Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005732.1 Hibiscus syriacus cultivar Beakdansim tig00013399_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: 96799
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Found at i:4515 original size:10 final size:10
Alignment explanation
Indices: 4500--4585 Score: 64
Period size: 10 Copynumber: 7.4 Consensus size: 10
4490 ATAAATGAAT
4500 GAACATAAAC
1 GAACATAAAC
4510 GAACATAACCGAAC
1 GAACAT-A---AAC
4524 GAACATAAACGAAC
1 GAACAT-AA--A-C
4538 GAACATAAAC
1 GAACATAAAC
4548 GAACATAACCGAAC
1 GAACAT-A---AAC
4562 GAACATAAAC
1 GAACATAAAC
4572 GAACATAAAC
1 GAACATAAAC
4582 GAAC
1 GAAC
4586 GTTCACGAAC
Statistics
Matches: 65, Mismatches: 0, Indels: 22
0.75 0.00 0.25
Matches are distributed among these distances:
10 30 0.46
11 4 0.06
13 4 0.06
14 27 0.42
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:4527 original size:24 final size:24
Alignment explanation
Indices: 4521--4586 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
4511 AACATAACCG
4521 AACGAACATAAACGAACGAACATA
1 AACGAACATAAACGAACGAACATA
*
4545 AACGAACATAACCGAACGAACATA
1 AACGAACATAAACGAACGAACATA
4569 AACGAACATAAACGAACG
1 AACGAACATAAACGAACG
4587 TTCACGAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.56, C:0.23, G:0.14, T:0.08
Consensus pattern (24 bp):
AACGAACATAAACGAACGAACATA
Found at i:4542 original size:38 final size:38
Alignment explanation
Indices: 4487--4575 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
4477 GATTGAGTTA
* *
4487 AACATAAATGAATGAACATAAACGAACATAACCGAACG
1 AACATAAACGAACGAACATAAACGAACATAACCGAACG
4525 AACATAAACGAACGAACATAAACGAACATAACCGAACG
1 AACATAAACGAACGAACATAAACGAACATAACCGAACG
4563 AACATAAACGAAC
1 AACATAAACGAAC
4576 ATAAACGAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.10
Consensus pattern (38 bp):
AACATAAACGAACGAACATAAACGAACATAACCGAACG
Found at i:4586 original size:14 final size:14
Alignment explanation
Indices: 4507--4575 Score: 92
Period size: 14 Copynumber: 5.2 Consensus size: 14
4497 AATGAACATA
*
4507 AACGAACATAACCG
1 AACGAACATAAACG
4521 AACGAACATAAACG
1 AACGAACATAAACG
4535 AACGAACAT--A--
1 AACGAACATAAACG
*
4545 AACGAACATAACCG
1 AACGAACATAAACG
4559 AACGAACATAAACG
1 AACGAACATAAACG
4573 AAC
1 AAC
4576 ATAAACGAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.19
12 1 0.02
14 38 0.79
ACGTcount: A:0.55, C:0.25, G:0.13, T:0.07
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:13771 original size:20 final size:20
Alignment explanation
Indices: 13746--13794 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
13736 TTTAAAACAT
13746 TATTTAAATATGTGTAACGC
1 TATTTAAATATGTGTAACGC
*
13766 TATTT-AA-ATGTGTAATGC
1 TATTTAAATATGTGTAACGC
13784 TATTTAAATAT
1 TATTTAAATAT
13795 TAAACTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 15 0.58
19 4 0.15
20 7 0.27
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (20 bp):
TATTTAAATATGTGTAACGC
Found at i:31125 original size:21 final size:21
Alignment explanation
Indices: 31082--31126 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31072 TATCGCATTA
**
31082 CGATTTCCCAAATTCGCGTTG
1 CGATTTCCCAAATTCGCAATG
* *
31103 CGATTTTCCTAATTCGCAATG
1 CGATTTCCCAAATTCGCAATG
31124 CGA
1 CGA
31127 ATACGTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (21 bp):
CGATTTCCCAAATTCGCAATG
Found at i:31148 original size:20 final size:20
Alignment explanation
Indices: 31116--31209 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
31106 TTTTCCTAAT
31116 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
31136 TCACAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
31157 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
31177 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
31197 TCGCAATGCGAAT
1 TCGCAATGCGAAT
31210 CTGACTATCG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:31161 original size:41 final size:40
Alignment explanation
Indices: 31116--31209 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
31106 TTTTCCTAAT
