Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002241.1 Hibiscus syriacus cultivar Beakdansim tig00004559_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: 74687
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:370 original size:13 final size:13
Alignment explanation
Indices: 349--382 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
339 TTTATAGAGA
349 AAATGATATGAAT
1 AAATGATATGAAT
* *
362 AAGTGATATGTAT
1 AAATGATATGAAT
375 AAATGATA
1 AAATGATA
383 ATGCCCATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (13 bp):
AAATGATATGAAT
Found at i:509 original size:59 final size:60
Alignment explanation
Indices: 442--590 Score: 237
Period size: 60 Copynumber: 2.5 Consensus size: 60
432 GAGTCGAGGG
* *
442 TTACCTATGTTCTTCGAGACATATGGACTGTTTACATAT-TCTTCGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGTTTACATATGTCTTCGGACATATGGACTGA
* *
501 TTACCTATGTTCTTCGGGACATATGGACTGTTTATATATGTCTTTGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGTTTACATATGTCTTCGGACATATGGACTGA
* *
561 TTATCTATGTTCTTCGGGACATATGTACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
591 ATTCCTAGGT
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 37 0.45
60 46 0.55
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (60 bp):
TTACCTATGTTCTTCGGGACATATGGACTGTTTACATATGTCTTCGGACATATGGACTGA
Found at i:524 original size:31 final size:31
Alignment explanation
Indices: 442--604 Score: 194
Period size: 31 Copynumber: 5.5 Consensus size: 31
432 GAGTCGAGGG
*
442 TTACCTATGTTCTTCGAGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
473 TTA-C-ATATTCTTC-GGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
501 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
** * *
532 TTATATATG-TCTT-TGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* * *
561 TTATCTATGTTCTTCGGGACATATGTACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
592 TT-CCTAGGTTCTT
1 TTACCTATGTTCTT
605 ATTGACCTAT
Statistics
Matches: 115, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
28 17 0.15
29 31 0.27
30 26 0.23
31 41 0.36
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:3081 original size:31 final size:31
Alignment explanation
Indices: 3043--3165 Score: 183
Period size: 31 Copynumber: 4.0 Consensus size: 31
3033 GAGTCGAGGG
*
3043 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGA
3074 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
*
3105 TTACCTATGTTCTTCGGGATATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* * ** *
3136 TTACCTAGGTTGTTATGGACTTATGGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
3166 GTCATTCGGG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 84 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:7802 original size:12 final size:13
Alignment explanation
Indices: 7776--7804 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
7766 TGACCTGTCT
7776 TTCTCTTCTTCGC
1 TTCTCTTCTTCGC
7789 TTCTCTTC-TCGC
1 TTCTCTTCTTCGC
7801 TTCT
1 TTCT
7805 GTAACCTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.00, C:0.38, G:0.07, T:0.55
Consensus pattern (13 bp):
TTCTCTTCTTCGC
Found at i:8262 original size:23 final size:23
Alignment explanation
Indices: 8228--8296 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
8218 CACCATAACT
* *
8228 CGTATAAATGCACCGAAGTGCTA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
8251 CGTAGAATTGCACCAAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
8274 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
8297 TATAAAATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:8872 original size:2 final size:2
Alignment explanation
Indices: 8807--8857 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
8797 ACTCATAGTG
8807 TA TA TA 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
8849 TA TA TA TA T
1 TA TA TA TA T
8858 TTAATAACTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12319 original size:14 final size:14
Alignment explanation
