Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007785.1 Hibiscus syriacus cultivar Beakdansim tig00110070_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: 140209
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5185 original size:13 final size:13
Alignment explanation
Indices: 5167--5201 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
5157 TCATTCCATG
5167 CACAAGGCTGCAC
1 CACAAGGCTGCAC
5180 CACAAGGCTGCAC
1 CACAAGGCTGCAC
5193 CACAAGGCT
1 CACAAGGCT
5202 TCCTAGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.37, G:0.23, T:0.09
Consensus pattern (13 bp):
CACAAGGCTGCAC
Found at i:6130 original size:28 final size:28
Alignment explanation
Indices: 6080--6138 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
6070 AAATCAAAAA
* *
6080 AAAGAAATTGAAGCACTC-CAAAAGAAAG
1 AAAGAAATTCAAGCACTCAAAAAAG-AAG
* *
6108 AAAGAAATTCCAGCACTTAAAAAAGAAG
1 AAAGAAATTCAAGCACTCAAAAAAGAAG
6136 AAA
1 AAA
6139 AGCAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.59, C:0.14, G:0.15, T:0.12
Consensus pattern (28 bp):
AAAGAAATTCAAGCACTCAAAAAAGAAG
Found at i:10650 original size:179 final size:178
Alignment explanation
Indices: 10352--10708 Score: 671
Period size: 179 Copynumber: 2.0 Consensus size: 178
10342 TGAAGGTTAA
10352 TGAACATGTTCTTTATAATTTCAACTAACACGTTTTTGGAATTTCAAAGATATGATGCTTGAATC
1 TGAACATGTTCTTTATAATTTCAACTAACACGTTTTTGGAATTTCAAAGATATGATGCTTGAATC
10417 ATCTTGAATGTCCCTTGGAATAACCTGCAAATTCAAAGAATGAATAGAAGAAAAAAATTGATTAG
66 ATCTTGAATGTCCCTTGGAATAACCTGCAAATTCAAAGAATGAATAGAAGAAAAAAATTGATTAG
10482 TATAAAGCAAACCTTCCTTTTCCTCGCACTC-TTTCATTCATGCTCAT
131 TATAAAGCAAACCTTCCTTTTCCTCGCACTCTTTTCATTCATGCTCAT
10529 TGAACATGTTCTTTATAATTTCAACTAACACGTCTTTTGGAATTTCAAAAGATATGATGCTTGAA
1 TGAACATGTTCTTTATAATTTCAACTAACACGT-TTTTGGAATTTC-AAAGATATGATGCTTGAA
* *
10594 TCATCTTGAATGTCGCTTGGAATAACCTGCAAATTCAAAGAATGGATAGAAGAAAAAAATTGATT
64 TCATCTTGAATGTCCCTTGGAATAACCTGCAAATTCAAAGAATGAATAGAAGAAAAAAATTGATT
10659 AGTATAAAGCAAACCTTCCTTTTCCTCGCACTCTTTTCATTCATGCTCAT
129 AGTATAAAGCAAACCTTCCTTTTCCTCGCACTCTTTTCATTCATGCTCAT
10709 GTTTTTCAAC
Statistics
Matches: 175, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
177 33 0.19
178 12 0.07
179 114 0.65
180 16 0.09
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (178 bp):
TGAACATGTTCTTTATAATTTCAACTAACACGTTTTTGGAATTTCAAAGATATGATGCTTGAATC
ATCTTGAATGTCCCTTGGAATAACCTGCAAATTCAAAGAATGAATAGAAGAAAAAAATTGATTAG
TATAAAGCAAACCTTCCTTTTCCTCGCACTCTTTTCATTCATGCTCAT
Found at i:23469 original size:91 final size:91
Alignment explanation
Indices: 23314--23496 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
23304 GGTAGTTGAT
*
23314 GCTTGGCCGAATAGGGAGTGAACTCTTCATCTTGACGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGACGCCTAAATGAACCACATGCAAGGCACATG
*
23379 GGGGCTGATCACATGCAAAACACATG
66 GAGGCTGATCACATGCAAAACACATG
* *
23405 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGACGCCTAAATGAACCACATGCAAGGCACATG
* * **
23470 GAGGCTGGTCATATGCAAGGCACATG
66 GAGGCTGATCACATGCAAAACACATG
23496 G
1 G
23497 GTATTCTAGG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.20
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGACGCCTAAATGAACCACATGCAAGGCACATG
GAGGCTGATCACATGCAAAACACATG
Found at i:25228 original size:24 final size:21
Alignment explanation
Indices: 25193--25235 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
25183 GGCACATTCT
*
25193 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
25216 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
25236 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:27682 original size:22 final size:18