**
31116 TCGCAATGCGAATACGTAAATCACAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCACAACGCGAA-TACGAAAA
* * * *
31157 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCACAACGCGAATACGAAAA
31197 TCGCAATGCGAAT
1 TCGCAATGCGAAT
31210 CTGACTATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 17 0.37
41 29 0.63
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCACAACGCGAATACGAAAA
Found at i:31197 original size:61 final size:60
Alignment explanation
Indices: 31116--31229 Score: 174
Period size: 61 Copynumber: 1.9 Consensus size: 60
31106 TTTTCCTAAT
*
31116 TCGCAATGCGAATACGTAAATCACAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCACAACGCGAATCT-GAAAATCGCAATGCGATTACGTAAA
* * **
31177 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACTATCGCAATGCGATT
1 TCGCAATGCGAATACGTAAATCACAACGCGAATCTGAAAATCGCAATGCGATT
31230 TACATAGCGT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 16 0.33
61 32 0.67
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCACAACGCGAATCTGAAAATCGCAATGCGATTACGTAAA
Found at i:31861 original size:20 final size:20
Alignment explanation
Indices: 31836--31885 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
31826 TGCGATTCCT
31836 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
31856 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
31876 GTGTTGCGAT
1 GCGTTGCGAT
31886 TTTTATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:31893 original size:20 final size:20
Alignment explanation
Indices: 31870--31907 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
31860 TGCGATAGTC
31870 ATTTTCGTGTTGCGATTTTT
1 ATTTTCGTGTTGCGATTTTT
31890 ATTTTCGTGTTGCGATTT
1 ATTTTCGTGTTGCGATTT
31908 AAAGTTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.58
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTT
Found at i:31915 original size:20 final size:20
Alignment explanation
Indices: 31872--31915 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
31862 CGATAGTCAT
** *
31872 TTTCGTGTTGCGATTTTTAT
1 TTTCGTGTTGCGATTTAAAG
31892 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
31912 TTTC
1 TTTC
31916 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:33805 original size:20 final size:20
Alignment explanation
Indices: 33780--33923 Score: 174
Period size: 20 Copynumber: 7.5 Consensus size: 20
33770 AGAATAGTTT
33780 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
** *
33800 ACTATCGCAACACAAAAATG
1 ACTATCGCAATGCGAAAATG
*
33820 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
33836 A--ATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
33854 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
33874 ACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
**
33894 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
33914 ACTATCGCAA
1 ACTATCGCAA
33924 CGAAAAAATC
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.07
16 3 0.03
17 4 0.04
18 3 0.03
20 89 0.84
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:33892 original size:40 final size:40
Alignment explanation
Indices: 33780--33923 Score: 192
Period size: 40 Copynumber: 3.8 Consensus size: 40
33770 AGAATAGTTT
*
33780 ACTATCGCAATGCGAAAATGACTATCGCAACACAAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATACAAAAATG
* *
33820 ACTATCGCAA--CG-AGA-GA--ATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATACAAAAATG
*
33854 ACTATCGCAATGCGAAAATGACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATACAAAAATG
**
33894 ACTATCGCAATGCGAATTTGACTATCGCAA
1 ACTATCGCAATGCGAAAATGACTATCGCAA
33924 CGAAAAAATC
Statistics
Matches: 90, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
34 25 0.28
36 4 0.04
37 4 0.04
38 4 0.04
40 53 0.59
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATACAAAAATG
Found at i:34571 original size:21 final size:21
Alignment explanation
Indices: 34474--34576 Score: 84
Period size: 21 Copynumber: 4.9 Consensus size: 21
34464 AAGCCCGACT
34474 CCCCTGTCATCGTTCAAGAGG
1 CCCCTGTCATCGTTCAAGAGG
