Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006965.1 Hibiscus syriacus cultivar Beakdansim tig00017926_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: 75815
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3673 original size:19 final size:19
Alignment explanation
Indices: 3651--3687 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3641 TTTTTTTATG
*
3651 ATTAGGAAATTACATATTA
1 ATTAGGAAATTAAATATTA
*
3670 ATTAGTAAATTAAATATT
1 ATTAGGAAATTAAATATT
3688 CAAAGAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (19 bp):
ATTAGGAAATTAAATATTA
Found at i:7051 original size:2 final size:2
Alignment explanation
Indices: 7044--7087 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
7034 TTATTATCAT
* *
7044 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7085 TA T
1 TA T
7088 TTGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14502 original size:97 final size:94
Alignment explanation
Indices: 14346--14522 Score: 228
Period size: 97 Copynumber: 1.9 Consensus size: 94
14336 ATCTGATCAG
* * * * * * *
14346 AAAATATATAATATCCCTCGACTCAAAATATATATTTTCCATCTAACTCTGACTTCGACCTAAAT
1 AAAATATATAATATCCCCCGACTCAAAACATATATTTCCCACCTAACTCTGAATCCGACCCAAAT
14411 ATTTAGAGTATAAATCCAACCCGGTCTTA
66 ATTTAGAGTATAAATCCAACCCGGTCTTA
* *
14440 AAAATATATAATATCCACCCGACTCAAAACATATATTCTCCCCACCTAGCTCTGAATCCGACCCG
1 AAAATATATAATATCC-CCCGACTCAAAACATATATT-T-CCCACCTAACTCTGAATCCGACCCA
* *
14505 AATTTTTAGGGTATAAAT
63 AATATTTAGAGTATAAAT
14523 TCGACCCAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
94 16 0.23
95 18 0.26
96 1 0.01
97 34 0.49
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (94 bp):
AAAATATATAATATCCCCCGACTCAAAACATATATTTCCCACCTAACTCTGAATCCGACCCAAAT
ATTTAGAGTATAAATCCAACCCGGTCTTA
Found at i:15394 original size:14 final size:14
Alignment explanation
Indices: 15375--15402 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15365 AAGTGAAAAA
15375 ATAGTTATATAATT
1 ATAGTTATATAATT
15389 ATAGTTATATAATT
1 ATAGTTATATAATT
15403 TTGTTATGAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:19797 original size:20 final size:20
Alignment explanation
Indices: 19774--19823 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
19764 ACAGGTTCCA
**
19774 AAATCGCAACTCGAATAGGT
1 AAATCGCAACGAGAATAGGT
* *
19794 AAATCGCAACGATAATATGT
1 AAATCGCAACGAGAATAGGT
19814 AAATCGCAAC
1 AAATCGCAAC
19824 ACAGAAGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATAGGT
Found at i:20006 original size:22 final size:23
Alignment explanation
Indices: 19974--20036 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 23
19964 AGTGTTGCGA
* *
19974 AATTCGAGTTGCGAATTTGGA-G
1 AATTCGCGTTGCGAATTTGGATC
19996 AATTCGCGTTGCG-ATTT--ATC
1 AATTCGCGTTGCGAATTTGGATC
*
20016 TATTCGCGTTGCGAATTTGGA
1 AATTCGCGTTGCGAATTTGGA
20037 AAATCGCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 1 0.03
20 12 0.35
21 8 0.24
22 12 0.35
23 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (23 bp):
AATTCGCGTTGCGAATTTGGATC
Found at i:20319 original size:20 final size:20
Alignment explanation
Indices: 20291--20341 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
20281 TGGAAAATTA
* **
20291 CAACACGAATTTTGTTTTCG
1 CAACGCGAATTTCATTTTCG
20311 CAACGCGAATTTCATTTTCG
1 CAACGCGAATTTCATTTTCG
*
20331 CAACGCTAATT
1 CAACGCGAATT
20342 ACCTATATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (20 bp):
CAACGCGAATTTCATTTTCG
Found at i:20510 original size:20 final size:20
Alignment explanation
Indices: 20464--20512 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
20454 TGGAGAATTT
20464 GCGTTGCGATTTACATATTA
1 GCGTTGCGATTTACATATTA
* * * *
20484 TCATTGCGATTTACCTATTC
1 GCGTTGCGATTTACATATTA
20504 GCGTTGCGA
1 GCGTTGCGA
20513 ATTTGGAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
