTCTTTTCGG
* ** * * *
470 TCGAGGGATCGATCTTTTTTTCTGAGGGATCGATCCTTTTGGAAATGGATCGATCCTTTGCAAAA
1 TCGAGGGATCAATCTTTTTCCCCGAGGGATCGATCCTTTTGAAAAGGGATCGATCCTTTGCAAAA
535 CAAAAAGTTTGGGAT
66 CAAAAAGTTTGGGAT
550 CGATCATTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 70 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (92 bp):
TCGAGGGATCAATCTTTTTCCCCGAGGGATCGATCCTTTTGAAAAGGGATCGATCCTTTGCAAAA
CAAAAAGTTTGGGATTGGTCTTTTCGG
Found at i:568 original size:92 final size:92
Alignment explanation
Indices: 378--569 Score: 251
Period size: 92 Copynumber: 2.1 Consensus size: 92
368 ATCCTTTCTT
** ** * * *
378 TCGAGGGATTAATCTTTTTCCCCGAGGGATCGATCCTTTTGAAAAGGGATTGATCCTTTGCACAA
1 TCGAGGGATCGATCTTTTTTTCTGAGGGATCGATCCTTTTGAAAAGGGATCGATCCTTTGCAAAA
* * *
443 CAGAAAGTTTGGGATTGGTCTTTTCGG
66 CAAAAAGTTTGGGATCGATCTTTTCGG
* *
470 TCGAGGGATCGATCTTTTTTTCTGAGGGATCGATCCTTTTGGAAATGGATCGATCCTTTGCAAAA
1 TCGAGGGATCGATCTTTTTTTCTGAGGGATCGATCCTTTTGAAAAGGGATCGATCCTTTGCAAAA
535 CAAAAAGTTTGGGATCGATCATTTT-GG
66 CAAAAAGTTTGGGATCGATC-TTTTCGG
*
562 TGGAGGGA
1 TCGAGGGA
570 AAAGTAATCC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
92 82 0.95
93 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (92 bp):
TCGAGGGATCGATCTTTTTTTCTGAGGGATCGATCCTTTTGAAAAGGGATCGATCCTTTGCAAAA
CAAAAAGTTTGGGATCGATCTTTTCGG
Found at i:3821 original size:15 final size:15
Alignment explanation
Indices: 3801--3835 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3791 TTACTTCAAC
*
3801 ATACTTCAATAATCT
1 ATACTTCAATAATAT
3816 ATACTTCAATAATAT
1 ATACTTCAATAATAT
3831 ATACT
1 ATACT
3836 GTATTTTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (15 bp):
ATACTTCAATAATAT
Found at i:6667 original size:59 final size:60
Alignment explanation
Indices: 6594--6708 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
6584 ACTATGGTCG
* *
6594 CTCAACTAAACCCTACCAAAC-ATGTGGCCATCTAAGAATTTTTACTATCAATTTGTCCA
1 CTCAACTAAACCCTACCAAACAATGAGGCCATCTAAGAATTTATACTATCAATTTGTCCA
* * * * *
6653 CTCAACTATACCCTATCAAACAATGAGGCCATTTAAGAGTTTATGCTATCAATTTG
1 CTCAACTAAACCCTACCAAACAATGAGGCCATCTAAGAATTTATACTATCAATTTG
6709 GCCTCCCAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 19 0.40
60 29 0.60
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (60 bp):
CTCAACTAAACCCTACCAAACAATGAGGCCATCTAAGAATTTATACTATCAATTTGTCCA
Found at i:8381 original size:12 final size:12
Alignment explanation
Indices: 8364--8388 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8354 AAGATCAAAC
8364 TCCAAATTGACA
1 TCCAAATTGACA
8376 TCCAAATTGACA
1 TCCAAATTGACA
8388 T
1 T
8389 GAATTCCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (12 bp):
TCCAAATTGACA
Found at i:8585 original size:11 final size:10
Alignment explanation
Indices: 8566--8592 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
8556 AAAGTTTCTG
8566 AAAAGAAAAA
1 AAAAGAAAAA
8576 AAAAGAAAAA
1 AAAAGAAAAA
8586 AAAAGAA
1 AAAAGAA
8593 GCAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:9841 original size:18 final size:19
Alignment explanation
Indices: 9802--9839 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9792 TGATTTAAGC
* *
9802 ATTTAAATTTTATTAAAAA
1 ATTTAAATATAATTAAAAA
9821 ATTTAAATATAATTAAAAA
1 ATTTAAATATAATTAAAAA
9840 TTCATACATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTAAATATAATTAAAAA
Found at i:10380 original size:30 final size:30
Alignment explanation
Indices: 10346--10413 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
10336 TTATCGTTTA
*
10346 TTATAAATTGGTCACTAACGTTATAATTTG
1 TTATAAATTAGTCACTAACGTTATAATTTG
**
10376 TTATAAATTAGTCACTAACGTTATTGTTTG
1 TTATAAATTAGTCACTAACGTTATAATTTG
*
10406 TTACAAAT
1 TTATAAAT
10414 CAATCATGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (30 bp):