**
34495 CCTCCCCT-ATCGTTCAAGAGG
1 CC-CCTGTCATCGTTCAAGAGG
* ** *
34516 CCCCTATCATCCCTCAAGAGT
1 CCCCTGTCATCGTTCAAGAGG
* *
34537 CCCCT-CCTACCGTTCAAGAGG
1 CCCCTGTC-ATCGTTCAAGAGG
* *
34558 CCACTGTCATCGTTGAAGA
1 CCCCTGTCATCGTTCAAGA
34577 TGTCCCTCCC
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
20 4 0.06
21 54 0.87
22 4 0.06
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
CCCCTGTCATCGTTCAAGAGG
Found at i:34584 original size:42 final size:41
Alignment explanation
Indices: 34477--34585 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
34467 CCCGACTCCC
* * * *
34477 CTGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CTCCTACCGTTCAAGAGGCCA
* **
34519 CTATCATCCCTCAAGAGTCCCCTCCTACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGT-CCCTCCTACCGTTCAAGAGGCCA
*
34561 CTGTCATCGTTGAAGATGTCCCTCC
1 CTGTCATCGTTCAAGA-GTCCCTCC
34586 CAACATTCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
42 50 0.93
43 4 0.07
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (41 bp):
CTGTCATCGTTCAAGAGTCCCTCCTACCGTTCAAGAGGCCA
Found at i:36152 original size:33 final size:34
Alignment explanation
Indices: 36092--36167 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
36082 CGCAACTTCG
*
36092 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCAATGCGATTCACT
* *
36126 CGTTGTGATTTTCA-TTTCGCAATGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCAATGCGATTCACT
36159 CGTTGCGAT
1 CGTTGCGAT
36168 AGTCATTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 25 0.66
34 13 0.34
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCAATGCGATTCACT
Found at i:36174 original size:33 final size:33
Alignment explanation
Indices: 36092--36176 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
36082 CGCAACTTCG
*
36092 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCAATGCGATTCACT
* *
36126 CGTTGTGATTTTCATTTCGCAATGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCAATGCGATTCACT
**
36159 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
36177 AGCGTTGCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 32 0.71
34 13 0.29
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCAATGCGATTCACT
Found at i:36184 original size:20 final size:19
Alignment explanation
Indices: 36159--36247 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 19
36149 GCGATTCTCT
36159 CGTTGCGATAGTCATTTCAG
1 CGTTGCGATAGTCATTTC-G
*
36179 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTC-ATTTCG
36199 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTC-G
*
36219 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAT-TTCG
36239 CGTTGCGAT
1 CGTTGCGAT
36248 TTCCGCGTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.06
20 51 0.82
21 7 0.11
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:36203 original size:40 final size:40
Alignment explanation
Indices: 36159--36247 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
36149 GCGATTCTCT
36159 CGTTGCGATAGTCATTTCAGCGTTGCGATAGTCA-ATTCCG
1 CGTTGCGATAGTCATTTCAGCGTTGCGATAGTCATATT-CG
* *
36199 CGTTGCGATAGTCATTTCTGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCAGCGTTGCGATAGTCATATTCG
36239 CGTTGCGAT
1 CGTTGCGAT
36248 TTCCGCGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 43 0.93
41 3 0.07
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCAGCGTTGCGATAGTCATATTCG
Found at i:38585 original size:23 final size:23
Alignment explanation
Indices: 38551--38613 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
38541 CATATAAATG
*
38551 CACCGAAGTGCCATATAGAATTA
1 CACCGTAGTGCCATATAGAATTA
* *** *
38574 CATCGTAGTGCCGCGTAGAATTG
1 CACCGTAGTGCCATATAGAATTA
38597 CACCGTAGTGCCATATA
1 CACCGTAGTGCCATATA
38614 ATAATGTCCA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
CACCGTAGTGCCATATAGAATTA
Found at i:38795 original size:103 final size:103
Alignment explanation
Indices: 38625--38944 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
38615 TAATGTCCAT
38625 AAGGACCACATATCATTCCTTAAGAAT-ATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
