Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006817.1 Hibiscus syriacus cultivar Beakdansim tig00017325_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: 62574
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:4740 original size:12 final size:12
Alignment explanation
Indices: 4720--4751 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4710 TAGCATTTAC
*
4720 AATAGATCAAAA
1 AATAAATCAAAA
4732 AATAAATCAAAA
1 AATAAATCAAAA
4744 AATAAATC
1 AATAAATC
4752 CGACGAGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.19
Consensus pattern (12 bp):
AATAAATCAAAA
Found at i:5718 original size:25 final size:25
Alignment explanation
Indices: 5690--5743 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
5680 TTTTATTTAA
5690 ATTTTAAGAATTAA-ATT-AATAAA-
1 ATTTTAA-AATTAAGATTAAATAAAT
*
5713 ATATTTAAATTTAAGATTAAATAAAT
1 AT-TTTAAAATTAAGATTAAATAAAT
5739 ATTTT
1 ATTTT
5744 TATCTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 7 0.27
24 8 0.31
25 9 0.35
26 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
ATTTTAAAATTAAGATTAAATAAAT
Found at i:5719 original size:24 final size:24
Alignment explanation
Indices: 5687--5742 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
5677 ATATTTTATT
5687 TAAAT-TTTAAGAATTAA-ATT-AA
1 TAAATATTTAA-AATTAAGATTAAA
*
5709 TAAAATATTTAAATTTAAGATTAAA
1 T-AAATATTTAAAATTAAGATTAAA
5734 TAAATATTT
1 TAAATATTT
5743 TTATCTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 1 0.03
23 9 0.31
24 16 0.55
25 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TAAATATTTAAAATTAAGATTAAA
Found at i:5759 original size:24 final size:24
Alignment explanation
Indices: 5705--5760 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
5695 AAGAATTAAA
* *
5705 TTAATAAAATATTTAAATTTAAGAT
1 TTAAT-AAATATTTAAATCTAAAAT
* **
5730 TAAATAAATATTTTTATCTAAAAT
1 TTAATAAATATTTAAATCTAAAAT
5754 TTAATAA
1 TTAATAA
5761 TCAAATTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAATAAATATTTAAATCTAAAAT
Found at i:12375 original size:24 final size:24
Alignment explanation
Indices: 12346--12418 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
12336 AACGATTCAT
*
12346 CTGGAAGAAAAAGTTATGTCAGCA
1 CTGGAAGAAAAAGTCATGTCAGCA
*
12370 CTGGAAGAAACAGTCATGTCAGCA
1 CTGGAAGAAAAAGTCATGTCAGCA
** *
12394 -TGGGAAGAAGCAGTCATGGCAGCA
1 CT-GGAAGAAAAAGTCATGTCAGCA
12418 C
1 C
12419 AATTACCCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.02
24 42 0.98
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (24 bp):
CTGGAAGAAAAAGTCATGTCAGCA
Found at i:13172 original size:184 final size:182
Alignment explanation
Indices: 12837--13205 Score: 607
Period size: 184 Copynumber: 2.0 Consensus size: 182
12827 TTCCCAGTAA
*
12837 TTTACAGAGAAAGTGTAAGTATAGAATCCGTTATATAATGTATGTTGTGACCATATGATCCTAGC
1 TTTACAGAGAAAGTGTAAGTATAGAATCCATTATATAATGTATGTTGTGACCATATGATCCTAGC
* *
12902 ATGAACATTGAAAAAATTTGGTAAGATAAATGAGCCAAACTGAATGGTCTGTCTATCAAATATTA
66 ATGAAAATTGAAAAAATTTGGTAAGATAAATGAGCCAAACTGAATGGTCTGTCTATCAAATATCA
*
12967 AGAATGTGTTAACAACAGTTCCTAATCTTTTTGCTTTCATCCCTTGTTTTCT
131 AGAATGTGTTAACAACAGTTCCTAATCTTTTTGCTTTCATCCCTTGCTTTCT
* * *
13019 TTTACAGAGAAAATGTTGTAATTATAGAATCCATTATATAATGTATGTTGTGACCCTGTGATCCT
1 TTTACAGAG-AAA-G-TGTAAGTATAGAATCCATTATATAATGTATGTTGTGACCATATGATCCT
*
13084 ATCATGAAAATTG-AAAAATTCTGG-AAGATAAATGAGCCAAACTGAATGGTCTGTCTATCAAAT
63 AGCATGAAAATTGAAAAAATT-TGGTAAGATAAATGAGCCAAACTGAATGGTCTGTCTATCAAAT
*
13147 ATCAAGAATGTGTTAACAGCAGTTCCTAATCTTTTTGCTTTCATCCCTTGCTTTCT
127 ATCAAGAATGTGTTAACAACAGTTCCTAATCTTTTTGCTTTCATCCCTTGCTTTCT
13203 TTT
1 TTT
13206 TCTTTCTTCT
Statistics
Matches: 174, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 9 0.05
183 3 0.02
184 103 0.59
185 59 0.34