Alignment explanation
Indices: 27636--27679 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
27626 GTCTCATTCA
27636 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
27654 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
27672 AGCTAGCT
1 AGCTAGCT
27680 AGCAAACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (18 bp):
AGCTAGCTTGAGTTGTGG
Found at i:56779 original size:24 final size:22
Alignment explanation
Indices: 56752--56808 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
56742 GGAGTGCAAA
56752 AAGAAAAGAAAAGACAAAAAGAAG
1 AAGAAAAGAAAAGAC-AAAA-AAG
** *
56776 AAGAAAA-AAAATTCAGAAAAG
1 AAGAAAAGAAAAGACAAAAAAG
56797 AAGAAAAGAAAA
1 AAGAAAAGAAAA
56809 AGAAGTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 10 0.34
22 7 0.24
23 5 0.17
24 7 0.24
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (22 bp):
AAGAAAAGAAAAGACAAAAAAG
Found at i:56800 original size:27 final size:26
Alignment explanation
Indices: 56766--56827 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
56756 AAAGAAAAGA
56766 CAAAAAGAAG--AAGAAAAA-AAATT
1 CAAAAAGAAGAAAAGAAAAAGAAATT
*
56789 CAGAAAAGAAGAAAAGAAAAAGAAGTT
1 CA-AAAAGAAGAAAAGAAAAAGAAATT
56816 CAAAAAG-AGAAA
1 CAAAAAGAAGAAA
56828 GCAAGCCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 2 0.06
24 8 0.24
25 5 0.15
26 13 0.38
27 6 0.18
ACGTcount: A:0.71, C:0.05, G:0.18, T:0.06
Consensus pattern (26 bp):
CAAAAAGAAGAAAAGAAAAAGAAATT
Found at i:56828 original size:24 final size:23
Alignment explanation
Indices: 56751--56828 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
56741 TGGAGTGCAA
**
56751 AAAGAAAAGAAAAGACAAAAAGA-
1 AAAGAAAA-AAAATTCAAAAAGAG
56774 AGAAGAAAAAAAATTCAGAAAAGAAG
1 A-AAGAAAAAAAATTCA-AAAAG-AG
*
56800 AAAAGAAAAAGAAGTTCAAAAAGAG
1 -AAAGAAAAA-AAATTCAAAAAGAG
56825 AAAG
1 AAAG
56829 CAAGCCAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
23 7 0.15
24 16 0.35
25 3 0.07
26 13 0.28
27 7 0.15
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.05
Consensus pattern (23 bp):
AAAGAAAAAAAATTCAAAAAGAG
Found at i:59354 original size:19 final size:20
Alignment explanation
Indices: 59313--59362 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
59303 GAAATCCCTT
*
59313 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
59333 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
59352 TGAAGATACAT
1 TGAAAATACAT
59363 TCTCTTGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:60300 original size:30 final size:31
Alignment explanation
Indices: 60261--60320 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
60251 ACATGCTGCC
**
60261 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
60292 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
60321 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:73668 original size:99 final size:99
Alignment explanation
Indices: 73497--73694 Score: 396
Period size: 99 Copynumber: 2.0 Consensus size: 99
73487 GCTATTATGG
73497 AGCTTCAAAGGACTCGGCTAGGAAGATCATTCACAAACAGCCCCATGCTTGCTAGCTAGCTCAAC
1 AGCTTCAAAGGACTCGGCTAGGAAGATCATTCACAAACAGCCCCATGCTTGCTAGCTAGCTCAAC
73562 ACTCAAGCTAGCTTGGAGGAGACACATGCACGCC
66 ACTCAAGCTAGCTTGGAGGAGACACATGCACGCC
73596 AGCTTCAAAGGACTCGGCTAGGAAGATCATTCACAAACAGCCCCATGCTTGCTAGCTAGCTCAAC
1 AGCTTCAAAGGACTCGGCTAGGAAGATCATTCACAAACAGCCCCATGCTTGCTAGCTAGCTCAAC
73661 ACTCAAGCTAGCTTGGAGGAGACACATGCACGCC
66 ACTCAAGCTAGCTTGGAGGAGACACATGCACGCC
73695 TAAGAAGAAG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.18
Consensus pattern (99 bp):
AGCTTCAAAGGACTCGGCTAGGAAGATCATTCACAAACAGCCCCATGCTTGCTAGCTAGCTCAAC