TTATAAATTAGTCACTAACGTTATAATTTG
Found at i:12292 original size:15 final size:15
Alignment explanation
Indices: 12272--12301 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12262 GAACTTTCTA
12272 ATGAAAATGTGAATG
1 ATGAAAATGTGAATG
*
12287 ATGAAAATTTGAATG
1 ATGAAAATGTGAATG
12302 TGACGATACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (15 bp):
ATGAAAATGTGAATG
Found at i:21460 original size:6 final size:6
Alignment explanation
Indices: 21449--21489 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
21439 GTGTCGAAGA
21449 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
21490 GCCGAGCCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:23405 original size:21 final size:21
Alignment explanation
Indices: 23379--23427 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
23369 AGTGTCTAAC
23379 AATAATAAAATCAATAGAAAA-
1 AATAATAAAATCAATA-AAAAT
*
23400 AATAATAAAATCGATAAAAAT
1 AATAATAAAATCAATAAAAAT
23421 AATAATA
1 AATAATA
23428 TTTTCGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (21 bp):
AATAATAAAATCAATAAAAAT
Found at i:23885 original size:22 final size:23
Alignment explanation
Indices: 23860--23905 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
23850 AATTTTGTAC
*
23860 TCTTACAAGTTTAATATAA-TTT
1 TCTTAAAAGTTTAATATAACTTT
*
23882 TCTTAAAATTTTAATATAACTTT
1 TCTTAAAAGTTTAATATAACTTT
23905 T
1 T
23906 TGAATGACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (23 bp):
TCTTAAAAGTTTAATATAACTTT
Found at i:26057 original size:31 final size:31
Alignment explanation
Indices: 26019--26080 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
26009 AACGGTCAGG
* *
26019 GACCATATTGCAAACAAACTAAATGTTAGGA
1 GACCATATTACAAACAAACTAAATATTAGGA
**
26050 GACCATATTACAAACGGACTAAATATTAGGA
1 GACCATATTACAAACAAACTAAATATTAGGA
26081 AACAGTATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (31 bp):
GACCATATTACAAACAAACTAAATATTAGGA
Found at i:28729 original size:20 final size:20
Alignment explanation
Indices: 28701--28748 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
28691 TTAGGTGGAA
*
28701 ATATTATTATTGTAAAA-AAT
1 ATATAATTATT-TAAAATAAT
28721 ATATAATTATTTAAAATAAT
1 ATATAATTATTTAAAATAAT
*
28741 ATTTAATT
1 ATATAATT
28749 TTGAGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATAATTATTTAAAATAAT
Found at i:29429 original size:15 final size:15
Alignment explanation
Indices: 29409--29450 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
29399 TATATGTTCT
29409 TTTTAATATATTAAA
1 TTTTAATATATTAAA
29424 TTTT-A-ATATTAAA
1 TTTTAATATATTAAA
*
29437 TTATAATA-ATTAAA
1 TTTTAATATATTAAA
29451 ATAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.46
14 8 0.33
15 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTAATATATTAAA
Found at i:32381 original size:35 final size:37
Alignment explanation
Indices: 32309--32381 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
32299 GTTGGAAAAT
* *
32309 ATTTATATATTTTCTTTAAAAAAATTTAAATTCATAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAAATCATAA
*
32346 ATTTATATAATTTT-TTT-ACAAAATTAAAAAT-ATAA
1 ATTTATAT-ATTTTCTTTAAAAAAATTAAAAATCATAA
32381 A
1 A
32382 AAAGATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 5 0.16
36 11 0.34
37 11 0.34
38 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAAATCATAA
Found at i:32506 original size:14 final size:14
Alignment explanation
Indices: 32487--32518 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
32477 GGATAAATTT
32487 GTAATTTAACCTTC
1 GTAATTTAACCTTC
32501 GTAATTTAACCTTC
1 GTAATTTAACCTTC
32515 GTAA
1 GTAA
32519 AAATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (14 bp):
GTAATTTAACCTTC
Found at i:32904 original size:42 final size:42