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (182 bp):
TTTACAGAGAAAGTGTAAGTATAGAATCCATTATATAATGTATGTTGTGACCATATGATCCTAGC
ATGAAAATTGAAAAAATTTGGTAAGATAAATGAGCCAAACTGAATGGTCTGTCTATCAAATATCA
AGAATGTGTTAACAACAGTTCCTAATCTTTTTGCTTTCATCCCTTGCTTTCT
Found at i:15043 original size:14 final size:14
Alignment explanation
Indices: 15024--15071 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 14
15014 AAATTTTATG
15024 TAATTATTTAAAAA
1 TAATTATTTAAAAA
15038 TAATTATTTAAAAAAA
1 TAATTATTT--AAAAA
15054 TAATATAATTTAAAAA
1 TAAT-T-ATTTAAAAA
15070 TA
1 TA
15072 TAAAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.30
16 16 0.53
17 1 0.03
18 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTATTTAAAAA
Found at i:15066 original size:18 final size:16
Alignment explanation
Indices: 15024--15074 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 16
15014 AAATTTTATG
15024 TAATTATTT--AAAAA
1 TAATTATTTAAAAAAA
15038 TAATTATTTAAAAAAA
1 TAATTATTTAAAAAAA
*
15054 TAATATAATTTAAAAATA
1 TAAT-T-ATTTAAAAAAA
15072 TAA
1 TAA
15075 AATTTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 9 0.28
16 9 0.28
17 1 0.03
18 13 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATTATTTAAAAAAA
Found at i:15571 original size:21 final size:21
Alignment explanation
Indices: 15547--15604 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
15537 TAACAATAAC
15547 CAAATAATTCGAGGGTATCCA
1 CAAATAATTCGAGGGTATCCA
*
15568 CAAATGTAAATC--GGGTATCCA
1 CAAA--TAATTCGAGGGTATCCA
**
15589 CATCTAATTCGAGGGT
1 CAAATAATTCGAGGGT
15605 CCAAAGCATG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
19 5 0.17
21 19 0.66
23 5 0.17
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
CAAATAATTCGAGGGTATCCA
Found at i:22107 original size:7 final size:7
Alignment explanation
Indices: 22095--22136 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
22085 ATAAATTTAA
22095 AAATTTT
1 AAATTTT
22102 AAATTTT
1 AAATTTT
22109 AAATTTT
1 AAATTTT
22116 AAA-TTT
1 AAATTTT
*
22122 AAACTTT
1 AAATTTT
*
22129 AAACTTT
1 AAATTTT
22136 A
1 A
22137 TATTATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTT
Found at i:22124 original size:20 final size:20
Alignment explanation
Indices: 22099--22136 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22089 ATTTAAAAAT
* *
22099 TTTAAATTTTAAATTTTAAA
1 TTTAAACTTTAAACTTTAAA
22119 TTTAAACTTTAAACTTTA
1 TTTAAACTTTAAACTTTA
22137 TATTATTATT
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:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAACTTTAAACTTTAAA
Found at i:22891 original size:25 final size:25
Alignment explanation
Indices: 22851--22901 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
22841 AATATGGGTT
* *
22851 CATGATTTAGTTAGACACAAATTTA
1 CATGATTTAATGAGACACAAATTTA
*
22876 CATGATTTAATGAGACATAAATTTA
1 CATGATTTAATGAGACACAAATTTA
22901 C
1 C
22902 TTAGAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (25 bp):
CATGATTTAATGAGACACAAATTTA
Found at i:26833 original size:18 final size:19
Alignment explanation
Indices: 26812--26854 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
26802 TTAAAGAACG
26812 AAAATAATTT-ATTAATA-A
1 AAAAT-ATTTAATTAATATA
26830 AAAATATTTAAATTAATATA
1 AAAATATTT-AATTAATATA
26850 AAAAT
1 AAAAT
26855 TAAAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.18
18 5 0.23
19 7 0.32
20 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATATTTAATTAATATA
Found at i:30117 original size:45 final size:46
Alignment explanation
Indices: 30001--30119 Score: 141
Period size: 46 Copynumber: 2.6 Consensus size: 46
29991 TAAAATCTCA
* * * **
30001 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCTTGAAGAAC
1 TTTGAAAACATCATGCACTGAAGGTCTTATAGATGACCCGAAGAAC
* * * **
30047 TTTAAAAACATCTTGCACTGTAGGTCTTATAGATGACCCGAAG-GT