38689 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
38727 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTATCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
38792 GACTTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
38830 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
38895 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
38933 AAGGACCACATA
1 AAGGACCACATA
38945 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
102 27 0.13
103 183 0.87
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:43800 original size:23 final size:23
Alignment explanation
Indices: 43747--43803 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
43737 CTCATATAAA
*
43747 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
43770 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
43793 TGCACCGTAGT
1 TGCACCGTAGT
43804 ACCATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:43994 original size:103 final size:103
Alignment explanation
Indices: 43827--44143 Score: 616
Period size: 103 Copynumber: 3.1 Consensus size: 103
43817 GTCCATAAGA
43827 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
43892 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
43930 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
43995 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
* *
44033 ACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTTTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
44098 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
44136 ACCACATA
1 ACCACATA
44144 GACCCTCAAC
Statistics
Matches: 212, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
Found at i:47169 original size:24 final size:24
Alignment explanation
Indices: 47135--47188 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
47125 CTGAAAAATC
*
47135 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* *
47159 ATCAAAGTCCGGGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
47183 ATCAAA
1 ATCAAA
47189 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:48063 original size:20 final size:20
Alignment explanation
Indices: 48040--48155 Score: 87
Period size: 20 Copynumber: 5.8 Consensus size: 20
48030 TTGCGATAGT
* *
48040 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
48060 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
* *
48080 C-GTATTCGCATTGCGATAGT-
1 CAG-AATCGCATTGCGAT-TTA
* *
48100 CAGATTCGCATTGCGATAGT-
1 CAGAATCGCATTGCGAT-TTA
*
48120 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
48140 C-GTATTCGCATTGCGA
1 CAG-AATCGCATTGCGA
48156 ATTAGGAAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.03
20 81 0.94
21 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTTA
Found at i:48076 original size:40 final size:40
Alignment explanation
Indices: 48029--48155 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
48019 GAAATTCAGT
48029 ATTGCGATAGTCAGAATCTCGTTGCGATTTACAGATTCGC
1 ATTGCGATAGTCAGAATCTCGTTGCGATTTACAGATTCGC
* * *
48069 ATTGCGAT--TTACGTAT-TCGCATTGCGATAGT-CAGATTCGC
1 ATTGCGATAGTCA-GAATCTCG--TTGCGAT-TTACAGATTCGC
* * *
48109 ATTGCGATAGTCAGATTCGCATTGCGATTTAC-GTATTCGC
1 ATTGCGATAGTCAGAATCTCGTTGCGATTTACAG-ATTCGC
48149 ATTGCGA
1 ATTGCGA
48156 ATTAGGAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
38 5 0.07
39 5 0.07
40 53 0.77
41 3 0.04
42 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (40 bp):
ATTGCGATAGTCAGAATCTCGTTGCGATTTACAGATTCGC
Found at i:48101 original size:60 final size:60
Alignment explanation
Indices: 48029--48155 Score: 202
Period size: 60 Copynumber: 2.1 Consensus size: 60
48019 GAAATTCAGT
* * *
48029 ATTGCGATAGTCAGAATCTCGTTGCGAT-TTACAGATTCGCATTGCGATTTACGTATTCGC
1 ATTGCGATAGTCAGAATCGCATTGCGATAGT-CAGATTCGCATTGCGATTTACGTATTCGC
*
48089 ATTGCGATAGTCAGATTCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGC
1 ATTGCGATAGTCAGAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGC
48149 ATTGCGA
1 ATTGCGA