Alignment explanation
Indices: 32820--32905 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
32810 TCAATAATTA
* **
32820 TAAAAGAGTATGAATAAATATTACCTTTTAACCATCTCATAT
1 TAAAAGAGTATAAATAAATATTACCTTTTAACCATCAAATAT
32862 TAAAAGAGTATAAATAAATATTACCTTTTAACCATCAAATAT
1 TAAAAGAGTATAAATAAATATTACCTTTTAACCATCAAATAT
32904 TA
1 TA
32906 TTTAAGAAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.35
Consensus pattern (42 bp):
TAAAAGAGTATAAATAAATATTACCTTTTAACCATCAAATAT
Found at i:33126 original size:42 final size:41
Alignment explanation
Indices: 33064--33142 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 41
33054 CTAAATTATT
*
33064 TTTAAAAATCCAGAAGAGACTCTAAGAATTGATTCATGTAA
1 TTTAAAAATCCAAAAGAGACTCTAAGAATTGATTCATGTAA
*
33105 TTTATAAAATCCAAAAGAGACTTTAAGAATTGATTCAT
1 TTTA-AAAATCCAAAAGAGACTCTAAGAATTGATTCAT
33143 CGTTTTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 4 0.11
42 31 0.89
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (41 bp):
TTTAAAAATCCAAAAGAGACTCTAAGAATTGATTCATGTAA
Found at i:36995 original size:22 final size:22
Alignment explanation
Indices: 36942--37009 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
36932 AATCATGCAG
* *
36942 TTTGTAACTCATGCAATAAAACC
1 TTTGTAACTCTTGC-ATTAAACC
* *
36965 TCTGTAACTCTTGCATTAAAGC
1 TTTGTAACTCTTGCATTAAACC
36987 TTTGTAACTCTTGCATTAAACC
1 TTTGTAACTCTTGCATTAAACC
37009 T
1 T
37010 ACAACAACTC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 27 0.69
23 12 0.31
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (22 bp):
TTTGTAACTCTTGCATTAAACC
Found at i:42881 original size:21 final size:21
Alignment explanation
Indices: 42839--42881 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
42829 TTTCTGGGCT
*
42839 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
42860 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
42881 A
1 A
42882 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:42934 original size:20 final size:20
Alignment explanation
Indices: 42909--42946 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42899 AAATGCTAGA
*
42909 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
42929 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
42947 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:43653 original size:103 final size:103
Alignment explanation
Indices: 43429--43654 Score: 389
Period size: 103 Copynumber: 2.2 Consensus size: 103
43419 GTAGAGGGTC
43429 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGCGAGACACATAC
1 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGCGAGACACATAC
43494 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
* * * *
43532 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGCGAGACACATAC
*
43597 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
* *
43635 TATGTGGTATTTCTGGACAT
1 TATGTGGTCTTTCGGGACAT
43655 TATTATATGG
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGCGAGACACATAC
TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:43700 original size:23 final size:23
Alignment explanation
Indices: 43663--43725 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
43653 ATTATTATAT
*
43663 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
43686 GGTACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
**
43709 GGCACTTAGGTGCAATT
1 GGCACTCCGGTGCAATT
43726 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:44484 original size:22 final size:22
Alignment explanation
Indices: 44426--44485 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
44416 TCCAATAGTT
* * *
44426 TGTAACTCATGCAATAAAACTC
1 TGTAACTCTTGCATTAAAACTA
* *
44448 TGTAACTCTTACATTAAAGCTA
1 TGTAACTCTTGCATTAAAACTA