1 TTTGAAAACATCATGCACTGAAGGTCTTATAGATGACCCGAAGAAC
30092 TTTGAAAACATCATGCACTGAAGGTCTT
1 TTTGAAAACATCATGCACTGAAGGTCTT
30120 TGAAAACATC
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
45 25 0.41
46 36 0.59
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (46 bp):
TTTGAAAACATCATGCACTGAAGGTCTTATAGATGACCCGAAGAAC
Found at i:30123 original size:26 final size:25
Alignment explanation
Indices: 30086--30276 Score: 103
Period size: 25 Copynumber: 8.2 Consensus size: 25
30076 TAGATGACCC
30086 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
*
30111 GAAGGTCTTTGAAAACATCCTGCACT
1 GAAGGT-TTTGAAAACATCATGCACT
** * *
30137 GAAGGGCTT----ACA-GATG-ACCC
1 GAAGGTTTTGAAAACATCATGCA-CT
30157 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
** * *
30182 GAAGGGCTT----ACA-GATG-ACCC
1 GAAGGTTTTGAAAACATCATGCA-CT
30202 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
** * *
30227 GAAGGGCTT----ACA-GATG-ACCC
1 GAAGGTTTTGAAAACATCATGCA-CT
30247 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATGCACT
30272 GAAGG
1 GAAGG
30277 GCTTACAGAT
Statistics
Matches: 118, Mismatches: 26, Indels: 44
0.63 0.14 0.23
Matches are distributed among these distances:
19 3 0.03
20 32 0.27
21 9 0.08
24 9 0.08
25 39 0.33
26 26 0.22
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (25 bp):
GAAGGTTTTGAAAACATCATGCACT
Found at i:30135 original size:71 final size:71
Alignment explanation
Indices: 30046--30186 Score: 237
Period size: 71 Copynumber: 2.0 Consensus size: 71
30036 GCTTGAAGAA
* * * *
30046 CTTTAAAAACATCTTGCACTGTAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 CTTTAAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
30111 GAAGGT
66 GAAGGT
*
30117 CTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 CTTTAAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
30182 GAAGG
66 GAAGG
30187 GCTTACAGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (71 bp):
CTTTAAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
GAAGGT
Found at i:30180 original size:45 final size:45
Alignment explanation
Indices: 30111--30287 Score: 336
Period size: 45 Copynumber: 3.9 Consensus size: 45
30101 ATCATGCACT
*
30111 GAAGGTCTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCC
1 GAAGGT-TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
30157 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
1 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
30202 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
1 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
30247 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
30288 TGGGAAATAG
Statistics
Matches: 130, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
45 124 0.95
46 6 0.05
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (45 bp):
GAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
Found at i:30206 original size:116 final size:117
Alignment explanation
Indices: 30001--30231 Score: 338
Period size: 116 Copynumber: 2.0 Consensus size: 117
29991 TAAAATCTCA
* ** * ** *
30001 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCTTGAAGAACTTTAAAAACATCTTGCACT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGAACTTTAAAAACATCATGCACT
* * *
30066 GTAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTC
66 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTC
** *
30118 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAG-GTTTTGAAAACATCATGCACT
1 TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGAACTTTAAAAACATCATGCACT
30182 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGG
66 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGG
30232 GCTTACAGAT
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