GCGTTGCGATTTACATATTA
Found at i:20570 original size:146 final size:146
Alignment explanation
Indices: 20387--20815 Score: 556
Period size: 154 Copynumber: 2.9 Consensus size: 146
20377 TCGCGTTGCA
* * *
20387 AATTTCGTTTTCGCAACGCTAGTTACCTATATCGGTAATTGGCGTTGTGAAATTCGAGTTGCGAA
1 AATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTGCGAA
*
20452 TTTGGAGAATTTGCGTTGCGATTTACATATTATCATTGCGATTTACCTATTCGCGTTGCGAATTT
66 TTTGGAGAATTTGCGTTGCGATTTACATATTATCGTTGCGATTTACCTATTCGCGTTGCGAATTT
20517 GGAAAATCACAACGCG
131 GGAAAATCACAACGCG
** * * *
20533 AATTTCGTTTTCGCAACGCTAATTACCGCTATAGGTAATTAGCGTTGCGAATTTCAAGTTGCGAA
1 AATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTGCGAA
* * * * * * *
20598 TTTCAAGTTGCGAAATTCGAGTTGCGAATTTGGAGA-ATTCGT-GTTGCGATTTACATATTCGCA
66 TTT---G--GAG-AATTTGCGTTGCG-ATTT--ACATATT-ATCGTTGCGATTTACCTATTCGCG
* *
20661 TTGCGAATTTGGAAAATCGCAATGCG
121 TTGCGAATTTGGAAAATCACAACGCG
*
20687 AATTTCGTTTTCGCAATGCTAATTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTGCGAA
1 AATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTGCGAA
* * *
20752 TTTGGAGAATTTGCGTTGTGATTTACATATTATCGTTGAGATTTACCTATTTGCGTTGCGAATT
66 TTTGGAGAATTTGCGTTGCGATTTACATATTATCGTTGCGATTTACCTATTCGCGTTGCGAATT
20816 ACATATTATC
Statistics
Matches: 237, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
145 3 0.01
146 89 0.38
147 4 0.02
148 10 0.04
149 3 0.01
151 3 0.01
152 11 0.05
153 4 0.02
154 107 0.45
155 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (146 bp):
AATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTGCGAA
TTTGGAGAATTTGCGTTGCGATTTACATATTATCGTTGCGATTTACCTATTCGCGTTGCGAATTT
GGAAAATCACAACGCG
Found at i:20595 original size:14 final size:14
Alignment explanation
Indices: 20576--20628 Score: 88
Period size: 14 Copynumber: 3.8 Consensus size: 14
20566 GGTAATTAGC
20576 GTTGCGAATTTCAA
1 GTTGCGAATTTCAA
20590 GTTGCGAATTTCAA
1 GTTGCGAATTTCAA
* *
20604 GTTGCGAAATTCGA
1 GTTGCGAATTTCAA
20618 GTTGCGAATTT
1 GTTGCGAATTT
20629 GGAGAATTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (14 bp):
GTTGCGAATTTCAA
Found at i:20794 original size:20 final size:20
Alignment explanation
Indices: 20765--20825 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
20755 GGAGAATTTG
*
20765 CGTTGTGATTTACATATTAT
1 CGTTGAGATTTACATATTAT
*
20785 CGTTGAGATTTACCTATT-T
1 CGTTGAGATTTACATATTAT
* *
20804 GCGTTGCGAATTACATATTAT
1 -CGTTGAGATTTACATATTAT
20825 C
1 C
20826 ATTGCAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (20 bp):
CGTTGAGATTTACATATTAT
Found at i:20818 original size:40 final size:40
Alignment explanation
Indices: 20760--20855 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
20750 AATTTGGAGA
* * * *
20760 ATTTGCGTTGTGATTTACATATTATCGTTG-AGATTTACCT
1 ATTTGCGTTGCGAATTACATATTATCATTGCA-ATTTAACT
20800 ATTTGCGTTGCGAATTACATATTATCATTGCAATTTAACT
1 ATTTGCGTTGCGAATTACATATTATCATTGCAATTTAACT
*
20840 ATTCGCGTTGCGAATT
1 ATTTGCGTTGCGAATT
20856 TGACTTTGGC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 49 0.98
41 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.44
Consensus pattern (40 bp):
ATTTGCGTTGCGAATTACATATTATCATTGCAATTTAACT
Found at i:20830 original size:20 final size:20
Alignment explanation
Indices: 20774--20834 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
20764 GCGTTGTGAT
* *
20774 TTACATATTATCGTTGAGAT
1 TTACATATTATCGTTGCGAA
*
20794 TTACCTATT-TGCGTTGCGAA
1 TTACATATTAT-CGTTGCGAA
*
20814 TTACATATTATCATTGC-AA
1 TTACATATTATCGTTGCGAA
20833 TT
1 TT
20835 TAACTATTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 5 0.15
20 28 0.82
21 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
TTACATATTATCGTTGCGAA
Found at i:20850 original size:20 final size:19
Alignment explanation
Indices: 20827--20895 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