Indices: 12300--12327 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12290 ATCATAACAA
12300 AATTATATAACTAT
1 AATTATATAACTAT
12314 AATTATATAACTAT
1 AATTATATAACTAT
12328 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:13668 original size:54 final size:54
Alignment explanation
Indices: 13583--13693 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 54
13573 TTCGAAAGAA
*
13583 TGATTTTATGTTGTCTATATCTTCTGTATTTGGTTTACTTAGGATCTCCTGTTC
1 TGATTTTATGTTGTCTATATCTTCTGCATTTGGTTTACTTAGGATCTCCTGTTC
* *
13637 TGATTTTCTGTTGTTTATATCTTCTGCATTTGGTTTACTTAGGATCTCCTGTTC
1 TGATTTTATGTTGTCTATATCTTCTGCATTTGGTTTACTTAGGATCTCCTGTTC
13691 TGA
1 TGA
13694 GGTTAAGTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.14, C:0.15, G:0.17, T:0.53
Consensus pattern (54 bp):
TGATTTTATGTTGTCTATATCTTCTGCATTTGGTTTACTTAGGATCTCCTGTTC
Found at i:20550 original size:17 final size:17
Alignment explanation
Indices: 20528--20562 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20518 AATATGTTCA
* *
20528 TAATAATTCTCAAGCAT
1 TAATAATGCTCAAACAT
20545 TAATAATGCTCAAACAT
1 TAATAATGCTCAAACAT
20562 T
1 T
20563 GATCCTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (17 bp):
TAATAATGCTCAAACAT
Found at i:20730 original size:21 final size:22
Alignment explanation
Indices: 20696--20758 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
20686 TATATTTACT
*
20696 TTATAAAAATATATTA-AATATAA
1 TTAT-AAATTATATTATAA-ATAA
*
20719 -TATTAATTATATTATAAATAA
1 TTATAAATTATATTATAAATAA
* *
20740 TTATAAATTAAACTATAAA
1 TTATAAATTATATTATAAA
20759 ATTAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 13 0.39
22 20 0.61
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTATAAATTATATTATAAATAA
Found at i:20734 original size:34 final size:38
Alignment explanation
Indices: 20696--20766 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
20686 TATATTTACT
*
20696 TTATAAA-AA-TAT-ATTAAA-TATAATATTAATTATA
1 TTATAAATAATTATAATTAAACTATAAAATTAATTATA
20730 TTATAAATAATTATAAATTAAACTATAAAATTAATTA
1 TTATAAATAATTAT-AATTAAACTATAAAATTAATTA
20767 ATATAGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 7 0.23
35 2 0.06
36 3 0.10
38 6 0.19
39 13 0.42
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (38 bp):
TTATAAATAATTATAATTAAACTATAAAATTAATTATA
Found at i:31257 original size:15 final size:15
Alignment explanation
Indices: 31235--31272 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
31225 ATTTATAAAA
*
31235 AATAATAAAAATATT
1 AATAATAAAAATAAT
*
31250 ATTAAT-AAAATAAT
1 AATAATAAAAATAAT
31264 AATAATAAA
1 AATAATAAA
31273 TAATTAAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAATAAAAATAAT
Found at i:36103 original size:3 final size:3
Alignment explanation
Indices: 36090--36141 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
36080 GGCCTGCAAA
36090 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
36137 AAT AA
1 AAT AA
36142 AATGTTTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 3 0.07
3 42 0.91
4 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:36581 original size:84 final size:84
Alignment explanation
Indices: 36473--36639 Score: 226
Period size: 84 Copynumber: 2.0 Consensus size: 84
36463 TCGAAGGTCT
* * *
36473 TTGGCAGATAACCCTTCTTGCCTTGACCTATACTGCAAATGATGTGCCTTTGAGCTGAGTGCAAT
1 TTGGCAAATAACCCTTCTTGCCTTGACCTATACTGCAAATGATGTGCATTCGAGCTGAGTGCAAT
36538 CGAACTCAAAGGTCTTTTG
66 CGAACTCAAAGGTCTTTTG
* * * ** * * *
36557 TTGGCAAATAACCCTTTTTGCCTTGAGCTTTGTTGCAAATGATGTGCATTCGAGCTGTGTGTAGT
1 TTGGCAAATAACCCTTCTTGCCTTGACCTATACTGCAAATGATGTGCATTCGAGCTGAGTGCAAT
*
36622 CGAACTCGAAGGTCTTTT
66 CGAACTCAAAGGTCTTTT
36640 TGTTTCAAGA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (84 bp):
TTGGCAAATAACCCTTCTTGCCTTGACCTATACTGCAAATGATGTGCATTCGAGCTGAGTGCAAT
CGAACTCAAAGGTCTTTTG
Found at i:36789 original size:18 final size:18
Alignment explanation
Indices: 36768--36824 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