48156 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 61 0.98
61 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (60 bp):
ATTGCGATAGTCAGAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGC
Found at i:48176 original size:21 final size:21
Alignment explanation
Indices: 48152--48197 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
48142 TATTCGCATT
48152 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
48173 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
48194 GCGA
1 GCGA
48198 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:51391 original size:51 final size:51
Alignment explanation
Indices: 51326--51459 Score: 153
Period size: 51 Copynumber: 2.6 Consensus size: 51
51316 CACCCGTAGC
* * * * *
51326 AGTAAAGCGCGCCCCCTGAACCGCGCTATATGTTGATTTGG-CACCACGTGG
1 AGTATAGCGCGCCCCCTGAACCGCGCTATACGTTGAATGGGTCA-CACATGG
* *
51377 AGTATAGCGCGCCCCCTGTACCGCGCTATACGTTGAATGGGTTACACATGG
1 AGTATAGCGCGCCCCCTGAACCGCGCTATACGTTGAATGGGTCACACATGG
* * **
51428 GGTATAGCGTGCCCCCTGCTCCGCGCTATACG
1 AGTATAGCGCGCCCCCTGAACCGCGCTATACG
51460 CCACGTAGGG
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 70 0.99
52 1 0.01
ACGTcount: A:0.19, C:0.31, G:0.28, T:0.22
Consensus pattern (51 bp):
AGTATAGCGCGCCCCCTGAACCGCGCTATACGTTGAATGGGTCACACATGG
Found at i:57795 original size:25 final size:26
Alignment explanation
Indices: 57761--57814 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
57751 TACACCGCGT
57761 TATTCCCCACGT-TTAGATACCCAGG
1 TATTCCCCACGTGTTAGATACCCAGG
57786 TATTCCCCACGTGTTAGATACCCAGG
1 TATTCCCCACGTGTTAGATACCCAGG
57812 TAT
1 TAT
57815 AGCGCGGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (26 bp):
TATTCCCCACGTGTTAGATACCCAGG
Found at i:58162 original size:2 final size:2
Alignment explanation
Indices: 58155--58184 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
58145 CGTCCCATTT
*
58155 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58185 GTTTGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:58244 original size:37 final size:36
Alignment explanation
Indices: 58168--58534 Score: 280
Period size: 36 Copynumber: 10.2 Consensus size: 36
58158 ATATATATAT
* * * *
58168 ATATACATATATATATAGTTTGAAAATATTTTTAAAAAA
1 ATATATATA-ATATATAGTTTTAAAACATTTTT--GAAA
* *
58207 CATATATATAATATATAG-TTTGAAACATGTTTGAAA
1 -ATATATATAATATATAGTTTTAAAACATTTTTGAAA
*
58243 ACT-TGTAT-ATATATAGTTTTTAAAAACA-TTTTGAAA
1 A-TATATATAATATATAG-TTTT-AAAACATTTTTGAAA
* *
58279 ATAAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 ATATATATAATATATAG-TTTTAAAACATTTTTGAAA
* **
58316 ATATATAT--TATATAGCTTTTAAAATA-TTTCAAAA
1 ATATATATAATATATAG-TTTTAAAACATTTTTGAAA
* *
58350 ATAAATATAATATATAGTTTTTAAAATATTTTTGAAA
1 ATATATATAATATATAG-TTTTAAAACATTTTTGAAA
*
58387 ATATATATATTATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATATAATATATAG-TTTTAAAACATTTTTGAAA
* * *
58423 ATATATGT-A-GT-T--TTTAAAAACA-TTTTGAAAA
1 ATATATATAATATATAGTTTTAAAACATTTTTG-AAA
* * *
58454 CATATATATATTATATAATTTTGAAATCATTTTTGAAA
1 -ATATATATAATATATAGTTTT-AAAACATTTTTGAAA
58492 AT-TATATAAT-TATAGTTTTAAAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTT--AAAACATTTTTGAAA
*
58528 CTATATA
1 ATATATA
58535 ATTTTAAAAA
Statistics
Matches: 269, Mismatches: 37, Indels: 45
0.77 0.11 0.13
Matches are distributed among these distances:
30 14 0.05
31 3 0.01
32 7 0.03
33 1 0.00
34 23 0.09
35 32 0.12
36 77 0.29
37 73 0.27
38 18 0.07
39 13 0.05
40 8 0.03
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTAAAACATTTTTGAAA
Found at i:58276 original size:36 final size:36
Alignment explanation
Indices: 58208--58534 Score: 258
Period size: 37 Copynumber: 9.2 Consensus size: 36
58198 TTTAAAAAAC
*
58208 ATATATATAATATATAG--TTT-GAAACATGTTTGAAA
1 ATATATAT-ATATATAGTTTTTAAAAACAT-TTTGAAA
*
58243 ACT-TGTATATATATAGTTTTTAAAAACATTTTGAAA
1 A-TATATATATATATAGTTTTTAAAAACATTTTGAAA
* *
58279 ATAAATATAATATATAGTTTTTAAAATA-TTTTTGAAA
1 ATATATAT-ATATATAGTTTTTAAAA-ACATTTTGAAA
* * **
58316 ATATATAT-TATATAGCTTTT-AAAATATTTCAAAA
1 ATATATATATATATAGTTTTTAAAAACATTTTGAAA