20817 CATATTATCA
20827 TTGCAATTTAACTATTCGCG
1 TTGCAATTTAACT-TTCGCG
* *
20847 TTGCGAATTTGACTTTGGCG
1 TTGC-AATTTAACTTTCGCG
* *
20867 TTGCAATTTTGACTTTTGCG
1 TTGCAA-TTTAACTTTCGCG
*
20887 TTGCGATTT
1 TTGCAATTT
20896 TGGAACCTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
19 5 0.12
20 30 0.70
21 8 0.19
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (19 bp):
TTGCAATTTAACTTTCGCG
Found at i:20896 original size:20 final size:20
Alignment explanation
Indices: 20844--20897 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
20834 TTAACTATTC
*
20844 GCGTTGCGAATTTGACTTTG
1 GCGTTGCGATTTTGACTTTG
* *
20864 GCGTTGCAATTTTGACTTTT
1 GCGTTGCGATTTTGACTTTG
20884 GCGTTGCGATTTTG
1 GCGTTGCGATTTTG
20898 GAACCTGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.44
Consensus pattern (20 bp):
GCGTTGCGATTTTGACTTTG
Found at i:22103 original size:40 final size:40
Alignment explanation
Indices: 22048--22128 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
22038 TCCGTGATGC
22048 TTTACGAGCGTCGTTGAGCACTATTAATTTTATAAAAACT
1 TTTACGAGCGTCGTTGAGCACTATTAATTTTATAAAAACT
22088 TTTACGAGCGTCGTTGAGCACTATTAATTTTATAAAAACT
1 TTTACGAGCGTCGTTGAGCACTATTAATTTTATAAAAACT
22128 T
1 T
22129 AAATCTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (40 bp):
TTTACGAGCGTCGTTGAGCACTATTAATTTTATAAAAACT
Found at i:24055 original size:23 final size:23
Alignment explanation
Indices: 24029--24095 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
24019 CCACAGCTCA
24029 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* *
24052 TATAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
*
24075 TAGAATTGCACC-ATAGTGCCA
1 TATAATTGCACCGA-AGTGCCA
24096 TATAATAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.22
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:24282 original size:103 final size:103
Alignment explanation
Indices: 24111--24326 Score: 396
Period size: 103 Copynumber: 2.1 Consensus size: 103
24101 TAATGTCCAT
* * *
24111 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACACATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
24176 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
24214 AAGGACCACACATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACACATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
24279 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
24317 AAGGACCACA
1 AAGGACCACA
24327 TAGACCCTCG
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACACATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:25197 original size:64 final size:64
Alignment explanation
Indices: 25064--25220 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
25054 TAATGAAGGT
* * * ** *
25064 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATATTGTATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATATTGTATTATTAAAGAG
* *
25128 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATT-TATT-TTAAA-A
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGA--TATTGTATTATTAAAGA
25190 G
64 G
* * *
25191 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
25221 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
63 2 0.03
64 69 0.87
65 4 0.05
66 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATATTGTATTATTAAAGAG
Found at i:26183 original size:15 final size:15
Alignment explanation
Indices: 26160--26201 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
26150 AATTATTTTT
*
26160 AAATCTTAAATATAA
1 AAATATTAAATATAA
*
26175 AAATATTAAAAAT-A
1 AAATATTAAATATAA
26189 AAA-ATTAAATATA
1 AAATATTAAATATA
26202 TATATTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 8 0.35
14 4 0.17
15 11 0.48
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTAAATATAA
Found at i:26214 original size:36 final size:35