36758 TCTCAAGAGA
36768 GAAAACTTTGTTTCAAGG
1 GAAAACTTTGTTTCAAGG
*
36786 G-AAAC--TGTCTCAAGAG
1 GAAAACTTTGTTTCAAG-G
36802 AGAAAACTTTGTTTCAAGG
1 -GAAAACTTTGTTTCAAGG
36821 GAAA
1 GAAA
36825 CTGTCTCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
15 8 0.25
16 1 0.03
17 5 0.16
18 9 0.28
19 1 0.03
20 8 0.25
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (18 bp):
GAAAACTTTGTTTCAAGG
Found at i:36790 original size:17 final size:17
Alignment explanation
Indices: 36770--36826 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
36760 TCAAGAGAGA
36770 AAACTTTGTTTCAAGGG
1 AAACTTTGTTTCAAGGG
*
36787 AAAC--TGTCTCAAGAGAG
1 AAACTTTGTTTCAAG-G-G
36804 AAAACTTTGTTTCAAGGG
1 -AAACTTTGTTTCAAGGG
36822 AAACT
1 AAACT
36827 GTCTCAAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 8 0.24
16 1 0.03
17 10 0.30
18 5 0.15
19 1 0.03
20 8 0.24
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (17 bp):
AAACTTTGTTTCAAGGG
Found at i:36861 original size:36 final size:34
Alignment explanation
Indices: 36741--37048 Score: 290
Period size: 36 Copynumber: 8.9 Consensus size: 34
36731 CAAAGGTTGG
*
36741 TGTTTCAATAGAAACTGTCTCAAGAGAGAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAA-TT
*
36776 TGTTTCAAGGGAAACTGTCTCAAGAGAGAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAA-TT
*
36811 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AA-ATT
* *
36847 TGTTTCAAGAGAAACTATCTCAACAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTC-A-AGAGAGAAAA-TT
* * * *
36884 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA--AAATT
*
36920 TGTTTCAAG-GAAAACATAT-TC-A-A-AG---ATT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGAAAATT
*
36948 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAG--AAAATT
*
36984 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAG--AAAATT
* * *
37020 TATTTCATGATAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA
37049 CAAAACTTTG
Statistics
Matches: 233, Mismatches: 21, Indels: 39
0.80 0.07 0.13
Matches are distributed among these distances:
27 2 0.01
28 18 0.08
29 2 0.01
30 1 0.00
31 2 0.01
33 2 0.01
34 1 0.00
35 69 0.30
36 102 0.44
37 28 0.12
38 6 0.03
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (34 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAATT
Found at i:36965 original size:137 final size:137
Alignment explanation
Indices: 36750--37061 Score: 389
Period size: 137 Copynumber: 2.2 Consensus size: 137
36740 GTGTTTCAAT
* *
36750 AGAAACTGTCTCAAGAGAG--AAAACTTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGAAAACTTT
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACATAT-TC-A-A-AG---A-TTT
* *
36812 GTTTCAAGGGAAACTGTCTCAAGAGAGATAAGATTTGTTTCAAGAGAAACTATCTCAACAGAGAC
58 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAACAGAGAC
36877 AAAACTTAGTTCCAAA
123 AAAACTTA-TTCCAAA
* *
36893 AGAAACTGTCTCAAGGGAGACGAAA-TTTGTTTCAAGGAAAACATATTCAAAGATTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACATATTCAAAGATTTGTTTCAAG
* * * *
36957 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAACAGAGACAAAACTTA
* **
37022 TTTCATG
131 TTCCAAA
*
37029 ATAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
37062 TGAGTAAATT
Statistics
Matches: 149, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
136 26 0.17
137 77 0.52
138 1 0.01
141 2 0.01
142 1 0.01
143 19 0.13
144 18 0.12
145 5 0.03
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (137 bp):
AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACATATTCAAAGATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAACAGAGACAAAACTTA
TTCCAAA
Found at i:36976 original size:101 final size:100
Alignment explanation
Indices: 36841--37026 Score: 273
Period size: 100 Copynumber: 1.9 Consensus size: 100
36831 CAAGAGAGAT
36841 AAGATTTGTTTCAAGAGAAACTATCTCAACAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCA
1 AAGATTTGTTTCAAGAGAAACTATCTCAACAGAGACAAAA-TTAGTTCCAAAAGAAACTGTCTCA
* * *