ACTCAAGCTAGCTTGGAGGAGACACATGCACGCC
Found at i:75982 original size:57 final size:57
Alignment explanation
Indices: 75894--76007 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
75884 AAAGTACAAG
75894 GCTCATGGAATGCTAAGGGAAGCTCGATTCAGCTGGAGAAGCTTCAGGCTAGCTAAA
1 GCTCATGGAATGCTAAGGGAAGCTCGATTCAGCTGGAGAAGCTTCAGGCTAGCTAAA
75951 GCTCATGGAATGCTAAGGGAAGCTCGATTCAGCTGGAGAAGCTTCAGGCTAGCTAAA
1 GCTCATGGAATGCTAAGGGAAGCTCGATTCAGCTGGAGAAGCTTCAGGCTAGCTAAA
76008 CTTAGCTAGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (57 bp):
GCTCATGGAATGCTAAGGGAAGCTCGATTCAGCTGGAGAAGCTTCAGGCTAGCTAAA
Found at i:87799 original size:19 final size:21
Alignment explanation
Indices: 87756--87806 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
87746 GAAACCCCTT
87756 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
87777 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
87796 TGAAGATACAT
1 TGAAAATACAT
87807 ACTCTTGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:88757 original size:30 final size:31
Alignment explanation
Indices: 88717--88776 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
88707 ACATGCTGCC
**
88717 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
88748 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
88777 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:88876 original size:44 final size:44
Alignment explanation
Indices: 88828--88960 Score: 127
Period size: 44 Copynumber: 3.1 Consensus size: 44
88818 ATCATATAGT
88828 TGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGA
1 TGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGA
* * * ** * *
88872 TGCAAATGTATGCTCATAA-ATAT-A-TAGT---GCATA-AATGAGT
1 TGCAAGTGAATG---ATAACATATGATTATTCAAGCATAGTTTAAGA
88912 TGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGA
1 TGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGA
88956 TGCAA
1 TGCAA
88961 ATGTATGCTC
Statistics
Matches: 65, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
37 4 0.06
38 4 0.06
39 1 0.02
40 16 0.25
41 5 0.08
43 5 0.08
44 21 0.32
45 1 0.02
46 4 0.06
47 4 0.06
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.32
Consensus pattern (44 bp):
TGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGA
Found at i:88916 original size:84 final size:85
Alignment explanation
Indices: 88825--88996 Score: 337
Period size: 84 Copynumber: 2.0 Consensus size: 85
88815 AAAATCATAT
88825 AGTTGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGATGCAAATGTATGCTCATA
1 AGTTGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGATGCAAATGTATGCTCATA
88890 A-ATATATAGTGCATAAATG
66 ATATATATAGTGCATAAATG
88909 AGTTGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGATGCAAATGTATGCTCATA
1 AGTTGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGATGCAAATGTATGCTCATA
88974 ATATATATAGTGCATAAATG
66 ATATATATAGTGCATAAATG
88994 AGT
1 AGT
88997 AAATATAATA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 66 0.76
85 21 0.24
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (85 bp):
AGTTGCAAGTGAATGATAACATATGATTATTCAAGCATAGTTTAAGATGCAAATGTATGCTCATA
ATATATATAGTGCATAAATG
Found at i:91605 original size:19 final size:20
Alignment explanation
Indices: 91570--91617 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
91560 AATAAAGGGT
91570 AATAATATAGTAATGAAAAT-A
1 AATAATA-AGTAATG-AAATGA
91591 AATAATAAG-AATGAAATGA
1 AATAATAAGTAATGAAATGA
91610 AATAATAA
1 AATAATAA
91618 AAGATAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 2 0.08
21 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