Alignment explanation
Indices: 26172--26262 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 35
26162 ATCTTAAATA
26172 TAAAAATATTAAAAATAAAAATTAAATATATATAT
1 TAAAAATATTAAAAATAAAAATTAAATATATATAT
** *
26207 TATAAAATTACTT--TTAGAAAAATTAAATATATATAT
1 TA-AAAA-TA-TTAAAAATAAAAATTAAATATATATAT
*
26243 TAAAAAT-TCTAAAATTAAAA
1 TAAAAATAT-TAAAAATAAAA
26263 TGGTAACTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
32 1 0.02
33 1 0.02
34 1 0.02
35 10 0.23
36 26 0.60
37 2 0.05
38 2 0.05
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (35 bp):
TAAAAATATTAAAAATAAAAATTAAATATATATAT
Found at i:31586 original size:50 final size:52
Alignment explanation
Indices: 31434--31555 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 52
31424 AGTAAAGCGT
* * * ** **
31434 GCCCCCTGCACTGCGCTATACGATGATTTGGCGTCACGTGGGGTATAGCGC-
1 GCCCCATGCACCGCGCTATACGGTGAGCTGGCACCACGTGGGGTATAGCGCG
*
31485 GCCCCATGCACCTCGCTATACGGTGAGCTGGCACCACGT-GGGTATAGCGCG
1 GCCCCATGCACCGCGCTATACGGTGAGCTGGCACCACGTGGGGTATAGCGCG
*
31536 GCCCC-TGCAGCGCGCTATAC
1 GCCCCATGCACCGCGCTATAC
31556 CTGTATATCT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
50 24 0.40
51 36 0.60
ACGTcount: A:0.16, C:0.34, G:0.30, T:0.20
Consensus pattern (52 bp):
GCCCCATGCACCGCGCTATACGGTGAGCTGGCACCACGTGGGGTATAGCGCG
Found at i:31744 original size:13 final size:14
Alignment explanation
Indices: 31716--31744 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31706 ATATTTTATA
31716 ATATTTTTACTATT
1 ATATTTTTACTATT
31730 ATATTTTTACT-TT
1 ATATTTTTACTATT
31743 AT
1 AT
31745 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:36797 original size:49 final size:51
Alignment explanation
Indices: 36690--36812 Score: 205
Period size: 49 Copynumber: 2.5 Consensus size: 51
36680 TTATACAAAA
*
36690 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTGAGGAGTAAATGTATAT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTGAGGAGTAAATGTATAG
36741 CGCGGTACCTGCCCCGCGCTATATAAAATTAT-T-AGGAGTAAATGTATAG
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTGAGGAGTAAATGTATAG
**
36790 CGCGGTACCTGATCCGCGCTATA
1 CGCGGTACCTGCCCCGCGCTATA
36813 CCCTTACGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
49 36 0.52
50 1 0.01
51 32 0.46
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (51 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTGAGGAGTAAATGTATAG
Found at i:46110 original size:60 final size:60
Alignment explanation
Indices: 45973--46110 Score: 136
Period size: 60 Copynumber: 2.3 Consensus size: 60
45963 AAACATATGA
* * * * * * *
45973 ATAGTCGAGTGACCATTTTGTAACTTTTAATAGTCGGATGACTCAATAAAGTAACGCCCT
1 ATAGTAGAGGGACCATTTTATAACTTTTAATAATCAGATGACTCAACAAAGTAACACCCT
* * * * *
46033 ATAGTTGAGGGATCATTTTATAACTTTTAATAATCAAGA-GACTTAACAAAGTAACATCTT
1 ATAGTAGAGGGACCATTTTATAACTTTTAATAATC-AGATGACTCAACAAAGTAACACCCT
46093 ATAGTCAG-GGGACCATTT
1 ATAGT-AGAGGGACCATTT
46111 GTGTACTTTA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
60 60 0.95
61 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (60 bp):
ATAGTAGAGGGACCATTTTATAACTTTTAATAATCAGATGACTCAACAAAGTAACACCCT
Found at i:46476 original size:26 final size:27
Alignment explanation
Indices: 46447--46502 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
46437 AGTACTTGAT
46447 TACACAGAGAACTTACAT-AAAAAATC
1 TACACAGAGAACTTACATGAAAAAATC
*
46473 TACACAGAGAACTTACATGAAAAGATC
1 TACACAGAGAACTTACATGAAAAAATC
46500 TAC
1 TAC
46503 TCAAATTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.50, C:0.20, G:0.11, T:0.20
Consensus pattern (27 bp):
TACACAGAGAACTTACATGAAAAAATC
Found at i:46859 original size:55 final size:55
Alignment explanation
Indices: 46774--46883 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
46764 AATTGAATTC
46774 AAGTCTTGTTCAAGTTTAGATGTACGAGACTACTTAGTCTTCACATTGTTAAGAT