116 64 0.63
117 37 0.37
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (117 bp):
TTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGAACTTTAAAAACATCATGCACT
GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTC
Found at i:30990 original size:22 final size:22
Alignment explanation
Indices: 30947--31003 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
30937 AATAAGGTTT
* * *
30947 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
30969 TCAGT-TTTGAAGAGAGAATCTA
1 TCA-TCTTTGAAGAGAGAATCTA
30991 TCATCTTTGAAGA
1 TCATCTTTGAAGA
31004 ATGTAGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:32394 original size:70 final size:72
Alignment explanation
Indices: 32291--32455 Score: 208
Period size: 75 Copynumber: 2.3 Consensus size: 72
32281 GATATAGGCC
* * * * *
32291 TTCAGCATGCCCCAGCATTTACTGATATGAACGTTCAAAAT-G-TTATTCTAATTTCTGATTGAA
1 TTCAGCATGCCCCAACATTTACTAATATAAACGTTCAAAATCGCATATTCCAATTTCTGATTGAA
32354 ATGGGCT
66 ATGGGCT
* *
32361 TTCAGCATGCCCCAATATTTGCTAATATAAACGTTCAAAATGCGCCAATATTCCAATTTCTGATT
1 TTCAGCATGCCCCAACATTTACTAATATAAACGTTCAAAAT-CG-C-ATATTCCAATTTCTGATT
*
32426 GAAATGGGTT
63 GAAATGGGCT
*
32436 TTCAGCATGCCTCAACATTT
1 TTCAGCATGCCCCAACATTT
32456 TCTTCTTGTT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
70 36 0.45
72 1 0.01
75 43 0.54
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (72 bp):
TTCAGCATGCCCCAACATTTACTAATATAAACGTTCAAAATCGCATATTCCAATTTCTGATTGAA
ATGGGCT
Found at i:40269 original size:28 final size:28
Alignment explanation
Indices: 40217--40274 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
40207 ACATTAATAA
40217 AATAATATATATAAAATATTATGAAAAT
1 AATAATATATATAAAATATTATGAAAAT
*
40245 AATAAGTATATATAAAA-ATTTTGAAAAT
1 AATAA-TATATATAAAATATTATGAAAAT
40273 AA
1 AA
40275 AGAATTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.34
Consensus pattern (28 bp):
AATAATATATATAAAATATTATGAAAAT
Found at i:40274 original size:25 final size:26
Alignment explanation
Indices: 40215--40271 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 26
40205 AAACATTAAT
40215 AAAATAATATATATAAAATATTATGAA
1 AAAATAATATATATAAAATATTATG-A
*
40242 AATAATAAGTATATATAAAA-ATTTTGA
1 AA-AATAA-TATATATAAAATATTATGA
40269 AAA
1 AAA
40272 TAAAGAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 1 0.04
27 5 0.19
28 10 0.37
29 11 0.41
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATATATAAAATATTATGA
Found at i:40283 original size:25 final size:29
Alignment explanation
Indices: 40223--40285 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
40213 ATAAAATAAT
*
40223 ATATATAAAATATTATGAAAATAATAAGT
1 ATATATAAAATATTATGAAAATAATAAGA
*
40252 ATATATAAAA-ATTTTGAAAAT-A-AAGA
1 ATATATAAAATATTATGAAAATAATAAGA
40278 AT-TATAAA
1 ATATATAAA
40286 TTAAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 6 0.19
26 5 0.16
27 1 0.03
28 10 0.31
29 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (29 bp):
ATATATAAAATATTATGAAAATAATAAGA
Found at i:40283 original size:29 final size:29
Alignment explanation
Indices: 40222--40298 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
40212 AATAAAATAA
*
40222 TATATATAAAATATTATGAAAATAATAAG
1 TATATATAAAATATTATGAAAATAAGAAG
* *
40251 TATATATAAAA-ATTTTGAAAATAAAGAAT
1 TATATATAAAATATTATGAAAAT-AAGAAG
* *
40280 TATAAATTAAATA-TATGAA
1 TATATATAAAATATTATGAA
40299 TTTTTAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 10 0.25
29 29 0.73
30 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (29 bp):
TATATATAAAATATTATGAAAATAAGAAG
Found at i:40737 original size:47 final size:48
Alignment explanation
Indices: 40677--40767 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
40667 AATTTGTCTT
* * *
40677 TATTATTAGAAATTTA-AATATTCA-AAAATGTATTTAATTTATAATCC
