Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001257.1 Hibiscus syriacus cultivar Beakdansim tig00002474_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: 66199
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:11471 original size:2 final size:2
Alignment explanation
Indices: 11459--11514 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
11449 TTTTAATGAT
*
11459 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11501 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
11515 AATCATTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:14686 original size:21 final size:20
Alignment explanation
Indices: 14662--14705 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
14652 ATTATAATTT
*
14662 TTAATTCAAAAAATTTTATAA
1 TTAATTCAAAAAA-TATATAA
* *
14683 TTAATTTAAATAATATATAA
1 TTAATTCAAAAAATATATAA
14703 TTA
1 TTA
14706 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTCAAAAAATATATAA
Found at i:14886 original size:186 final size:184
Alignment explanation
Indices: 14659--14995 Score: 559
Period size: 186 Copynumber: 1.8 Consensus size: 184
14649 AAAATTATAA
*
14659 TTTTTAATTCAAAAAATTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTAGA
1 TTTTTAATTCAAAAAATTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTAGA
14724 TAAATTTTTTAATTAAATAATATTGATTTAGGTTT-AAAAGTTATTAGATCTTAAATTATTAATT
66 TAAATTTTTTAATTAAATAATATTGATTTAGGTTTAAAAAGTTATTAGATCTTAAATTATTAATT
* *
14788 GAGTTTTAAATGGTTTGGGCTGAGCTCATATGTTATATATAATATATATAATAT
131 AAGTTGTAAATGGTTTGGGCTGAGCTCATATGTTATATATAATATATATAATAT
*
14842 TTTTTAATTCAAAAAATCAGTTTACAATTAATTTAAATAATATATATTTATAAAATAAAAATTTT
1 TTTTTAATTCAAAAAAT---TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTT
* * * * *
14907 ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAAGTTATTGGATTTTAAATTATTA
63 AGATAAATTTTTTAATTAAATAATATTGATTTAGGTTTAAAAAGTTATTAGATCTTAAATTATTA
14972 ATTAAGTTGTAAATGGTTTGGGCT
128 ATTAAGTTGTAAATGGTTTGGGCT
14996 CATATAATAT
Statistics
Matches: 141, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
183 17 0.12
186 78 0.55
187 46 0.33
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.47
Consensus pattern (184 bp):
TTTTTAATTCAAAAAATTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTAGA
TAAATTTTTTAATTAAATAATATTGATTTAGGTTTAAAAAGTTATTAGATCTTAAATTATTAATT
AAGTTGTAAATGGTTTGGGCTGAGCTCATATGTTATATATAATATATATAATAT
Found at i:15494 original size:12 final size:12
Alignment explanation
Indices: 15477--15509 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15467 TTGATTAAAG
*
15477 ACTCAAGCTTAA
1 ACTCAAACTTAA
15489 ACTCAAACTTAA
1 ACTCAAACTTAA
15501 AC-CAAACTT
1 ACTCAAACTT
15510 GAACCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.45, C:0.27, G:0.03, T:0.24
Consensus pattern (12 bp):
ACTCAAACTTAA
Found at i:18443 original size:44 final size:44
Alignment explanation
Indices: 18385--18503 Score: 193
Period size: 44 Copynumber: 2.7 Consensus size: 44
18375 ATCTTGGATT
18385 GCATTTCCGTCTCTCTTAGGGATGGGCACGGCCCCAAACACATC
1 GCATTTCCGTCTCTCTTAGGGATGGGCACGGCCCCAAACACATC
18429 GCATTTCCGTCTCTCTTAGGGATGGGCACGGCCCCAAACACATC
1 GCATTTCCGTCTCTCTTAGGGATGGGCACGGCCCCAAACACATC
* * * * *
18473 GCATTTCTGTCGCTTTTAGGAATGGGGACGG
1 GCATTTCCGTCTCTCTTAGGGATGGGCACGG
18504 GCCGGGACAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.25
Consensus pattern (44 bp):
GCATTTCCGTCTCTCTTAGGGATGGGCACGGCCCCAAACACATC
Found at i:21406 original size:19 final size:19
Alignment explanation
Indices: 21382--21437 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
21372 GAACGTTGGA
21382 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
21401 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