36906 AGGGAGACGAAATTTGTTTCAAGGAAAACATATTCA
65 AGAGAGACAAAATTTATTTCAAGGAAAACATATTCA
* * * * * **
36942 AAGATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAA
1 AAGATTTGTTTCAAGAGAAACTATCTCAACAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAA
37007 GAGAGACAAAATTTATTTCA
66 GAGAGACAAAATTTATTTCA
37027 TGATAAACTG
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
100 38 0.51
101 37 0.49
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (100 bp):
AAGATTTGTTTCAAGAGAAACTATCTCAACAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAA
GAGAGACAAAATTTATTTCAAGGAAAACATATTCA
Found at i:38853 original size:11 final size:11
Alignment explanation
Indices: 38829--38866 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
38819 CTTGTTTTCT
*
38829 TTTTTC-TTTA
1 TTTTTCATTTG
38839 TTTTTCATTTG
1 TTTTTCATTTG
38850 TTTTTTCATTTG
1 -TTTTTCATTTG
38862 TTTTT
1 TTTTT
38867 TGTTTTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 6 0.24
11 8 0.32
12 11 0.44
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTTCATTTG
Found at i:38879 original size:12 final size:12
Alignment explanation
Indices: 38839--38867 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
38829 TTTTTCTTTA
38839 TTTTTCATTTGT
1 TTTTTCATTTGT
38851 TTTTTCATTTGT
1 TTTTTCATTTGT
38863 TTTTT
1 TTTTT
38868 GTTTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTCATTTGT
Found at i:38892 original size:11 final size:12
Alignment explanation
Indices: 38876--38921 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
38866 TTGTTTTTTG
38876 TTTTT-TTCTCT
1 TTTTTCTTCTCT
38887 TTTTT-TTCTCT
1 TTTTTCTTCTCT
38898 TTTTTCTTCTTCT
1 TTTTTCTTC-TCT
*
38911 ATTTTTGTTCT
1 -TTTTTCTTCT
38922 TGATTGGTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 16 0.52
12 3 0.10
13 4 0.13
14 8 0.26
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTCTTCTCT
Found at i:41814 original size:6 final size:5
Alignment explanation
Indices: 41780--41813 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
41770 AATCAAAGGA
41780 AAAAT AAAAT AAAAT AAAAT AATAAT AATAAT AA
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AA
41814 TTTTAAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:42834 original size:2 final size:2
Alignment explanation
Indices: 42827--42852 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42817 TATTTACCTC
42827 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
42853 TTCATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45206 original size:17 final size:18
Alignment explanation
Indices: 45172--45212 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
45162 CGATTGTCGC
45172 TATTTTTTATTGTCTTTT
1 TATTTTTTATTGTCTTTT
*
45190 TATTTTTTCTTGT-TTTT
1 TATTTTTTATTGTCTTTT
45207 TATTTT
1 TATTTT
45213 CAATAAGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (18 bp):
TATTTTTTATTGTCTTTT
Found at i:58465 original size:20 final size:20
Alignment explanation
Indices: 58440--58510 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
58430 CGATAATTAT
58440 CGTTGCGAATTTGAAAATCG
1 CGTTGCGAATTTGAAAATCG
*
58460 CGTTGCGAATTTGGAGAATCG
1 CGTTGCGAATTT-GAAAATCG
* *
58481 CATTGCAAATTTGAAAA-CTG
1 CGTTGCGAATTTGAAAATC-G
*
58501 AGTTGCGAAT
1 CGTTGCGAAT
58511 AGTTGTGTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.02
20 24 0.57
21 17 0.40
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAATCG
Found at i:58682 original size:113 final size:113
Alignment explanation
Indices: 58473--58689 Score: 265
Period size: 113 Copynumber: 1.9 Consensus size: 113
58463 TGCGAATTTG
* ** *
58473 GAGAATCGCATTGCAAATTTGAAAACTGAGTTGCGAATAGTTGTGTTCACCTATATCGGTAATTA
1 GAGAATCGCATTGCAAATATGAAAACTGAACTGCGAATAATTGTGTTCACCTATATCGGTAATTA
* * * *
58538 ACATTGCGAAATTCGAGTTGCGAAAACGAAATTCGCGTTGAATTTTTA
66 ACATTGCGAAATTAGAGTTACAAAAACGAAATTCACGTTGAATTTTTA
* ** * *
58586 GAGAATCGCGTTGTGAATATGAAAACTGAACTGTGAATAATTGTGTTTACCTATATCGGTAATTA
1 GAGAATCGCATTGCAAATATGAAAACTGAACTGCGAATAATTGTGTTCACCTATATCGGTAATTA