44470 TGTAACTCTTGCATTA
1 TGTAACTCTTGCATTA
44486 CACTTGTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (22 bp):
TGTAACTCTTGCATTAAAACTA
Found at i:45785 original size:18 final size:18
Alignment explanation
Indices: 45762--45798 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
45752 ATTTGTGCTT
45762 TAAGCAAACCCTGCATGA
1 TAAGCAAACCCTGCATGA
45780 TAAGCAAACCCTGCATGA
1 TAAGCAAACCCTGCATGA
45798 T
1 T
45799 TTGAGTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (18 bp):
TAAGCAAACCCTGCATGA
Found at i:55326 original size:15 final size:15
Alignment explanation
Indices: 55306--55334 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55296 AACCGAACCG
55306 AACCGAATTAACCAT
1 AACCGAATTAACCAT
55321 AACCGAATTAACCA
1 AACCGAATTAACCA
55335 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:55495 original size:26 final size:26
Alignment explanation
Indices: 55431--55496 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
55421 AATTTTCGAA
* *
55431 TTAATAAAAAAAAAATTTAAAATTTT
1 TTAATTAAATAAAAATTTAAAATTTT
* * *
55457 CTAATTTATATAAAAA-TTAAATGTTTT
1 TTAA-TTAAATAAAAATTTAAA-ATTTT
55484 TTAATTAAATAAA
1 TTAATTAAATAAA
55497 TTATAATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAATTAAATAAAAATTTAAAATTTT
Found at i:55511 original size:20 final size:19
Alignment explanation
Indices: 55484--55525 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
55474 TAAATGTTTT
55484 TTAATTAAATAA-ATTATAA
1 TTAATTAAATAATA-TATAA
55503 TTAATTTAAATAATATATAA
1 TTAA-TTAAATAATATATAA
55523 TTA
1 TTA
55526 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 16 0.76
21 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAATTAAATAATATATAA
Found at i:55765 original size:181 final size:182
Alignment explanation
Indices: 55501--55846 Score: 565
Period size: 181 Copynumber: 1.9 Consensus size: 182
55491 AATAAATTAT
*
55501 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATA
1 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAACA
* * * *
55566 TTGATTTATATTTAAAAGTTATTGGATCTTAAATTATTAATT-GAGTTTTAAATGGTTTGGGCTT
66 TTGATTTAGATTTAAAAGTTATTAGATCTTAAATTATTAATTAG-GTTTTAAATGGTTTCGGCTG
*
55630 AG-CCTATATGTTATATATAATATATTTAATATTTAATTAAAAAAACAGTTTAC
130 AGATC-ATATGTTATATATAATATATTTAATATTTAATTAAAAAAACAGTTTAC
*
55683 AATTAATTTAAATAATATATAATTATAAAATAAAAAATTT-ATAT-AATTTTTTAATTAATTAAC
1 AATTAATTTAAATAATATATAATTATAAAAT-AAAAATTTCAGATAAATTTTTTAATTAATTAAC
*
55746 ATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAATTAGGTTTTAAATGGTTTCGGCTG
65 ATTGATTTAGATTTAAAAGTTATTAGATCTTAAATTATTAATTAGGTTTTAAATGGTTTCGGCTG
55811 AGATCATATGTTATATATAATATATTTAATATTTAA
130 AGATCATATGTTATATATAATATATTTAATATTTAA
55847 AATTTAATTT
Statistics
Matches: 153, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
181 109 0.71
182 36 0.24
183 8 0.05
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (182 bp):
AATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAACA
TTGATTTAGATTTAAAAGTTATTAGATCTTAAATTATTAATTAGGTTTTAAATGGTTTCGGCTGA
GATCATATGTTATATATAATATATTTAATATTTAATTAAAAAAACAGTTTAC
Found at i:56112 original size:8 final size:9
Alignment explanation
Indices: 56094--56134 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
56084 AAACCAAATT
56094 AAAATGAAA
1 AAAATGAAA
56103 AAAATGAAAA
1 AAAATG-AAA
56113 AAAAT-AAA
1 AAAATGAAA
*
56121 AAAA-GAGA
1 AAAATGAAA
56129 AAAATG
1 AAAATG
56135 TTGATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
8 13 0.46
9 7 0.25
10 8 0.29
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (9 bp):
AAAATGAAA
Found at i:56130 original size:19 final size:19
Alignment explanation
Indices: 56094--56132 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
56084 AAACCAAATT