1 AAGTCTTGTTCAAGTTTAGATGTACGAGACTACTTAGTCTTCACATTGTTAAGAT
* *
46829 AAGTCTTGTTCAAGTTTAGATGTACTAGACTACTTAGTCTTCATATTGTTAAGAT
1 AAGTCTTGTTCAAGTTTAGATGTACGAGACTACTTAGTCTTCACATTGTTAAGAT
46884 CATCACAAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (55 bp):
AAGTCTTGTTCAAGTTTAGATGTACGAGACTACTTAGTCTTCACATTGTTAAGAT
Found at i:65571 original size:91 final size:90
Alignment explanation
Indices: 65476--65747 Score: 449
Period size: 90 Copynumber: 3.0 Consensus size: 90
65466 AATTTTAGTG
*
65476 ATCCAAATTTTTGATTATCTAAAATTTTAGATCAGATAATGTACGATATCCAATAATACACACCT
1 ATCCAAATTTTTGAATATCTAAAATTTTAGATC-GATAATGTACGATATCCAATAATACACACCT
65541 CTATTGTTATCTATCAAATATTTTTT
65 CTATTGTTATCTATCAAATATTTTTT
65567 ATCCAAATTTTTGAATATCTAAAATTTTAGATCGGATAATGTACG-TATCCAATAATACACACCT
1 ATCCAAATTTTTGAATATCTAAAATTTTAGATC-GATAATGTACGATATCCAATAATACACACCT
*
65631 CTATTGTTATCTATCAAATA-ATTTT
65 CTATTGTTATCTATCAAATATTTTTT
* * *
65656 ATCCAAATTTTTGAATATCTAAAATTTTAGATCGAATAATTTACAATATCCAATAATACACACCC
1 ATCCAAATTTTTGAATATCTAAAATTTTAGATCG-ATAATGTACGATATCCAATAATACACACCT
65721 CTATTGTTATCTATCAAATAATTTTTT
65 CTATTGTTATCTATCAAAT-ATTTTTT
65748 CCCAACAGCA
Statistics
Matches: 170, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
88 1 0.01
89 45 0.26
90 76 0.45
91 44 0.26
92 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (90 bp):
ATCCAAATTTTTGAATATCTAAAATTTTAGATCGATAATGTACGATATCCAATAATACACACCTC
TATTGTTATCTATCAAATATTTTTT
Found at i:66858 original size:58 final size:60
Alignment explanation
Indices: 66748--66862 Score: 162
Period size: 58 Copynumber: 1.9 Consensus size: 60
66738 AAATAGTTGG
* * **
66748 ATGACCATTTTATAATTTTTAATAGTCTAAGGACTCAACAAAATAATATCTTATAATTAA
1 ATGACCATTTTATAACTTTTAATAATCTAACAACTCAACAAAATAATATCTTATAATTAA
* *
66808 ATGACTATTTTATAACTTTTAA-AAT-TAACAACTCAATAAAATAATATCTTATAAT
1 ATGACCATTTTATAACTTTTAATAATCTAACAACTCAACAAAATAATATCTTATAAT
66863 AATGAATCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 27 0.55
59 2 0.04
60 20 0.41
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.39
Consensus pattern (60 bp):
ATGACCATTTTATAACTTTTAATAATCTAACAACTCAACAAAATAATATCTTATAATTAA
Found at i:71711 original size:10 final size:10
Alignment explanation
Indices: 71696--71720 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
71686 CATCCTCTGC
71696 AAGAAAAAAA
1 AAGAAAAAAA
71706 AAGAAAAAAA
1 AAGAAAAAAA
71716 AAGAA
1 AAGAA
71721 CCCGTGAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:73096 original size:148 final size:145
Alignment explanation
Indices: 72796--73069 Score: 319
Period size: 148 Copynumber: 1.9 Consensus size: 145
72786 AATAATTTCA
* *
72796 TAATATTTATTTAATATTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTG
1 TAATATTTATTTAATATTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCCTTTTCTA
* * * *
72861 ATATTCTTAAATAAATAAATATCCTATTTTTATAAATTATATATATTAATTTATTTTAATTATAT
66 ATATTCTTAAATAAATAAATA--CTATTTTAATAAATTATATATATTAAATTATATTAATTAAAT
* * *
72926 TTAGAGAAATGTTTTAT
129 TTAAAGAAAAGTTTAAT
* * *
72943 TAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCTTTTTCT
1 TAATATTTATTTA-ATATTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCCTTTTCT
* *
73008 AATATT-TCTAAGTAAATAAATA-TATTATTAATATATT-T-T-T-TTAAAATTATATTAA-TAA
65 AATATTCT-TAAATAAATAAATACTATT-TTAATAAATTATATATATT-AAATTATATTAATTAA
73066 ATTT
127 ATTT
73070 GAAATAACAA
Statistics
Matches: 112, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
142 8 0.07
143 11 0.10
144 1 0.01
145 5 0.04
146 8 0.07
147 14 0.12
148 65 0.58
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (145 bp):
TAATATTTATTTAATATTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCCTTTTCTA
ATATTCTTAAATAAATAAATACTATTTTAATAAATTATATATATTAAATTATATTAATTAAATTT
AAAGAAAAGTTTAAT
Done.