AATAATAAGTAATGAAATGA
Found at i:92065 original size:19 final size:21
Alignment explanation
Indices: 92022--92073 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
92012 GAAACCCCTT
92022 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
92043 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
92062 TGAAGATACATG
1 TGAAAATACATG
92074 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:95513 original size:35 final size:37
Alignment explanation
Indices: 95444--95522 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
95434 ATACTATTTC
*
95444 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
95481 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
95516 -ATCACCA
1 CATCACCA
95523 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
34 7 0.17
35 14 0.35
36 3 0.08
37 16 0.40
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:97445 original size:90 final size:91
Alignment explanation
Indices: 97291--97472 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 91
97281 CCTAGAACAC
*
97291 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
97356 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * *
97382 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
97446 AAGAGCTCTCTCCCTATTGGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
97472 C
1 C
97473 ATCATTTCCC
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 63 0.77
91 19 0.23
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:98247 original size:25 final size:22
Alignment explanation
Indices: 98218--98263 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
98208 CTTTTAACCC
98218 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
98243 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
98264 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:101983 original size:20 final size:19
Alignment explanation
Indices: 101960--102025 Score: 78
Period size: 21 Copynumber: 3.3 Consensus size: 19
101950 TATTTTGAAA
*
101960 TTTTGGGTTTTTTTTTTGT
1 TTTTTGGTTTTTTTTTTGT
**
101979 TTTTTGCCTTTTTTTTTGCCT
1 TTTTTGGTTTTTTTTTTG--T
102000 TTTTTGGTTTTTTTTTTGGT
1 TTTTTGGTTTTTTTTTT-GT
102020 TTTTTG
1 TTTTTG
102026 AAAAAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.38
20 7 0.18
21 16 0.41
22 1 0.03
ACGTcount: A:0.00, C:0.06, G:0.17, T:0.77
Consensus pattern (19 bp):
TTTTTGGTTTTTTTTTTGT
Found at i:101991 original size:21 final size:20
Alignment explanation
Indices: 101967--102025 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
101957 AAATTTTGGG
101967 TTTTTTTTTT-GTTTTTTGCC
1 TTTTTTTTTTCGTTTTTTG-C
* * *
101987 TTTTTTTTTGCCTTTTTTGG
1 TTTTTTTTTTCGTTTTTTGC
*
102007 TTTTTTTTTTGGTTTTTTG
1 TTTTTTTTTTCGTTTTTTG
102026 AAAAAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.00, C:0.07, G:0.14, T:0.80
Consensus pattern (20 bp):
TTTTTTTTTTCGTTTTTTGC
Found at i:101993 original size:12 final size:12
Alignment explanation
Indices: 101978--102004 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
101968 TTTTTTTTTG
101978 TTTTTTGCCTTT
1 TTTTTTGCCTTT
101990 TTTTTTGCCTTT
1 TTTTTTGCCTTT
102002 TTT
1 TTT
102005 GGTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTGCCTTT
Found at i:102014 original size:12 final size:12
Alignment explanation
Indices: 101999--102024 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
101989 TTTTTTTGCC
101999 TTTTTTGGTTTT
1 TTTTTTGGTTTT
102011 TTTTTTGGTTTT
1 TTTTTTGGTTTT
102023 TT
1 TT
102025 GAAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (12 bp):
TTTTTTGGTTTT
Found at i:102899 original size:25 final size:22