* ** *
58651 ACGTTTTGAAATTA-AGGTTACAAAAATGAAATTCACGTT
66 ACATTGCGAAATTAGA-GTTACAAAAACGAAATTCACGTT
58690 ACGAATTTGA
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
112 1 0.01
113 85 0.99
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (113 bp):
GAGAATCGCATTGCAAATATGAAAACTGAACTGCGAATAATTGTGTTCACCTATATCGGTAATTA
ACATTGCGAAATTAGAGTTACAAAAACGAAATTCACGTTGAATTTTTA
Found at i:58700 original size:20 final size:19
Alignment explanation
Indices: 58677--58741 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
58667 GTTACAAAAA
58677 TGAAATTCACGTTACGAATT
1 TGAAA-TCACGTTACGAATT
*
58697 TGAAAATCGCGTTACGAATT
1 TG-AAATCACGTTACGAATT
* * *
58717 TGAGAATCTCGTTGCGATTT
1 TGA-AATCACGTTACGAATT
58737 TGAAA
1 TGAAA
58742 ACTGCGTTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 3 0.08
20 33 0.85
21 3 0.08
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (19 bp):
TGAAATCACGTTACGAATT
Found at i:58749 original size:20 final size:20
Alignment explanation
Indices: 58686--58758 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
58676 ATGAAATTCA
*
58686 CGTTACGAATTTGAAAA-TCG
1 CGTTGCGAATTTGAAAACT-G
* *
58706 CGTTACGAATTTGAGAATCT-
1 CGTTGCGAATTTGA-AAACTG
*
58726 CGTTGCGATTTTGAAAACTG
1 CGTTGCGAATTTGAAAACTG
58746 CGTTGCGAATTTG
1 CGTTGCGAATTTG
58759 TTGGTTATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 4 0.09
20 38 0.84
21 2 0.04
22 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAACTG
Found at i:66214 original size:19 final size:19
Alignment explanation
Indices: 66187--66225 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
66177 ATTAAGTAAC
* *
66187 AAAATTAATATTTTCGATA
1 AAAAATAATATTTTAGATA
66206 AAAAATAATATTTTAGATA
1 AAAAATAATATTTTAGATA
66225 A
1 A
66226 TATTTCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAAATAATATTTTAGATA
Found at i:68902 original size:16 final size:14
Alignment explanation
Indices: 68883--68917 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
68873 AAAAATTATT
68883 AATTTTAATTTGTATA
1 AATTTTAATTT-T-TA
68899 AATTTTAATTTTTA
1 AATTTTAATTTTTA
68913 AATTT
1 AATTT
68918 AATGTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 1 0.05
16 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
AATTTTAATTTTTA
Found at i:70358 original size:39 final size:39
Alignment explanation
Indices: 70293--70379 Score: 120
Period size: 39 Copynumber: 2.2 Consensus size: 39
70283 TCCTATTGGT
* * * *
70293 CTGAAGACGCCGTGCACTCATGGGGTCTTCTCCGTTTGC
1 CTGAAGACGCCATGCACTCATAGGGTCTTCTCCATTTGA
* *
70332 CTGAAGACGCCATGCAGTCATAGGGTCTTCTCCATTTTA
1 CTGAAGACGCCATGCACTCATAGGGTCTTCTCCATTTGA
70371 CTGAAGACG
1 CTGAAGACG
70380 ATGCAATCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (39 bp):
CTGAAGACGCCATGCACTCATAGGGTCTTCTCCATTTGA
Found at i:70777 original size:23 final size:24
Alignment explanation
Indices: 70729--70779 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
70719 TAAAAGAATT
*
70729 TTGATTTGTCTAGTTGACGAGTCTTA
1 TTGATTTGTCGAGTT-A-GAGTCTTA
70755 TTGATTTGTCGAGTT-GAGTCTTA
1 TTGATTTGTCGAGTTAGAGTCTTA
70778 TT
1 TT
70780 TTACAACTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
26 14 0.58
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.49
Consensus pattern (24 bp):
TTGATTTGTCGAGTTAGAGTCTTA
Found at i:73583 original size:43 final size:43
Alignment explanation
Indices: 73456--73571 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
73446 ATATAAGGGT
* * *
73456 TTCAATAATGGATATAAGGTTTTCGATACCGATCGTTTTGGAT
1 TTCAATAATGAATATAAGGTTTTCGATACTGATCGTTTTGGAG
* * * *
73499 TTCGATAATGAATA-CATGTCTTTCGATAGTGATCGTTTTGGAG
1 TTCAATAATGAATATAAGGT-TTTCGATACTGATCGTTTTGGAG
*
73542 TTCAATGATGAATATAAGGTTTTCGATACT
1 TTCAATAATGAATATAAGGTTTTCGATACT
73572 AACCATTTTG
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 3 0.05
43 53 0.90
44 3 0.05
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (43 bp):
TTCAATAATGAATATAAGGTTTTCGATACTGATCGTTTTGGAG
Done.