1 TATTATTACAAATTTATAATATTAAGAAAATCTA-TTAATTTATAATCC
* *
40724 TATTATTTCAAATTTATAATTTTAAGAAAATCTATTAATTTATA
1 TATTATTACAAATTTATAATATTAAGAAAATCTATTAATTTATA
40768 TATATAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
47 14 0.38
48 16 0.43
49 7 0.19
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (48 bp):
TATTATTACAAATTTATAATATTAAGAAAATCTATTAATTTATAATCC
Found at i:41068 original size:3 final size:3
Alignment explanation
Indices: 41062--41092 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
41052 ATAGATATTT
*
41062 ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41093 ATGTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:42488 original size:24 final size:26
Alignment explanation
Indices: 42440--42501 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
42430 CTGTAATATG
42440 TAATAATTATTTATTATTTAATAATAA
1 TAAT-ATTATTTATTATTTAATAATAA
*
42467 TAATATTA-TTATTATTATTAATAGTAA
1 TAATATTATTTATTA-T-TTAATAATAA
*
42494 TAAAATTA
1 TAATATTA
42502 ATAATAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 6 0.19
26 5 0.16
27 20 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TAATATTATTTATTATTTAATAATAA
Found at i:47403 original size:111 final size:111
Alignment explanation
Indices: 47256--47480 Score: 432
Period size: 111 Copynumber: 2.0 Consensus size: 111
47246 ATCATCTCTC
47256 TAAAGTTTATGCATAATTTTGATATTTTTATTGTAAGATTATTATTATTTTTTATATAATGAAAT
1 TAAAGTTTATGCATAATTTTGATATTTTTATTGTAAGATTATTATTATTTTTTATATAATGAAAT
*
47321 TTTGAATCATATTATTTATATTAATATTTAATTCTTTGATTAAGTT
66 TTTGAATCATATTATTTATATTAATATTTAATTCATTGATTAAGTT
*
47367 TAAAGTTTATGCATAATTTTGATATTTTTATTGTAAGATTCTTATTATTTTTTATATAATGAAAT
1 TAAAGTTTATGCATAATTTTGATATTTTTATTGTAAGATTATTATTATTTTTTATATAATGAAAT
47432 TTTGAATCATATTATTTATATTAATATTTAATTCATTGATTAAGTT
66 TTTGAATCATATTATTTATATTAATATTTAATTCATTGATTAAGTT
47478 TAA
1 TAA
47481 CATCAACGAT
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (111 bp):
TAAAGTTTATGCATAATTTTGATATTTTTATTGTAAGATTATTATTATTTTTTATATAATGAAAT
TTTGAATCATATTATTTATATTAATATTTAATTCATTGATTAAGTT
Found at i:47523 original size:111 final size:111
Alignment explanation
Indices: 47289--47524 Score: 264
Period size: 111 Copynumber: 2.1 Consensus size: 111
47279 ATTTTTATTG
*
47289 TAAGATTATTATTATTTTTTATATAATGAAATTTTGAATCATATTATTTATATTAATATTTAATT
1 TAAGATAATTATTATTTTTTATATAATGAAATTTTGAATCATATTATTTATATTAATATTTAATT
* ** * * * ** ***
47354 CTTTGATTAAGTTTAAAGTTTATGCATAATTTTGATATTTTTATTG
66 CATTGATTAAGTTTAAAGTCAACGCATAATTTAGACATAGTTACCC
**
47400 TAAGATTCTTATTATTTTTTATATAATGAAATTTTGAATCATATTATTTATATTAATATTTAATT
1 TAAGATAATTATTATTTTTTATATAATGAAATTTTGAATCATATTATTTATATTAATATTTAATT
* *
47465 CATTGATTAAGTTTAACA-TCAACG-ATTGA-TTAGACATCAGTTCCCC
66 CATTGATTAAGTTTAA-AGTCAACGCA-TAATTTAGACAT-AGTTACCC
47511 TAAAGA-AATTATTA
1 T-AAGATAATTATTA
47525 AATTATTCTT
Statistics
Matches: 105, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
110 7 0.07
111 93 0.89
112 5 0.05
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (111 bp):
TAAGATAATTATTATTTTTTATATAATGAAATTTTGAATCATATTATTTATATTAATATTTAATT
CATTGATTAAGTTTAAAGTCAACGCATAATTTAGACATAGTTACCC
Found at i:48190 original size:21 final size:21
Alignment explanation
Indices: 48166--48311 Score: 111
Period size: 21 Copynumber: 7.1 Consensus size: 21
48156 GCAAATTCGC
48166 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
48187 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
48207 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* *
48228 GTTGAAAATT-GCGTTGCGAT-
1 GTTG-CATTTCGCGTTGCGATA
* *
48248 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ***
48269 GTTGAAAACCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* * *
48289 TTTCCATTTCGCGTTGCAATA