Alignment explanation
Indices: 102870--102915 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
102860 ACTTTAACCC
102870 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
102895 AATCTAATCCTAAAATATAAT
1 AATCTAATCCTAAAAAATAAT
102916 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:107285 original size:63 final size:63
Alignment explanation
Indices: 107209--107338 Score: 235
Period size: 63 Copynumber: 2.1 Consensus size: 63
107199 AGCATATCCT
*
107209 TCAAATTGTATGGTGATCAGGTGAACTTGTTTAGCTTGGGGGCA-TCATGTTGCGAATATTAGA
1 TCAAATTGTATGGTGATCAGGTGAACTTGTTTAGCTTGGGGGCAGTCATG-TACGAATATTAGA
107272 TCAAATTGTATGGTGATCAGGTGAACTTGTTTAGCTTGGGGGCAGTCATGTACGAATATTAGA
1 TCAAATTGTATGGTGATCAGGTGAACTTGTTTAGCTTGGGGGCAGTCATGTACGAATATTAGA
107335 TCAA
1 TCAA
107339 CTTTTCCTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
63 60 0.92
64 5 0.08
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (63 bp):
TCAAATTGTATGGTGATCAGGTGAACTTGTTTAGCTTGGGGGCAGTCATGTACGAATATTAGA
Found at i:108538 original size:7 final size:7
Alignment explanation
Indices: 108528--108585 Score: 64
Period size: 7 Copynumber: 7.9 Consensus size: 7
108518 TTTTGGCTCT
108528 TTTTTTG
1 TTTTTTG
108535 TTTTTTTG
1 -TTTTTTG
*
108543 CCTTTTT-
1 -TTTTTTG
108550 TTTTTTG
1 TTTTTTG
108557 CCTTTTTTG
1 --TTTTTTG
108566 TTTTTTG
1 TTTTTTG
108573 TTTTTTG
1 TTTTTTG
108580 TTTTTT
1 TTTTTT
108586 TGAAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
6 5 0.11
7 20 0.45
8 12 0.27
9 7 0.16
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (7 bp):
TTTTTTG
Found at i:108538 original size:19 final size:17
Alignment explanation
Indices: 108516--108572 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
108506 AAATTTTGGC
108516 TTTTTTGGCTCTTTTTTT
1 TTTTTTGGC-CTTTTTTT
*
108534 GTTTTTTTGCC--TTTTT
1 -TTTTTTGGCCTTTTTTT
*
108550 TTTTTT-GCCTTTTTTG
1 TTTTTTGGCCTTTTTTT
108566 TTTTTTG
1 TTTTTTG
108573 TTTTTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 3 0.09
15 6 0.18
16 15 0.45
18 1 0.03
19 8 0.24
ACGTcount: A:0.00, C:0.11, G:0.12, T:0.77
Consensus pattern (17 bp):
TTTTTTGGCCTTTTTTT
Found at i:108553 original size:20 final size:20
Alignment explanation
Indices: 108516--108552 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
108506 AAATTTTGGC
*
108516 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTGT
108536 TTTTTTGCCT-TTTTTTT
1 TTTTTTGCCTCTTTTTTT
108553 TTTGCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (20 bp):
TTTTTTGCCTCTTTTTTTGT
Found at i:108569 original size:21 final size:20
Alignment explanation
Indices: 108527--108587 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 20
108517 TTTTTGGCTC
*
108527 TTTTTTTGTTTTTTTGCCTTTT
1 TTTTTTTGCTTTTTTG--TTTT
108549 TTTTTTTGCCTTTTTTGTTTTT
1 TTTTTTTG-CTTTTTTG-TTTT
*
108571 TGTTTTTTGTTTTTTTG
1 T-TTTTTTGCTTTTTTG
108588 AAAAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (20 bp):
TTTTTTTGCTTTTTTGTTTT
Found at i:108576 original size:14 final size:15
Alignment explanation
Indices: 108528--108585 Score: 75
Period size: 14 Copynumber: 3.9 Consensus size: 15
108518 TTTTGGCTCT
108528 TTTTTTGTTTTTTTGC
1 TTTTTTG-TTTTTTGC
*
108544 CTTTTT-TTTTTTGCC
1 TTTTTTGTTTTTTG-C
108559 TTTTTTGTTTTTTG-
1 TTTTTTGTTTTTTGC
108573 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
108586 TGAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 20 0.53
15 6 0.16
16 12 0.32
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (15 bp):
TTTTTTGTTTTTTGC
Found at i:115748 original size:70 final size:72
Alignment explanation