21422 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
21438 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:21417 original size:11 final size:11
Alignment explanation
Indices: 21382--21430 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
21372 GAACGTTGGA
21382 AACCGGTTTTG
1 AACCGGTTTTG
21393 -ACCGG-TTT-
1 AACCGGTTTTG
21401 AACCGGTTTTG
1 AACCGGTTTTG
21412 AACCGGTTTTG
1 AACCGGTTTTG
21423 -ACCGGTTT
1 AACCGGTTT
21431 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:21433 original size:9 final size:10
Alignment explanation
Indices: 21383--21437 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
21373 AACGTTGGAA
21383 ACCGGTTTTG
1 ACCGGTTTTG
*
21393 ACCGG-TTTA
1 ACCGGTTTTG
21402 ACCGGTTTTG
1 ACCGGTTTTG
21412 AACCGGTTTTG
1 -ACCGGTTTTG
21423 ACCGG-TTTG
1 ACCGGTTTTG
21432 ACCGGT
1 ACCGGT
21438 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:21468 original size:13 final size:13
Alignment explanation
Indices: 21450--21504 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
21440 CGACCCGTTT
*
21450 ACCCGTTTACCCG
1 ACCCGTTGACCCG
21463 ACCCGTTGACCCGACCCG
1 ACCCGTTGA--C---CCG
21481 ACCCGTTGACCCG
1 ACCCGTTGACCCG
21494 ACCCGTTGACC
1 ACCCGTTGACC
21505 GTTGACCGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 22 0.61
15 1 0.03
16 1 0.03
18 12 0.33
ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:21481 original size:18 final size:18
Alignment explanation
Indices: 21458--21498 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
21448 TTACCCGTTT
21458 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
21476 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
21494 ACCCG
1 ACCCG
21499 TTGACCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:28621 original size:19 final size:19
Alignment explanation
Indices: 28597--28652 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
28587 GAACGTTGGA
28597 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
28616 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
28637 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
28653 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:28632 original size:11 final size:11
Alignment explanation
Indices: 28597--28645 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
28587 GAACGTTGGA
28597 AACCGGTTTTG
1 AACCGGTTTTG
28608 -ACCGG-TTT-
1 AACCGGTTTTG
28616 AACCGGTTTTG
1 AACCGGTTTTG
28627 AACCGGTTTTG
1 AACCGGTTTTG
28638 -ACCGGTTT
1 AACCGGTTT
28646 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:28648 original size:9 final size:10
Alignment explanation
Indices: 28598--28652 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
28588 AACGTTGGAA
28598 ACCGGTTTTG
1 ACCGGTTTTG
*
28608 ACCGG-TTTA
1 ACCGGTTTTG
28617 ACCGGTTTTG
1 ACCGGTTTTG
28627 AACCGGTTTTG
1 -ACCGGTTTTG
28638 ACCGG-TTTG
1 ACCGGTTTTG
28647 ACCGGT
1 ACCGGT
28653 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:28683 original size:13 final size:13
Alignment explanation
Indices: 28665--28719 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
28655 CGACCCGTTT
*
28665 ACCCGTTTACCCG
1 ACCCGTTGACCCG
28678 ACCCGTTGACCCGACCCG
1 ACCCGTTGA--C---CCG
28696 ACCCGTTGACCCG
1 ACCCGTTGACCCG
28709 ACCCGTTGACC
1 ACCCGTTGACC
28720 GTTGACCGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 22 0.61
15 1 0.03
16 1 0.03
18 12 0.33
ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:28696 original size:18 final size:18
Alignment explanation
Indices: 28673--28713 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
28663 TTACCCGTTT
28673 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