*
56094 AAAATGAAAAAAATGAAAA
1 AAAATGAAAAAAAAGAAAA
56113 AAAAT-AAAAAAAGAGAAAA
1 AAAATGAAAAAAA-AGAAAA
56132 A
1 A
56133 TGTTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (19 bp):
AAAATGAAAAAAAAGAAAA
Found at i:59299 original size:22 final size:22
Alignment explanation
Indices: 59272--59314 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
59262 CATCTTTGTA
* *
59272 TTTGCATGAGCGTCTTTGCATC
1 TTTGCATGAGCATATTTGCATC
59294 TTTGCATGAGCATATTTGCAT
1 TTTGCATGAGCATATTTGCAT
59315 TAGTATCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (22 bp):
TTTGCATGAGCATATTTGCATC
Found at i:60574 original size:14 final size:13
Alignment explanation
Indices: 60550--60622 Score: 68
Period size: 12 Copynumber: 5.9 Consensus size: 13
60540 AGGTGAGGAT
60550 AAAAA-CAAAGAA
1 AAAAAGCAAAGAA
60562 AAAATAGCAAAGAA
1 AAAA-AGCAAAGAA
*
60576 GAAAAGGCAAA-AA
1 -AAAAAGCAAAGAA
*
60589 AAAGAGCAAAG--
1 AAAAAGCAAAGAA
60600 AAAAA-CAAAG-A
1 AAAAAGCAAAGAA
60611 AAAAAGCAAAGA
1 AAAAAGCAAAGA
60623 GAAACAAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
10 5 0.10
11 9 0.18
12 17 0.34
13 3 0.06
14 12 0.24
15 4 0.08
ACGTcount: A:0.74, C:0.08, G:0.16, T:0.01
Consensus pattern (13 bp):
AAAAAGCAAAGAA
Found at i:60608 original size:10 final size:10
Alignment explanation
Indices: 60595--60636 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
60585 AAAAAAAGAG
60595 CAAAGAAAAA
1 CAAAGAAAAA
60605 CAAAGAAAAAA
1 CAAAG-AAAAA
*
60616 GCAAAGAGAAA
1 -CAAAGAAAAA
60627 CAAAGAAAAA
1 CAAAGAAAAA
60637 TGATGACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 14 0.50
11 9 0.32
12 5 0.18
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (10 bp):
CAAAGAAAAA
Found at i:60608 original size:22 final size:22
Alignment explanation
Indices: 60550--60636 Score: 95
Period size: 22 Copynumber: 3.7 Consensus size: 22
60540 AGGTGAGGAT
60550 AAAAACAAAGAAAAAATAGCAAAG
1 AAAAACAAAG-AAAAA-AGCAAAG
60574 AAGAAAAGGCAAA-AAAAAGAGCAAAG
1 -A-AAAA--CAAAGAAAAA-AGCAAAG
60600 AAAAACAAAGAAAAAAGCAAAG
1 AAAAACAAAGAAAAAAGCAAAG
*
60622 AGAAACAAAGAAAAA
1 AAAAACAAAGAAAAA
60637 TGATGACAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
22 25 0.45
23 5 0.09
24 4 0.07
25 2 0.04
26 16 0.29
28 4 0.07
ACGTcount: A:0.75, C:0.08, G:0.16, T:0.01
Consensus pattern (22 bp):
AAAAACAAAGAAAAAAGCAAAG
Found at i:61843 original size:36 final size:36
Alignment explanation
Indices: 61803--61900 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 36
61793 TAGTTGGGTG
*
61803 TTTTTTTTCGAAACAAATTTTATCTCACTTGAGACA
1 TTTTTTTTCGAAACAAATTTCATCTCACTTGAGACA
** *
61839 TTTTTTCTCTTAAAACAAATTTCGTCTCACTTGAGACA
1 TTTTTT-T-TCGAAACAAATTTCATCTCACTTGAGACA
**
61877 TTTTCCTTCGAAACACAAATTTCA
1 TTTTTTTTCG-AA-ACAAATTTCA
61901 AAGTTATTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
36 7 0.14
37 4 0.08
38 38 0.78
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (36 bp):
TTTTTTTTCGAAACAAATTTCATCTCACTTGAGACA
Found at i:61932 original size:66 final size:67
Alignment explanation
Indices: 61840--61976 Score: 204
Period size: 66 Copynumber: 2.1 Consensus size: 67
61830 CTTGAGACAT
*
61840 TTTTTCTCTTAAAACAAATTTCGTCTCACTTGAGACATTTTCCTTCGAAACACAAATTTCAAAGT
1 TTTTTCTCTAAAAACAAATTTCGTCTCACTTGAGACATTTTCCTTCGAAACACAAATTTCAAAGT
61905 TA
66 TA
* * * * *
61907 TTTTTCT-TAAAAATAAATTTTGTCTCACTTGAGATATTTTTCTTCGGAACACAAATTTCAAAGT
1 TTTTTCTCTAAAAACAAATTTCGTCTCACTTGAGACATTTTCCTTCGAAACACAAATTTCAAAGT
*
61971 TC
66 TA
61973 TTTT
1 TTTT
61977 ACTTGAACCA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
66 56 0.89
67 7 0.11
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (67 bp):
TTTTTCTCTAAAAACAAATTTCGTCTCACTTGAGACATTTTCCTTCGAAACACAAATTTCAAAGT
TA
Done.