1 GTTGCATTTCGCGTTGCGATA
48310 GT
1 GT
48312 CTACAGTTGT
Statistics
Matches: 90, Mismatches: 30, Indels: 10
0.69 0.23 0.08
Matches are distributed among these distances:
19 3 0.03
20 40 0.44
21 44 0.49
22 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:48215 original size:41 final size:41
Alignment explanation
Indices: 48170--48311 Score: 257
Period size: 41 Copynumber: 3.5 Consensus size: 41
48160 ATTCGCGTTG
48170 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
48211 CATTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
48252 CATTTCGCGTTGCGATAGTTGAAAACCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
48293 CATTTCGCGTTGCAATAGT
1 CATTTCGCGTTGCGATAGT
48312 CTACAGTTGT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:48220 original size:20 final size:20
Alignment explanation
Indices: 48195--48305 Score: 98
Period size: 20 Copynumber: 5.5 Consensus size: 20
48185 TAGTTGAAAA
48195 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*** *
48215 TCGCGTTGCGATAGTTGAAAAT
1 TCGCGTTGCGAT--TTTCCATT
48237 T-GCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
48256 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
48277 CCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
48297 TCGCGTTGC
1 TCGCGTTGC
48306 AATAGTCTAC
Statistics
Matches: 67, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
19 5 0.07
20 33 0.49
21 24 0.36
22 5 0.07
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:48311 original size:82 final size:83
Alignment explanation
Indices: 48170--48336 Score: 275
Period size: 82 Copynumber: 2.0 Consensus size: 83
48160 ATTCGCGTTG
* *
48170 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAA
1 CATTTCGCGTTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTCT-AA
48234 AATTG-CGTTGCGATTTTC
65 AATTGTCGTTGCGATTTTC
*
48252 CATTTCGCGTTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTCTAAA
*
48317 GTTGTCGTTGCGATTTTC
66 ATTGTCGTTGCGATTTTC
48335 CA
1 CA
48337 AATTCGTTGC
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
82 63 0.80
83 16 0.20
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (83 bp):
CATTTCGCGTTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTCTAAA
ATTGTCGTTGCGATTTTC
Found at i:48376 original size:19 final size:19
Alignment explanation
Indices: 48336--48376 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
48326 GCGATTTTCC
*
48336 AAATTCGTTGCGATAGCGA
1 AAATTCGTTGCGATAGCAA
* *
48355 AAATTCGTTGTGATAGTAA
1 AAATTCGTTGCGATAGCAA
48374 AAA
1 AAA
48377 AAAAAGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (19 bp):
AAATTCGTTGCGATAGCAA
Found at i:48460 original size:6 final size:6
Alignment explanation
Indices: 48449--48477 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
48439 GACACGTATT
48449 ACCACG ACCACG ACCACG ACCACG ACCAC
1 ACCACG ACCACG ACCACG ACCACG ACCAC
48478 TACCCGAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.52, G:0.14, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:48492 original size:5 final size:5
Alignment explanation
Indices: 48482--48522 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
48472 GACCACTACC
*
48482 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA AGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
48523 GCGGCGGCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.39, C:0.20, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:49139 original size:22 final size:22
Alignment explanation
Indices: 49114--49164 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
49104 AATTTGGAAA
49114 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
49136 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
49158 ATCGCAA
1 ATCGCAA