28691 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
28709 ACCCG
1 ACCCG
28714 TTGACCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:28787 original size:29 final size:29
Alignment explanation
Indices: 28727--28792 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
28717 ACCGTTGACC
*** *
28727 GTGCTATTCTGGGAATTAATTCGGTTTTG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
28756 GTGCTATTCTGGGAATTAATTCGAAATGG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
28785 GTGCTATT
1 GTGCTATT
28793 TCGGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (29 bp):
GTGCTATTCTGGGAATTAATTCGAAATGG
Found at i:34074 original size:21 final size:22
Alignment explanation
Indices: 34038--34078 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
34028 TTTAAAAATA
*
34038 TAAAGGAAGTATCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
34060 TAAAGG-AGTACCGATACTC
1 TAAAGGAAGTACCGATACTC
34079 CCTGTCCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:34800 original size:79 final size:76
Alignment explanation
Indices: 34663--34805 Score: 180
Period size: 79 Copynumber: 1.8 Consensus size: 76
34653 CAATAAAATA
*
34663 TTATTTAACTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTATAATC-TTTAATGT
1 TTATTTAACTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGT
34727 TTATTTAAAAC
66 TTATTTAAAAC
* * * * * *
34738 TTATTTAATTATTTCGAATTATATATACCAATTAAAAGAGTTGTAATCTAAATTACATTCTTTTA
1 TTATTTAACTAATTC-AATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTACAATCTTTTA
34803 ATG
62 ATG
34806 CTTACTTACT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
75 13 0.23
76 10 0.18
77 1 0.02
78 3 0.05
79 22 0.39
80 7 0.12
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (76 bp):
TTATTTAACTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGT
TTATTTAAAAC
Found at i:39934 original size:45 final size:45
Alignment explanation
Indices: 39865--40032 Score: 254
Period size: 45 Copynumber: 3.8 Consensus size: 45
39855 TATAAAATTT
* *
39865 CTTATCATTTATCCTATAAGCTCGTAAGTTTATTTTACCAATATA
1 CTTACCATTTATCCTATAAGCTCGTAAGCTTATTTTACCAATATA
39910 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTA-TCCTATAAGCTCGTAAGCTTATTTTACCAATATA
*
39955 CTTACCATTTATCCTTTAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCTATAAGCTCGTAAGCTTATTTTACCAATATA
*
40000 CTTGCCA-TTATTCC-ATAAGCTCGT-AGCTTATTT
1 CTTACCATTTA-TCCTATAAGCTCGTAAGCTTATTT
40033 GCATGGTTAC
Statistics
Matches: 115, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
43 9 0.08
44 15 0.13
45 88 0.77
46 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (45 bp):
CTTACCATTTATCCTATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:44372 original size:21 final size:21
Alignment explanation
Indices: 44346--44385 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44336 TCTTTGAGTG
* *
44346 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGATTAAAGAAAGC
44367 TTATATAAGATTAAAGAAA
1 TTATATAAGATTAAAGAAA
44386 CAAGAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (21 bp):
TTATATAAGATTAAAGAAAGC
Found at i:45861 original size:21 final size:21
Alignment explanation
Indices: 45830--45881 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
45820 AGGAGTGATT
*
45830 CTTCAGGACATATATGTGGTC
1 CTTCGGGACATATATGTGGTC
* *
45851 CTTTGGGACATATATGTGGTT
1 CTTCGGGACATATATGTGGTC
45872 CTTCGGGACA
1 CTTCGGGACA
45882 AATTCTATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (21 bp):
CTTCGGGACATATATGTGGTC
Found at i:45887 original size:56 final size:56
Alignment explanation
Indices: 45772--45887 Score: 124
Period size: 56 Copynumber: 2.1 Consensus size: 56
45762 ATGTATGCGG
* * * ***
45772 TTCTTCGGGACACATATTTGGTCCTTTGGAATATATATGTGATCCTTAAGGAGTGA