* *
58350 ATAAATATAATATATAGTTTTTAAAATA-TTTTTGAAA
1 ATATATAT-ATATATAGTTTTTAAAA-ACATTTTGAAA
58387 ATATATATATTATATAGTTTTT-AAAACATTTTG---
1 ATATATATA-TATATAGTTTTTAAAAACATTTTGAAA
*
58420 A-A-A-ATATATGTAGTTTTTAAAAACATTTTGAAAA
1 ATATATATATATATAGTTTTTAAAAACATTTTG-AAA
* * *
58454 CATATATATATTATATA-ATTTTGAAATCATTTTTGAAA
1 -ATATATATA-TATATAGTTTTTAAAAACA-TTTTGAAA
*
58492 AT-TATATA-ATTATAGTTTTAAAAAACATTTTTGAAA
1 ATATATATATA-TATAGTTTTTAAAAACA-TTTTGAAA
*
58528 CTATATA
1 ATATATA
58535 ATTTTAAAAA
Statistics
Matches: 237, Mismatches: 27, Indels: 54
0.75 0.08 0.17
Matches are distributed among these distances:
29 11 0.05
30 14 0.06
31 1 0.00
32 1 0.00
33 2 0.01
34 25 0.11
35 23 0.10
36 60 0.25
37 73 0.31
38 17 0.07
39 10 0.04
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATATATATATATAGTTTTTAAAAACATTTTGAAA
Found at i:58294 original size:73 final size:72
Alignment explanation
Indices: 58212--58527 Score: 309
Period size: 71 Copynumber: 4.5 Consensus size: 72
58202 AAAAACATAT
* * * *
58212 ATATAATATATAG--TTTGAAACATGTTTGAAAACTTGTATA-TATATAGTTTTTAAAAACATTT
1 ATATAATATATAGTTTTTAAAATATTTTTGAAAA-TTATATATTATATAGTTTTT-AAAACATTT
58274 TGAAAATAA
64 TGAAAATAA
* * **
58283 ATATAATATATAGTTTTTAAAATATTTTTGAAAA-TATATATTATATAGCTTTTAAAATATTTCA
1 ATATAATATATAGTTTTTAAAATATTTTTGAAAATTATATATTATATAGTTTTTAAAACATTTTG
58347 AAAATAA
66 AAAATAA
58354 ATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTTT
1 ATATAATATATAGTTTTTAAAATATTTTTGAAAAT-TATATATTATATAGTTTTTAAAACATTTT
58419 G-----AA
65 GAAAATAA
* * * * *
58422 A-AT-ATATGTAGTTTTTAAAA-ACATTTTGAAAACATATATATATTATATAATTTTGAAATCAT
1 ATATAATATATAGTTTTTAAAATA-TTTTTG-AAA-AT-TATATATTATATAGTTTTTAAAACA-
*
58484 TTTTGAAAAT-T
61 TTTTGAAAATAA
* *
58495 ATATAAT-TATAGTTTTAAAAAACATTTTTGAAA
1 ATATAATATATAGTTTT-TAAAATATTTTTGAAA
58528 CTATATAATT
Statistics
Matches: 206, Mismatches: 21, Indels: 33
0.79 0.08 0.13
Matches are distributed among these distances:
65 1 0.00
66 21 0.10
67 5 0.02
68 28 0.14
69 5 0.02
71 67 0.33
72 11 0.05
73 43 0.21
74 13 0.06
75 11 0.05
76 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (72 bp):
ATATAATATATAGTTTTTAAAATATTTTTGAAAATTATATATTATATAGTTTTTAAAACATTTTG
AAAATAA
Found at i:58316 original size:12 final size:11
Alignment explanation
Indices: 58296--58426 Score: 50
Period size: 11 Copynumber: 11.1 Consensus size: 11
58286 TAATATATAG
58296 TTTTTAAAATA
1 TTTTTAAAATA
58307 TTTTTGAAAATA
1 TTTTT-AAAATA
* *
58319 TATATT-ATATA
1 T-TTTTAAAATA
*
58330 GCTTTTAAAATA
1 -TTTTTAAAATA
**
58342 TTTCAAAAATA
1 TTTTTAAAATA
** *
58353 AATATAATATATA
1 TTTTTAA-A-ATA
58366 GTTTTTAAAATA
1 -TTTTTAAAATA
58378 TTTTTGAAAATA
1 TTTTT-AAAATA
*
58390 TATATATT-ATATA
1 T-T-T-TTAAAATA
*
58403 GTTTTTAAAACA
1 -TTTTTAAAATA
*
58415 TTTTGAAAATA
1 TTTTTAAAATA
58426 T
1 T
58427 ATGTAGTTTT
Statistics
Matches: 87, Mismatches: 20, Indels: 26
0.65 0.15 0.20
Matches are distributed among these distances:
11 40 0.46
12 26 0.30
13 13 0.15
14 6 0.07
15 2 0.02
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:58436 original size:29 final size:30
Alignment explanation
Indices: 58401--58458 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
58391 ATATATTATA
*
58401 TAGTTTTT-AAAACATTTTGAAAATATATG
1 TAGTTTTTAAAAACATTTTGAAAACATATG
58430 TAGTTTTTAAAAACATTTTGAAAACATAT
1 TAGTTTTTAAAAACATTTTGAAAACATAT
58459 ATATATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (30 bp):
TAGTTTTTAAAAACATTTTGAAAACATATG
Found at i:58683 original size:21 final size:21
Alignment explanation
Indices: 58657--58697 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
58647 TATTTATTTT
58657 ATTTTATTTT-ATCTTTTATTA
1 ATTTTATTTTCAT-TTTTATTA
58678 ATTTTATTTTCATTTTTATT
1 ATTTTATTTTCATTTTTATT
58698 GTCAGGTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (21 bp):
ATTTTATTTTCATTTTTATTA
Found at i:60008 original size:21 final size:22
Alignment explanation
Indices: 59966--60016 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
59956 CCCCTGAGTT
*