49165 TGCGAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:49204 original size:41 final size:41
Alignment explanation
Indices: 49155--49415 Score: 495
Period size: 41 Copynumber: 6.4 Consensus size: 41
49145 ACAACTGTAG
*
49155 ACTATCGCAATGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
49196 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
49237 ACTATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
49278 ACTATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
49319 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
49360 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
49401 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
49416 TTTTCAATTA
Statistics
Matches: 217, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 217 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:51075 original size:21 final size:23
Alignment explanation
Indices: 51035--51098 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 23
51025 CATGATAGTT
* **
51035 CATGATACTGATGTTACAG-TC-
1 CATGATAATGATGTGGCAGTTCA
*
51056 CATGATATTGATGTGGCAGTTCA
1 CATGATAATGATGTGGCAGTTCA
51079 CGATGACTAATGATGTGGCA
1 C-ATGA-TAATGATGTGGCA
51099 AATGCCATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 16 0.46
22 2 0.06
23 1 0.03
24 4 0.11
25 12 0.34
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (23 bp):
CATGATAATGATGTGGCAGTTCA
Found at i:51223 original size:24 final size:24
Alignment explanation
Indices: 51203--51248 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
51193 AAGTTATTTT
51203 AAATTGTAAATATAAAATTATTCA
1 AAATTGTAAATATAAAATTATTCA
* *
51227 AAATTTTAAATATAAAAATATT
1 AAATTGTAAATATAAAATTATT
51249 AAGAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATTGTAAATATAAAATTATTCA
Found at i:51632 original size:25 final size:25
Alignment explanation
Indices: 51599--51664 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
51589 AGAAAACATA
* *
51599 GTAACTTTCAATTAATTCAAAATTT
1 GTAAGTTTCGATTAATTCAAAATTT
* * *
51624 GTAAGTTTCGCTTAATTTAAATTTT
1 GTAAGTTTCGATTAATTCAAAATTT
51649 GTAAGTTTCGATTAAT
1 GTAAGTTTCGATTAAT
51665 CCAATAAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (25 bp):
GTAAGTTTCGATTAATTCAAAATTT
Found at i:52824 original size:85 final size:85
Alignment explanation
Indices: 52722--52891 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
52712 TAATTAATTA
*
52722 AAAATGTTAAAGTTTTAATGTAGTTCACATGATATCTTACATGACAATTTATTTGTTCATGTAAT
1 AAAATGTTAAAGTTTTAATGTAATTCACATGATATCTTACATGACAATTTATTTGTTCATGTAAT
52787 TTTATTTTATTTTTATATTT
66 TTTATTTTATTTTTATATTT
52807 AAAATGTTAAAGTTTTAATGTAATTCACATGATATCTTACATGACAATTTATTTGTTCATGTAAT
1 AAAATGTTAAAGTTTTAATGTAATTCACATGATATCTTACATGACAATTTATTTGTTCATGTAAT
52872 TTTATTTTATTTTTATATTT
66 TTTATTTTATTTTTATATTT
52892 TTATAATTTT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (85 bp):
AAAATGTTAAAGTTTTAATGTAATTCACATGATATCTTACATGACAATTTATTTGTTCATGTAAT
TTTATTTTATTTTTATATTT
Found at i:56668 original size:32 final size:33
Alignment explanation
Indices: 56627--56693 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 33
56617 GAATAAGAGT
* * *
56627 TGGTGTAGCTGAAGTTGGTGTGTTGCGTG-AGC
1 TGGTGTAGCTGAAGGTGGTATGTTGCATGTAGC
56659 TGGTGTAGCTGAAGGTGGTATGTTGCATGTAGC
1 TGGTGTAGCTGAAGGTGGTATGTTGCATGTAGC
56692 TG
1 TG
56694 AAGGTGGTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.15, C:0.09, G:0.42, T:0.34
Consensus pattern (33 bp):
TGGTGTAGCTGAAGGTGGTATGTTGCATGTAGC
Found at i:59776 original size:2 final size:2
Alignment explanation
Indices: 59769--59814 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
59759 CTAAAATTTA
59769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59811 -T AT A
1 AT AT A
59815 AACTGATGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.