Indices: 115662--115799 Score: 167
Period size: 71 Copynumber: 1.9 Consensus size: 72
115652 TAAATTCATC
* * * * *
115662 CATTCATGCATATTCATACA-AGAAGCCAAAT-AGTCATGTTCACACAA-G-GGGAAGAATTTCA
1 CATTCATGAACATTCATACATAGAAGACAAATCA-ACAAGTTCACACAAGGTGGGAAGAA-TTCA
115723 GCCAAGATA
64 GCCAAGATA
* *
115732 CATTCATGAACATTCATCCATAGAAGACAAATCAACAAGTTCACACAAGGTGGGATGAATTCAGC
1 CATTCATGAACATTCATACATAGAAGACAAATCAACAAGTTCACACAAGGTGGGAAGAATTCAGC
115797 CAA
66 CAA
115800 AGGATGTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
70 17 0.30
71 22 0.39
72 11 0.19
73 7 0.12
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.22
Consensus pattern (72 bp):
CATTCATGAACATTCATACATAGAAGACAAATCAACAAGTTCACACAAGGTGGGAAGAATTCAGC
CAAGATA
Found at i:120309 original size:24 final size:21
Alignment explanation
Indices: 120274--120316 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
120264 GGCTCATTCT
*
120274 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
120297 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
120317 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:124112 original size:14 final size:14
Alignment explanation
Indices: 124093--124135 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
124083 ATAAGATACT
* *
124093 ATCTATTCATCATC
1 ATCTATCCATCACC
124107 ATCTATCCATCACC
1 ATCTATCCATCACC
*
124121 ATC-CTCCATCACC
1 ATCTATCCATCACC
124134 AT
1 AT
124136 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:127533 original size:30 final size:31
Alignment explanation
Indices: 127481--127540 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
127471 CTTAGCTTTA
**
127481 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
127511 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
127541 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:128468 original size:19 final size:20
Alignment explanation
Indices: 128444--128491 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
128434 CGTCCAAGAG
128444 CATGTATCTTCA-TT-AAAAT
1 CATGTAT-TTCATTTAAAAAT
*
128463 CATGTATTTTATTTAAAAAT
1 CATGTATTTCATTTAAAAAT
128483 CATGTATTT
1 CATGTATTT
128492 TCAAAGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 9 0.35
20 14 0.54
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAAT
Found at i:135005 original size:14 final size:13
Alignment explanation
Indices: 134988--135037 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
134978 GTGCAAAAAG
134988 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
135002 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
135015 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
135026 AAAGAAAAAGAA
1 AAAGAAAAAGAA
135038 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:135034 original size:19 final size:18
Alignment explanation
Indices: 134982--135037 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
134972 ATTGGAGTGC
134982 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
134999 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
135018 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
135037 A
1 A
135038 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:135035 original size:11 final size:11
Alignment explanation
Indices: 134982--135037 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
134972 ATTGGAGTGC
134982 AAAAAG-AAAG
1 AAAAAGAAAAG
134992 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
135006 AAGAAGAAAAG
1 AAAAAGAAAAG
135017 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
135030 AAAAAGAA
1 AAAAAGAA
135038 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Done.