59966 TTATTTTATTTTATTTACTATTA
1 TTATTTT-TTTTATTCACTATTA
*
59989 TTATTTTTTTTCTTCA-TATTA
1 TTATTTTTTTTATTCACTATTA
60010 TT-TTTTT
1 TTATTTTT
60017 ACCTTTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 7 0.27
22 7 0.27
23 7 0.27
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (22 bp):
TTATTTTTTTTATTCACTATTA
Found at i:61724 original size:32 final size:31
Alignment explanation
Indices: 61666--61725 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
61656 AAAGTAACAA
* *
61666 ATTAATTTTATCGATTTATAATAAATAAATT
1 ATTAATATTATCGATTTATAACAAATAAATT
* *
61697 ATTAATATTATTGATTTTATTACAAATAA
1 ATTAATATTATCGA-TTTATAACAAATAA
61726 GGGAACCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 12 0.50
32 12 0.50
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTAATATTATCGATTTATAACAAATAAATT
Found at i:63347 original size:17 final size:18
Alignment explanation
Indices: 63312--63352 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
63302 ATATTATGTA
*
63312 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
63330 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
63347 TTTACT
1 TTTACT
63353 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:65043 original size:18 final size:18
Alignment explanation
Indices: 65016--65057 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
65006 ACAGCAGCCA
*
65016 CCGCAACCATTTATGATG
1 CCGCAACCATATATGATG
* *
65034 TCGCAGCCATATATGATG
1 CCGCAACCATATATGATG
65052 CCGCAA
1 CCGCAA
65058 TCGCCTTTCC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:65460 original size:12 final size:12
Alignment explanation
Indices: 65409--65461 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
65399 TGCTCAGGAC
65409 GACGACGACGAT
1 GACGACGACGAT
* *
65421 GTCGACGATGAT
1 GACGACGACGAT
* * * *
65433 GACAACAATGAC
1 GACGACGACGAT
65445 GACGACGACGAT
1 GACGACGACGAT
65457 GACGA
1 GACGA
65462 TGATGACAGC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.30, T:0.11
Consensus pattern (12 bp):
GACGACGACGAT
Found at i:66839 original size:18 final size:18
Alignment explanation
Indices: 66816--66858 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
66806 AAAAAGTATA
* *
66816 ACTTACTAATTTGCTTTC
1 ACTTACCAACTTGCTTTC
*
66834 ACTTACCCACTTGCTTTC
1 ACTTACCAACTTGCTTTC
66852 ACTTACC
1 ACTTACC
66859 CATGCGCACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.42
Consensus pattern (18 bp):
ACTTACCAACTTGCTTTC
Found at i:66859 original size:18 final size:18
Alignment explanation
Indices: 66826--66860 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
66816 ACTTACTAAT
66826 TTGCTTTCACTTACCCAC
1 TTGCTTTCACTTACCCAC
66844 TTGCTTTCACTTACCCA
1 TTGCTTTCACTTACCCA
66861 TGCGCACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.37, G:0.06, T:0.40
Consensus pattern (18 bp):
TTGCTTTCACTTACCCAC
Found at i:68832 original size:23 final size:23
Alignment explanation
Indices: 68767--68835 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
68757 CACCACAACT
* *
68767 CGTATAAATGCACCGAAGTACCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
68790 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
68813 CGTAGAAATGTACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
68836 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:70276 original size:21 final size:21
Alignment explanation
Indices: 70252--70296 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
70242 TTTTGTTCGT
70252 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
70273 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
70294 TTG
1 TTG
70297 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:71213 original size:17 final size:16
Alignment explanation
Indices: 71191--71232 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
71181 TCATCAGTTC
71191 TTATCAATCAAAATCA
1 TTATCAATCAAAATCA
* *
71207 TTAATCAATCAAATTCC
1 TT-ATCAATCAAAATCA
71224 TTATCAATC
1 TTATCAATC
71233 TTTAATTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (16 bp):
TTATCAATCAAAATCA