1 TTCTTCAGGACACATATGTGGTCCTTTGGAACATATATGTGATCCTTAAGGACAAA
* * * * **
45828 TTCTTCAGGACATATATGTGGTCCTTTGGGACATATATGTGGTTCTTCGGGACAAA
1 TTCTTCAGGACACATATGTGGTCCTTTGGAACATATATGTGATCCTTAAGGACAAA
45884 TTCT
1 TTCT
45888 ATGTGCCCCT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (56 bp):
TTCTTCAGGACACATATGTGGTCCTTTGGAACATATATGTGATCCTTAAGGACAAA
Found at i:50104 original size:21 final size:21
Alignment explanation
Indices: 50079--50118 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
50069 AAGACTTTAT
50079 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
50100 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
50119 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:56471 original size:22 final size:22
Alignment explanation
Indices: 56443--56484 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
56433 AGATTACTCG
*
56443 GAGGGTACCGATTCGCCCTACA
1 GAGGGTACCGATTCCCCCTACA
56465 GAGGGTACCGATTCCCCCTA
1 GAGGGTACCGATTCCCCCTA
56485 TGTAACGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.19
Consensus pattern (22 bp):
GAGGGTACCGATTCCCCCTACA
Found at i:57811 original size:19 final size:18
Alignment explanation
Indices: 57755--57811 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
57745 ATTTGCATTC
*
57755 TTATTTATTTTTATCTTAT
1 TTATTTAATTTTATCTT-T
* *
57774 ATATTTAATTTAATC-TT
1 TTATTTAATTTTATCTTT
57791 TTATTTAATATTTATCTTT
1 TTATTTAAT-TTTATCTTT
57810 TT
1 TT
57812 GTTTTGTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 9 0.29
18 6 0.19
19 16 0.52
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTAATTTTATCTTT
Found at i:58041 original size:19 final size:19
Alignment explanation
Indices: 58017--58093 Score: 145
Period size: 19 Copynumber: 4.1 Consensus size: 19
58007 TCCTATCCAT
58017 TTTCATCTTCTTTGAACTC
1 TTTCATCTTCTTTGAACTC
58036 TTTCATCTTCTTTGAACTC
1 TTTCATCTTCTTTGAACTC
*
58055 TTTCATCTTCTTTGAGCTC
1 TTTCATCTTCTTTGAACTC
58074 TTTCATCTTCTTTGAACTC
1 TTTCATCTTCTTTGAACTC
58093 T
1 T
58094 AAGTTTTTCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 56 1.00
ACGTcount: A:0.14, C:0.26, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTCATCTTCTTTGAACTC
Found at i:58066 original size:10 final size:10
Alignment explanation
Indices: 58017--58086 Score: 65
Period size: 10 Copynumber: 7.3 Consensus size: 10
58007 TCCTATCCAT
58017 TTTCATCTTC
1 TTTCATCTTC
* *
58027 TTTGAAC-TC
1 TTTCATCTTC
58036 TTTCATCTTC
1 TTTCATCTTC
* *
58046 TTTGAAC-TC
1 TTTCATCTTC
58055 TTTCATCTTC
1 TTTCATCTTC
* *
58065 TTTGAGC-TC
1 TTTCATCTTC
58074 TTTCATCTTC
1 TTTCATCTTC
58084 TTT
1 TTT
58087 GAACTCTAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
9 21 0.47
10 24 0.53
ACGTcount: A:0.13, C:0.26, G:0.06, T:0.56
Consensus pattern (10 bp):
TTTCATCTTC
Found at i:63665 original size:17 final size:17
Alignment explanation
Indices: 63643--63689 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
63633 CGATACTTCT
63643 TCAAGGGGTATCGATAC
1 TCAAGGGGTATCGATAC
*
63660 TCAAGGTCTAGTATCGATAC
1 TCAAGG---GGTATCGATAC
63680 TCAAGGGGTA
1 TCAAGGGGTA
63690 GTATCAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 9 0.36
20 16 0.64
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (17 bp):
TCAAGGGGTATCGATAC
Found at i:63675 original size:20 final size:20
Alignment explanation
Indices: 63650--63700 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
63640 TCTTCAAGGG
*
63650 GTATCGATACTCAAGGTCTA
1 GTATCGATACTCAAGGGCTA
*
63670 GTATCGATACTCAAGGGGTA
1 GTATCGATACTCAAGGGCTA
*
63690 GTATCAATACT
1 GTATCGATACT
63701 GGTGACACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (20 bp):
GTATCGATACTCAAGGGCTA
Done.