Found at i:71892 original size:18 final size:18
Alignment explanation
Indices: 71871--71909 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
71861 TCCCTTCTAA
* *
71871 CTTAACTTCATATTTATT
1 CTTAACTCCATATTTAAT
*
71889 CTTAACTCCTTATTTAAT
1 CTTAACTCCATATTTAAT
71907 CTT
1 CTT
71910 CCAGTACCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.54
Consensus pattern (18 bp):
CTTAACTCCATATTTAAT
Found at i:73636 original size:20 final size:21
Alignment explanation
Indices: 73597--73636 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
73587 ATGTCACGAG
73597 AAACACACATATCATTATATCA
1 AAACACACATAT-ATTATATCA
*
73619 AAACATACATAT-TTATAT
1 AAACACACATATATTATAT
73637 ACAATCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (21 bp):
AAACACACATATATTATATCA
Found at i:73909 original size:23 final size:23
Alignment explanation
Indices: 73867--73958 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
73857 CACCACAGCT
* **
73867 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGTAGTGCCA
* * * *
73890 TGTAGAATTACACCGTAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCA
*
73913 CGTAGAAATGCACCGTAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCA
*
73936 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGTAGTGCCA
73959 TATAATAATG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGTAGTGCCA
Found at i:75403 original size:21 final size:21
Alignment explanation
Indices: 75379--75423 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
75369 TTTTGTTCGT
75379 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
75400 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
75421 TTG
1 TTG
75424 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:77550 original size:41 final size:41
Alignment explanation
Indices: 77505--77596 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
77495 CACTGATCCA
* *
77505 CGCTATACCCCTATGTGGCGTATAGCGCGGATCAGAGGCCG
1 CGCTATACCCCTATATGACGTATAGCGCGGATCAGAGGCCG
* * * *
77546 CGCTATACCCTTATATGATGTATAGTGCGGATCAGGGGCCG
1 CGCTATACCCCTATATGACGTATAGCGCGGATCAGAGGCCG
77587 CGCTATACCC
1 CGCTATACCC
77597 ACGTGTAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (41 bp):
CGCTATACCCCTATATGACGTATAGCGCGGATCAGAGGCCG
Found at i:78812 original size:3 final size:3
Alignment explanation
Indices: 78804--78853 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
78794 TGGGTTTCTT
78804 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
78852 TT
1 TT
78854 TCAAGCCTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:79590 original size:16 final size:18
Alignment explanation
Indices: 79569--79613 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
79559 TCAGATTCAT
79569 ATTCCAATTCC-T-ACAG
1 ATTCCAATTCCTTCACAG
79585 ATTCCAATTCCTTCACAG
1 ATTCCAATTCCTTCACAG
*
79603 ATTCTAATTCC
1 ATTCCAATTCC
79614 CTTATAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.36
Consensus pattern (18 bp):
ATTCCAATTCCTTCACAG
Found at i:83306 original size:14 final size:14
Alignment explanation
Indices: 83289--83329 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
83279 ACTGCTTACA
83289 ACATAACACTTAAT
1 ACATAACACTTAAT
* *
83303 ACATAACACTGATT
1 ACATAACACTTAAT
83317 ACATAACACTTAA
1 ACATAACACTTAA
83330 ACCAAAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (14 bp):
ACATAACACTTAAT
Found at i:88920 original size:74 final size:74
Alignment explanation
Indices: 88799--88946 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
88789 CTTCATCAAC
88799 TCTTCCAGACCTCTGCAACAGCAAACGGTTTCATTCTTAAAAATGTTTAGGGAAAAGATTTGCAT
1 TCTTCCAGACCTCTGCAACAGCAAACGGTTTCATTCTTAAAAATGTTTAGGGAAAAGATTTGCAT
88864 TTACTCATG
66 TTACTCATG
88873 TCTTCCAGACCTCTGCAACAGCAAACGGTTTCATTCTTAAAAATGTTTAGGGAAAAGATTTGCAT
1 TCTTCCAGACCTCTGCAACAGCAAACGGTTTCATTCTTAAAAATGTTTAGGGAAAAGATTTGCAT
88938 TTACTCATG
66 TTACTCATG
88947 AGCTCCTAAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (74 bp):
TCTTCCAGACCTCTGCAACAGCAAACGGTTTCATTCTTAAAAATGTTTAGGGAAAAGATTTGCAT
TTACTCATG
Done.